Patent Grant
7566694
Many pathogens have the ability to evade the natural defenses of an infected host cell or organism. Consequently, the infected host develops the disease or disorder which is associated with that pathogen.
Treatments for pathogenic infections typically target a distinguishing feature or characteristic of a specific pathogen. For example, acyclovir targets the replication stage of herpesvirus infection, zidovudine/AZT targets the reverse transcriptase of human immunodeficiency virus (HIV), and various protease inhibitors target HIV protease. Generally, however, these therapies have many disadvantages, including limited usefulness for only a specific pathogen, ineffectiveness due to pathogen variation, and toxic side effects. In addition, many of these therapies tend to be slow to develop.
A need exists therefore, for the development of anti-pathogen therapies that are effective for a broad spectrum of pathogens and which overcome disadvantages of existing therapies.
The present invention relates to an agent, such as a chimeric molecule, or components thereof, which are capable of being assembled together to form said chimeric molecule or agent, as described herein. The chimeric molecule or agent of the invention has at least one pathogen-detection domain (or a pathogen-recognition domain), or molecular structure that is capable of specifically interacting with a pathogen, pathogen component, pathogen product or pathogen-induced product, and/or at least one effector domain, or molecular structure capable of eliciting a desired effector function, these domains or molecular structures not being typically associated or bound together in nature. This invention also relates to the use of this agent for the treatment or prevention of a pathogen infection in a cell or an organism.
In one embodiment, a method for treating or preventing a pathogen infection in a cell includes administering to a cell chimeric molecules having at least one pathogen-detection domain and at least one effector domain, such pathogen-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen in the cell, the chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector domain, thus treating or preventing the pathogen infection in the cell.
In another embodiment, a method for treating or preventing a pathogen infection in a cell includes administering to a cell chimeric molecules having at least one pathogen-induced product-detection domain and at least one effector domain, such pathogen-induced product-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen-induced product in a cell, the chimeric molecules bind to the pathogen-induced product and activate the effector domain, thus treating or preventing the pathogen infection in the cell.
In a further embodiment, a method for treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism, chimeric molecules having at least one pathogen-detection domain and at least one effector domain, such pathogen-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen in the organism, the chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector domain, thus treating or preventing the spread of the pathogen infection in the organism.
In a still further embodiment, a method for treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism, chimeric molecules having at least one pathogen-induced product-detection domain and at least one effector domain, such pathogen-induced product-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen-induced product in the organism, the chimeric molecules bind to the pathogen-induced product and activate the effector domain, thus treating or preventing the spread of the pathogen infection in the organism.
In another embodiment of the invention, a method of treating or preventing a pathogen infection in a cell includes administering to a cell an agent having at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, such pathogen-interacting molecular structure and effector-mediating molecular structure being a non-naturally occurring agent in a cell, and wherein in the presence of a pathogen in a cell, the agent binds to the pathogen, pathogen component or pathogen product, and activates the effector-mediating molecular structure, thus treating or preventing the pathogen infection in the cell.
In still another embodiment of the invention, a method of treating or preventing a pathogen infection in a cell includes administering to a cell an agent having at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure, such pathogen-induced product-interacting molecular structure and effector-mediating molecular structure being a non-naturally occurring agent in a cell, and wherein in the presence of a pathogen-induced product in a cell, the agent binds to the pathogen-induced product and activates the effector-mediating molecular structure, thus treating or preventing the pathogen infection in the cell.
In a further embodiment, a method for treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism an agent having at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, such pathogen-interacting molecular structure and effector-mediating molecular structure being a non-naturally occurring agent in a cell, and wherein in the presence of a pathogen in the organism, the agent binds to the pathogen, pathogen component or pathogen product, and activates the effector-mediating molecular structure, thus treating or preventing the spread of the pathogen infection in the organism.
In another embodiment, a method for treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism an agent having at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure, such pathogen-induced product-interacting molecular structure and effector-mediating molecular structure being a non-naturally occurring agent in a cell, and wherein in the presence of a pathogen in the organism, the agent binds to the pathogen-induced product and activates the effector-mediating molecular structure, thus treating or preventing the spread of the pathogen infection in the organism.
In yet another embodiment of the invention, a method of treating or preventing a pathogen infection in a cell includes administering to the cell individual components of a chimeric molecule, such components being assembled together to form a chimeric molecule having at least one pathogen-detection domain and at least one effector domain, such pathogen-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen, pathogen component or pathogen product in the cell, the chimeric molecules bind to the pathogen, pathogen component or pathogen product in the cell, and activate the effector domain, thus treating or preventing the pathogen infection in the cell.
In another embodiment of the invention, a method of treating or preventing a pathogen infection in a cell includes administering to the cell individual components of a chimeric molecule, such components being assembled together to form a chimeric molecule having at least one pathogen-induced product-detection domain and at least one effector domain, such pathogen-induced product-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen-induced product in a cell, the chimeric molecules bind to the pathogen-induced product and activate the effector domain, thus treating or preventing the pathogen infection in the cell.
In still another embodiment of the invention, a method of treating or preventing a pathogen infection in an organism includes administering to the organism individual components of a chimeric molecule, such components being assembled together to form a chimeric molecule having at least one pathogen-detection domain and at least one effector domain, such pathogen-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen in the organism, the chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector domain, thus treating or preventing the spread of the pathogen infection in the organism.
In another embodiment of the invention, a method of treating or preventing a pathogen infection in an organism includes administering to the organism individual components of a chimeric molecule, such components being assembled together to form a chimeric molecule having at least one pathogen-induced product-detection domain and at least one effector domain, such pathogen-induced product-detection domain and effector domain being not normally bound to each other, and wherein in the presence of a pathogen-induced product in the organism, the chimeric molecules bind to the pathogen-induced product and activate the effector domain, thus treating or preventing the spread of the pathogen infection in the organism.
In a further embodiment of the invention, a chimeric molecule is provided which has at least one pathogen-detection domain and at least one effector domain, such pathogen-detection domain and effector domain being one that is non-naturally-occurring in a cell.
In a still further embodiment of the invention, a chimeric molecule is provided which has at least one pathogen-induced product-detection domain and at least one effector domain, such pathogen-induced product-detection domain and effector domain being one that is non-naturally-occurring in a cell.
In yet another embodiment of the invention, an agent is provided which has at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell.
In a further embodiment of the invention, an agent is provided which has at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell.
In another embodiment of the invention, an assay for the detection of a pathogen infection in a cell includes culturing the cell in a suitable cell culture medium and administering to the cell chimeric molecules having at least one pathogen-detection domain and at least one effector domain, such chimeric molecule being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product in the cell, the chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector domain, thus determining the presence or absence of apoptosis in the cell indicates the presence or absence of a pathogen infection in the cell.
In yet another embodiment of the invention, an assay for the detection of a pathogen infection in an organism includes obtaining a cell or cells from the organism and culturing the cell(s) in a suitable cell culture medium and administering to the cell(s) chimeric molecules having at least pathogen-detection domain and at least one effector domain, such chimeric molecule being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product, chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector domain. Thus, determining the presence or absence of apoptosis in the cell isolated from the organism indicates the presence or absence of a pathogen infection in the organism.
In a still further embodiment of the invention, an assay for the detection of a pathogen infection in an organism, includes obtaining a sample from the organism and adding the sample to an uninfected cell, then culturing this cell in a suitable cell culture medium and administering to that cell chimeric molecules having at least one pathogen-detection domain and at least one effector domain, such chimeric molecules are non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product, the chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector domain. Thus, determining the presence or absence of effector domain activation indicates the presence or absence of a pathogen infection in the sample obtained from the organism.
In a still further embodiment of the invention, an assay for the detection of a pathogen infection in an organism, includes obtaining a sample from the organism and adding the sample to an uninfected cell, then culturing this cell in a suitable cell culture medium and administering to that cell an agent having at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product in the cell, the agent binds to the pathogen, pathogen component or pathogen product, and activates the effector-mediating molecular structure. Thus, determining the presence or absence of activation of the effector-mediating molecular structure in the cell indicates the presence or absence of a pathogen infection in the sample obtained from the organism.
In further embodiment of the invention, an assay for the detection of a pathogen infection in a cell includes culturing the cell in a suitable cell culture medium and administering to that cell an agent having at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product in the cell, the agent binds to the pathogen, pathogen component or pathogen product, and activates the effector-mediating molecular structure. Thus, determining the presence or absence of activation of the effector-mediating molecular structure in the cell indicates the presence or absence of a pathogen infection in the cell.
In another embodiment of the invention, an assay for the detection of a pathogen infection in an organism includes obtaining a cell or cells from the organism and culturing the cell(s) in a suitable cell culture medium and administering to the cell(s) an agent having at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product, chimeric molecules bind to the pathogen, pathogen component or pathogen product, and activate the effector-mediating molecular structure. Thus, determining the presence or absence of activation of the effector-mediating molecular structure in the cell indicates the presence or absence of a pathogen infection in the organism.
In another embodiment of the invention, an assay for the detection of a pathogen infection in a cell includes culturing the cell in a suitable cell culture medium and administering to the cell chimeric molecules having at least one pathogen-induced product-detection domain and at least one effector domain, such chimeric molecule being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen-induced product in the cell, the chimeric molecules bind to the pathogen-induced product, and activate the effector domain, thus determining the presence or absence of apoptosis in the cell indicates the presence or absence of a pathogen infection in the cell.
In yet another embodiment of the invention, an assay for the detection of a pathogen infection in an organism includes obtaining a cell or cells from the organism and culturing the cell(s) in a suitable cell culture medium and administering to the cell(s) chimeric molecules having at least pathogen-induced product-detection domain and at least one effector domain, such chimeric molecule being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen, pathogen component or pathogen product, chimeric molecules bind to the pathogen-induced product, and activate the effector domain. Thus, determining the presence or absence of apoptosis in the cell isolated from the organism indicates the presence or absence of a pathogen infection in the organism.
In further embodiment of the invention, an assay for the detection of a pathogen infection in a cell includes culturing the cell in a suitable cell culture medium and administering to that cell an agent having at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen-induced product in the cell, the agent binds to the pathogen-induced product, and activates the effector-mediating molecular structure. Thus, determining the presence or absence of activation of the effector-mediating molecular structure in the cell indicates the presence or absence of a pathogen infection in the cell.
In a still further embodiment of the invention, an assay for the detection of a pathogen infection in an organism, includes obtaining a sample from the organism and adding the sample to an uninfected cell, then culturing this cell in a suitable cell culture medium and administering to that cell chimeric molecules having at least one pathogen-induced product-detection domain and at least one effector domain, such chimeric molecules are non-naturally-occurring in a cell, wherein in the presence of a pathogen-induced product, the chimeric molecules bind to the pathogen-induced product, and activate the effector domain. Thus, determining the presence or absence of effector domain activation indicates the presence or absence of a pathogen infection in the sample obtained from the organism.
In a still further embodiment of the invention, an assay for the detection of a pathogen infection in an organism, includes obtaining a sample from the organism and adding the sample to an uninfected cell, then culturing this cell in a suitable cell culture medium and administering to that cell an agent having at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen-induced product, chimeric molecules bind to the pathogen-induced product, and activate the effector-mediating molecular structure. Thus, determining the presence or absence of activation of the effector-mediating molecular structure in the cell indicates the presence or absence of a pathogen infection in the sample obtained from the organism.
In another embodiment of the invention, an assay for the detection of a pathogen infection in an organism includes obtaining a cell or cells from the organism and culturing the cell(s) in a suitable cell culture medium and administering to the cell(s) an agent having at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure, such agent being one that is non-naturally-occurring in a cell, wherein in the presence of a pathogen-induced product, chimeric molecules bind to the pathogen-induced product, and activate the effector-mediating molecular structure. Thus, determining the presence or absence of activation of the effector-mediating molecular structure in the cell indicates the presence or absence of a pathogen infection in the organism.
In another embodiment, a method for treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism, chimeric molecules having at least one pathogen-detection domain and at least one effector domain, such pathogen-detection domain and effector domain being not normally bound to each other, and wherein the presence of a pathogen in the organism, the chimeric molecules bind to the pathogen, pathogen component or pathogen product and activate the effector domain, thus treating or preventing the spread of the pathogen infection in the organism.
In yet another embodiment, the method includes administering to a cell chimeric molecules which have at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the chimeric molecule being one that is non-naturally-occurring in a cell, such that in the presence of a pathogen in the cell, chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain, thereby causing apoptosis of the cell, thus treating or preventing the pathogen infection in the cell.
In a further embodiment, the method includes administering to a cell an agent which has at least one double-stranded RNA-interacting molecular structure and at least one apoptosis-effector mediating molecular structure, the agent being one that is non-naturally-occurring in a cell, such that in the presence of a pathogen in the cell, the agent binds to the double-stranded RNA produced by the pathogen and activates the apoptosis-effector mediating molecular structure, thereby causing apoptosis of the cell, thus treating or preventing the pathogen infection in the cell.
In another embodiment of the invention, a method for treating or preventing a virus infection in a cell includes administering to the cell chimeric molecules that have at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the chimeric molecule being one not naturally-occurring in a cell, such that in the presence of a virus in the cell, the chimeric molecules bind to a double-stranded RNA produced by the virus and activate the apoptosis mediator domain, thereby causing apoptosis of the cell, thus treating or preventing the virus infection in the cell.
In an additional embodiment of the invention, a method of treating or preventing a pathogen infection in a cell includes administering to the cell chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one pro-enzymatic caspase-3 domain, such that in the presence of a pathogen in the cell, these chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate the pro-enzymatic caspase-3 domain thereby causing apoptosis of the cell, thus treating or preventing the pathogen infection in the cell.
In another embodiment of the invention, a method of treating or preventing a pathogen infection in a cell comprises administering to the cell chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one apoptosis mediator domain isolated from Fas-associated protein with death domain (FADD), such that in the presence of a pathogen in the cell, the chimeric molecules bind to double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain and cause apoptosis of the cell, thus treating or preventing the pathogen infection in the cell.
In still another embodiment of the invention, a method of treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism chimeric molecules that have at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of a pathogen in a cell or cells of the organism, the chimeric molecules bind to double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain, thereby causing apoptosis of the cell in the organism, thus treating or preventing the spread of the pathogen in the organism.
In yet another embodiment, a method of treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism an agent which has at least one double-stranded RNA-interacting molecular structure and at least one apoptosis-effector mediating molecular structure whereby, the agent being one that is non-naturally-occurring in a cell, such that in the presence of a pathogen in a cell or cells of the organism, the agent binds to the double-stranded RNA produced by the pathogen and activates the apoptosis-effector mediating molecular structure, thereby causing apoptosis of the cell in the organism, thus treating or preventing the spread of the pathogen in the organism.
In a further embodiment of the invention, a method of treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one pro-enzymatic caspase-3 domain, such that in the presence of the pathogen in a cell or cells of the organism, the chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate the pro-enzymatic caspase-3 domain, thereby causing apoptosis of the cell in the organism, thus treating or preventing the spread of the pathogen in the organism.
In another embodiment of the invention, a method for treating or preventing the spread of a pathogen infection in an organism, includes administering to the organism chimeric molecules that have at least one double-stranded RNA binding domain isolated from protein kinase R and at least one apoptosis mediator domain isolated from FADD, such that in the presence of the pathogen in a cell or cells of an organism, the chimeric molecules bind to double-stranded RNA produced by that pathogen and activate the apoptosis mediator domain, thereby causing apoptosis of the cell in the organism, thus treating or preventing the spread of the pathogen in the organism.
In yet another embodiment of the invention, a method of treating or preventing a pathogen infection in a cell includes administering to the cell individual components of a chimeric molecule, such components being assembled together to form a chimeric molecule at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, such that in the presence of a pathogen in the cell, the chimeric molecules bind to double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain, thus treating or preventing the pathogen infection in the cell.
In still another embodiment of the invention, a method of treating or preventing the spread of a pathogen infection in an organism includes administering to the organism individual components of a chimeric molecule, such components being assembled together to form a chimeric molecule having at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, such that in the presence of a pathogen, the chimeric molecules bind to double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain, thus treating or preventing the spread of a pathogen infection in the organism.
In a further embodiment of the invention, a method of mediating apoptosis in a cell infected with a pathogen, includes administering to the cell chimeric molecules having at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of a pathogen in the cell, the chimeric molecules bind to the double-stranded RNA produced by that pathogen and activate the apoptosis mediator domain, thus causing apoptosis of the cell.
In a further embodiment of the invention, a method of mediating apoptosis in a cell infected with a pathogen, includes administering to the cell an agent which has at least one double-stranded RNA-interacting molecular structure and at least one apoptosis-effector mediating molecular structure, the agent being one that is non-naturally-occurring in a cell, such that in the presence of a pathogen, the agent binds to the double-stranded RNA produced by the pathogen and activates the apoptosis-effector mediating molecular structure, thereby causing apoptosis of the cell.
In another embodiment of the invention, a method of mediating apoptosis in a cell infected with a pathogen, includes administering to the cell chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one pro-enzymatic caspase-3 domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of the pathogen in the cell, the chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate pro-enzymatic caspase-3, thus causing apoptosis of the cell.
In a further embodiment of the invention, a method of mediating apoptosis in a cell infected with a pathogen, includes administering to the cell chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one apoptosis mediator domain isolated from FADD, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of the pathogen in the cell, the chimeric molecules bind to the double-stranded RNA produced by that pathogen and activate the apoptosis mediator domain, and cause apoptosis of the cell.
In still another embodiment of the invention, a method of mediating apoptosis in an organism infected with a pathogen, includes administering to the organism chimeric molecules having at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of the pathogen in a cell or cells of the organism, the chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate apoptosis mediator domain, thereby causing apoptosis of the cell in the organism.
In another embodiment of the invention, a method of mediating apoptosis in an organism infected with a pathogen, includes administering to the organism an agent having at least one double-stranded RNA-interacting molecular structure and at least one apoptosis-effector mediating molecular structure, the agent being one that is non-naturally-occurring in a cell, such that in the presence of the pathogen in a cell or cells of the organism, the agent binds to the double-stranded RNA produced by the pathogen and activates the apoptosis-effector mediating molecular structure, thereby causing apoptosis of the cell in the organism.
In further embodiment of the invention, a method of mediating apoptosis in an organism infected with a pathogen, includes administering to the organism chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one pro-enzymatic caspase-3 domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of a pathogen in a cell or cells of the organism, the chimeric molecules bind to the double-stranded RNA produced by that pathogen and activate the pro-enzymatic caspase-3 domain, causing apoptosis of the cell in the organism.
Another embodiment of the invention is a method of mediating apoptosis in an organism infected with a pathogen, by administering to the organism chimeric molecules having at least one double-stranded RNA binding domain isolated from protein kinase R and at least one apoptosis mediator domain isolated from FADD, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of a pathogen in a cell or cells of the organism, the chimeric molecules bind to the double-stranded RNA produced by that pathogen and activate the apoptosis mediator domain, causing apoptosis of the cell in the organism.
In another embodiment of the invention, a chimeric molecule is provided which has at least one double-stranded pathogen-RNA binding domain and at least one apoptosis mediator domain.
In still another embodiment, is an agent that has at least one double-stranded RNA-interacting molecular structure and at least one apoptosis-effector mediating molecular structure.
In a further embodiment, a chimeric molecule is provided that has at least one double-stranded RNA binding domain isolated from protein kinase R and at least one apoptosis mediator domain isolated from pro-enzymatic caspase-3, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain.
In another embodiment, a chimeric molecule is provided that has at least one double-stranded RNA binding domain isolated from protein kinase R and at least one apoptosis mediator domain isolated from FADD apoptosis mediator, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain.
In a further embodiment of the invention, a chimeric molecule having more than one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domains being ones that are not naturally bound to the apoptosis mediator domain, is provided.
In an alternative embodiment, a chimeric molecule of the invention has at least one double-stranded RNA binding domain and more than one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domains.
In further embodiment of the invention, an assay for the detection of a pathogen infection in a cell includes, culturing the cell in a suitable cell culture medium and administering to that cell chimeric molecules having at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of a pathogen in the cell, the chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain, thus determining the presence or absence of apoptosis in the cell indicates the presence or absence of a pathogenic infection in the cell.
In further embodiment of the invention, an assay for the detection of a pathogen infection in a cell includes, culturing the cell in a suitable cell culture medium and administering to that cell an agent having at least one double-stranded RNA-interacting molecular structure, and at least one apoptosis-effector mediating molecular structure, the agent being one that is non-naturally occurring in a cell, such that in the presence of a pathogen in the cell, the agent binds to the double-stranded RNA produced by the pathogen and activates the apoptosis-effector mediating molecular structure, thus determining the presence or absence of apoptosis in the cell indicates the presence or absence of a pathogenic infection in the cell.
In still a further embodiment of the invention, an assay for the detection of double-stranded RNA in a sample includes the steps of administering to the sample chimeric molecules having at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of double-stranded RNA in the sample, the chimeric molecules will bind to that double-stranded RNA and activate the apoptosis mediator domain. A determination of the presence or absence of activation of the apoptosis mediator domain will indicate the presence or absence of double-stranded RNA in the sample.
In another embodiment of the invention, an assay for the detection of double-stranded RNA in a sample includes the steps of administering to the sample an agent having at least one double-stranded RNA-interacting molecular structure and at least one apoptosis-effector mediating molecular structure, the agent being one that is non-naturally occurring in a cell, such that in the presence of double-stranded RNA in the sample, the agent binds to that double-stranded RNA and activates the apoptosis-effector mediating molecular structure, thus a determination of the presence or absence of activation of the apoptosis-effector mediating molecular structure will indicate the presence or absence of double-stranded RNA in the sample.
In further embodiment of the invention, an assay for the detection of a pathogen infection in an organism includes, obtaining a cell or cells from the organism, culturing the cell(s) in a suitable cell culture medium, and administering to the cell(s) chimeric molecules having at least one double-stranded RNA binding domain and at least one apoptosis mediator domain, the double-stranded RNA binding domain being one that is not naturally bound to the apoptosis mediator domain, such that in the presence of a pathogen in the cell, the chimeric molecules bind to the double-stranded RNA produced by the pathogen and activate the apoptosis mediator domain. Determining the presence or absence of apoptosis in the cell indicates the presence or absence of a pathogenic infection in the organism.
In another embodiment of the invention, an assay for the detection of a pathogen infection in an organism includes, obtaining a cell or cells from the organism, culturing the cell(s) in a suitable cell culture medium and administering to the cell(s) an agent having at least one double-stranded RNA-interacting molecular structure, and at least one apoptosis-effector mediating molecular structure, the agent being one that is non-naturally occurring in a cell, such that in the presence of a pathogen in the cell, the agent binds to the double-stranded RNA produced by the pathogen and activates the apoptosis-effector mediating molecular structure. Determining the presence or absence of apoptosis in the cell indicates the presence or absence of a pathogenic infection in the organism.
The invention described herein provides chimeric molecules, and methods of use of said chimeric molecules, for treatment and prevention of pathogenic infections in a cell or an organism. Advantages of the claimed invention include, for example, its applicability to a broad spectrum of pathogenic infections, in addition to its use in both prophylactic methods and post-infection treatments. Furthermore, the claimed invention can overcome at least some disadvantages of existing therapies.
Organisms, such as humans, other animals, and plants, and their cells have natural defenses against pathogens, such as viruses, viroids, bacteria, rickettsia, chlamydia, mycoplasma, fungi, protozoa, helminths, and prions. These natural defenses include, for example and without limitation: (1) the interferon pathway, by which an infected cell can warn or prime nearby uninfected cells to increase their resistance to infection; (2) apoptosis, in which an infected cell can commit cell suicide to prevent further spread of the infection; (3) heat shock and other stress responses, which help cells survive under stress conditions, such as infection; (4) inflammatory responses, which can combat infections; (5) unfolded-protein responses or endoplasmic reticulum-associated protein degradation responses, which help cells respond to endoplasmic reticulum stress or protein accumulation, such as can be caused by a pathogen; (6) innate immune responses, which inhibit a broad spectrum of pathogens; and (7) adaptive immune responses, which identify and respond to specific pathogens.
However, many pathogens, for example: viruses such as variola major (smallpox), Ebola, HIV, hepatitis viruses, influenza viruses, papillomaviruses, herpesviruses, and adenoviruses; bacteria such as Mycobacterium species, Salmonella species, Yersinia species, Chlamydia species, Coxiella burnetti, Francisella tularensis, Brucella species, Bordetella species, Listeria monocytogenes, and Legionella pneumophila; fungi such as Histoplasma capsulatum; and protozoa such as Plasmodium species, Trypanosoma species, Leishmania species, and Toxoplasma gondii, have developed methods to evade some or all of these natural defenses.
This invention provides chimeric molecules, agents, and methods of use thereof, which manipulate or modify the natural defenses to be more effective against pathogen infections. This invention is also known as “Pharmacological Augmentation of Nonspecific Anti-pathogen Cellular Enzymes and Activities (PANACEA).”
A chimeric molecule of the invention, as described herein, is composed of at least two domains, said domains being not normally found in association together, or bound to one another, in a cell.
An agent of the invention, as described herein, is one that is non-naturally-occurring in a cell.
A broad spectrum of pathogens will be susceptible to treatment with the agents and chimeric molecules described herein, and include, for example and without limitation: viruses, including those belonging to the families of poxvirus (such as variola major), herpesvirus (such as herpes simplex virus types 1 and 2, varicella-zoster virus, cytomegaloviruses, and Epstein-Barr virus), adenovirus (such as various human adenovirus serotypes), papovavirus (such as human papillomaviruses), hepadnavirus (such as hepatitis B virus), parvovirus (such as parvovirus-like agent), picornavirus (such as poliovirus, Coxsachie viruses A and B, rhinoviruses, and foot-and-mouth disease virus), calicivirus (such as Norwalk agent and hepatitis E virus), togavirus (such as equine encephalitis viruses and rubella virus), flavivirus (such as West Nile virus, yellow fever virus, and Powassan), coronavirus (such as human coronaviruses), reovirus (such as Colorado tick fever virus), rhabdovirus (such as rabies virus), filovirus (such as Ebola and Marburg viruses), paramyxovirus (such as parainfluenza viruses, measles, distemper, rinderpest, and respiratory syncytial virus), orthomyxovirus (such as influenza viruses), bunyavirus (such as Rift Valley fever virus and Hantaan virus), arenavirus (such as Lassa virus), retrovirus (such as human immunodeficiency virus and human T cell leukemia virus), plant viruses, for example: dsDNA plant viruses (such as cauliflower mosaic virus and badnaviruses); ssDNA plant viruses (such as geminiviruses); dsRNA plant viruses (such as plant reoviruses and cryptoviruses); negative-sense or ambisense RNA plant viruses (such as rhabdoviruses, tomato spotted wilt virus, and tenuiviruses); positive-sense ssRNA plant viruses (such as tobacco mosaic virus, tobacco rattle virus, and alfalfa mosaic virus); and viroids (such as potato spindle tuber viroid); and other hepatitis viruses or other viruses; bacteria, such as Treponema pallidum, Borrelia bergdorferi, Helicobacter pylori, Pseudomonas aeruginosa, Legionella pneumophila, Neisseria meningitidis, Neisseria gonorrhoeae, Brucella species, Bordetella pertussis, Francisella tularensis, Escherichia coli, Shigella dysenteriae, Salmonella species, Klebsiella pneumoniae, Proteus species, Yersinia species, Vibrio cholerae, Haemophilus influenzae, Rickettsia species, Coxiella burnetii, Chlamydia species, Mycoplasma species, Staphylococcus species, Streptococcus species, Bacillus anthracis, Clostridium species, Listeria monocytogenes, Corynebacterium diphtheriae, Mycobacterium tuberculosis, Mycobacterium leprae, and other Mycobacterium species, and Nocardia asteroides; prions, such as the causitive agents of kuru, Creutzfeldt-Jakob disease, Gerstmann-Straussler syndrome, scrapie, bovine spongiform encephalopathy, and transmissible mink encephalopathy; protozoa, such as Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Plasmodium falciparum, Toxoplasma gondii, Pneumocystis carinii, Trypanosoma cruzi, Trypanasoma brucei gambiense, Trypanasoma brucei rhodesiense, Leishmania species, Naegleria, Acanthamoeba, Trichomonas vaginalis, Cryptosporidium species, Isospora species, Balantidium coli, Giardia lamblia, Entamoeba histolytica, and Dientamoeba fragilis; fungi, such as Candida albicans, Candida parasilosis, Cryptococcus neoformans, Apergillus fumigatus conidia and Aspergillus fumigatus hyphae; or multicellular parasites including Trichinella spiralis, nematode larvae, Schistosome larvae, Ascaris, Tricuris, filarila worms and the like.
As used herein, a pathogen, which can be detected by a chimeric molecule or agent of the invention, include those parts of the pathogen that are sufficient for their detection by the chimeric molecule or agent. For example, a pathogen component, a pathogen product or an epitope that is pathogen-specific are all encompassed by the term pathogen as used herein.
A pathogen-detection domain, as used herein, is generally directed to a domain that is capable of recognizing or binding a pathogen, pathogen component or product of the pathogen. As used herein, the term pathogen-detection domain is a region of the molecule that includes at least the minimal region necessary to perform the pathogen recognition (also referred to herein as pathogen detection) function of the domain. The pathogen-detection domain can also be encompassed within a larger region or structure, or smaller region or structure, but it still retains the pathogen recognition function of the domain.
More particularly, a detector domain, as used herein, is a molecule that binds to, is stimulated by, or is inhibited by one or more of the following: a pathogen (such as, for example, an extracellular domain of a toll-like receptor that binds to bacteria or other pathogens); a pathogen component (such as, for example, the domain from approximately amino acids 1-199 of human bactericidal/permeability-increasing protein (BPI) that binds to bacterial lipopolysaccharide (LPS)); a pathogen-produced product (such as, for example, the domain from approximately amino acids 1-174 of human PKR that binds to dsRNA produced in virus-infected cells); a pathogen-induced product (such as, for example, the domain from approximately amino acids 1-335 of human RNase L that binds to 2′,5′-oligoadenylate produced in virus-infected cells); or a pathogen-induced signaling molecule (such as, for example, the domain from approximately amino acids 98-1194 that binds to cytochrome c during pathogen-induced apoptotic pathway signaling). A molecule or structure that is detected can belong to multiple categories described supra. For example, dsRNA can be considered a pathogen component, a pathogen-produced product, or a pathogen-induced product.
Pathogen-detection domains can be isolated from naturally-occurring molecules that normally recognize a pathogen, pathogen component or product of said pathogen, such as a cellular protein. Suitable pathogen-detection domains can be isolated from a wide range of known cellular proteins from a number of different organisms, including for example, humans, non-human primates, rodents, plants, Drosophila, yeast, bacteria and the like, as will be appreciated by one of skill in the art. Alternatively, the pathogen-detection domain can be synthetically-derived, such as by chemically modifying a naturally-occurring molecule, or otherwise manipulating a naturally-occurring molecule to enhance, optimize, or modify the pathogen-detection domain, using standard techniques known to those of skill in the art. Additionally, the pathogen-detection domain can be a synthetic product such as a small molecule or a peptidomimetic. Furthermore, a pathogen-detection domain can be an antibody (including, for example, antibody fragments, such as Fab, Fab′, F(ab′)2, and fragments including either a VL or VH domain, single chain antibodies, bi-specific, chimeric or humanized antibodies), that recognizes a specific pathogen epitope, an epitope of a pathogen component or an epitope of a product of the pathogen.
In one embodiment, a pathogen, pathogen component or product of the pathogen, to which a pathogen-detection domain of the chimeric molecule of the invention can bind is double-stranded RNA (dsRNA), which is produced by said pathogen. In a preferred embodiment, the dsRNA is produced by a virus or a virus-infected cell.
Suitable dsRNA binding domains can be isolated from a wide range of known dsRNA-binding proteins from a number of different organisms, including for example, humans, non-human primates, rodents, plants, Drosophila, yeast, bacteria and the like, as will be appreciated by one of skill in the art. Examples of dsRNA-binding proteins include protein kinase R, 2′,5′-oligoadenylate synthases, RNA-specific adenosine deaminase 1 (ADAR1), vaccinia E3L, RNase III, Rnt1p, and Pac1. The identification and isolation of suitable domains from proteins or other molecules of interest can be readily achieved using standard techniques, as will be appreciated by one of skill in the art.
Examples of some dsRNA binding domain-containing proteins and the approximate amino acid position of the dsRNA binding domains are provided in Table 1. The protein, the approximate amino acid location of the dsRNA binding domain region within the protein, and the National Center for Biotechnology Information (NCBI) database accession number are provided in Table 1.
cerevisiae
sapiens
Homo sapiens
sapiens
musculus
dsRNA binding proteins that contain one or more dsRNA binding domains suitable for use in this invention include, for example and without limitation: 2′,5′-oligoadenylate synthetase 100 kDa form, Homo sapiens (NCBI Accession #AAD28543); 2′,5′-oligoadenylate synthetase 69 and 71 kDa forms, Homo sapiens (NCBI Accession #P29728); 2′,5′-oligoadenylate synthetase 41 and 46 kDa forms, Homo sapiens (NCBI Accession #P00973); 2′,5′-oligoadenylate synthetase 1A, Mus musculus (NCBI Accession #P11928); 2′,5′-oligoadenylate synthetase 1B, Mus musculus (NCBI Accession #P29080); 2′,5′-oligoadenylate synthetase 2, Mus musculus (NCBI Accession #SYMS02); 2′,5′-oligoadenylate synthetase 3, Mus musculus (NCBI Accession #SYMS03); RNase III, Homo sapiens (NCBI Accession #AAF80558); RNase III, Escherichia coli (NCBI Accession #NP—417062); Rnt1, Saccharomyces cerevisiae (NCBI Accession #S56053); and Pac1, Schizosaccharomyces pombe (NCBI Accession #S12605). Identification and isolation of a dsRNA binding domain from these or any other proteins will be readily appreciated by one of skill in the art using standard techniques.
Other pathogen-detection domains can be isolated from other dsRNA-binding compounds, including for example, antibiotics such as lividomycin or tobramycin.
A pathogen detection domain can also be a molecule that binds to lipopolysaccharide (LPS), such as the domain of approximately amino acids 1-197 of LPS-binding protein (LBP) (S. L. Abrahamson et al. (1997) Journal of Biological Chemistry 272, 2149-2155; L. J. Beamer et al. (1998) Protein Science 7, 906-914), the domain of approximately amino acids 1-193 of bactericidal/permeability-increasing protein (BPI) (S. L. Abrahamson et al. (1997) Journal of Biological Chemistry 272, 2149-2155; L. J. Beamer et al. (1998) Protein Science 7, 906-914), or a single-chain antibody that binds to LPS.
A pathogen-detection domain can also be a domain that recognizes an epitope which is present in multiple copies or is reiterated on the pathogen, pathogen component or pathogen product.
A pathogen-induced product-detection domain is generally directed to an isolated domain that is capable of recognizing or binding a pathogen-induced product. As used herein, the term pathogen-induced product-detection domain is a region of the molecule that includes at least the minimal region necessary to perform the function of the domain. The pathogen-induced product-detection domain can also be encompassed within a larger or smaller region or structure, but it still retains the pathogen-induced product-detection function of the domain.
Pathogen-induced product-detection domains can be isolated from naturally-occurring molecules that normally recognize a pathogen-induced product, such as a cellular protein that is induced to be expressed by a cell in response to a pathogen or pathogen stimulus. Suitable pathogen-induced product-detection domains can be isolated from a wide range of known cellular proteins from a number of different organisms, including for example, humans, non-human primates, rodents, plants, Drosophila, yeast, bacteria and the like, as will be appreciated by one of skill in the art. The pathogen-induced product-detection domain can also be synthetically-derived, such as by chemically modifying a naturally-occurring molecule, or otherwise manipulating a naturally-occurring molecule to enhance, optimize, or modify the pathogen-induced product-detection domain, using standard techniques known to those of skill in the art, or alternatively, they can be a synthetic product such as a small molecule or a peptidomimetic. Furthermore, a pathogen-induced product-detection domain can be an antibody (including, for example, antibody fragments, such as Fab, Fab′, F(ab′)2, and fragments including either a VL or VH domain, single chain antibodies, bi-specific, chimeric or humanized antibodies), that recognizes a specific pathogen-induced product.
A pathogen-induced product which can be recognized by a pathogen-induced product-detection domain includes, for example and without limitation, cytokines such as an interferon or interleukin, 2′,5′-oligoadenylate, unfolded-protein response or endoplasmic reticulum-associated protein degradation response signaling molecules, stress response or inflammatory response signaling molecules, and apoptosis signaling molecules.
Cytokines such as interferon alpha, interferon beta, or interferon omega are produced by cells in response to a pathogen infection and many genes are responsive to stimulation by such cytokines through suitable inducible promoters, for example and without limitation, promoters that contain one or more interferon-stimulated response elements (ISREs). Examples of suitable promoters are well known to those of skill in the art and include the promoters of the following genes: protein kinase R (K. L. Kuhen and C. E. Samuel (1999) Virology 254, 182-195; H. Tanaka and C. E. Samuel (2000) Gene 246, 373-382); 2′,5′-oligoadenylate synthetases (F. Yu, Q. Wang, and G. Floyd-Smith (1999) Gene 237, 177-184; G. Floyd-Smith, Q. Wang, and G. C. Sen (1999) Exp. Cell Res. 246, 138-147; Q. Wang and G. Floyd-Smith (1998) Gene 222, 83-90); Mx genes (T. Ronni et al. (1998) J. Interferon Cytokine Res. 18, 773-781); ADAR1 (C. X. George and C. E. Samuel (1999) Gene 229, 203-213). The ISRE-containing promoter of the Stratagene PathDetect® ISRE vector (Stratagene #219092) is another example of a promoter that can be induced by cytokines such as interferon alpha, interferon beta, or interferon omega. A pathogen-induced product-detection domain can be an ISRE-containing or other suitable promoter as defined supra that is operatively linked to a polynucleotide sequence encoding an effector domain as described herein, the effector domain being one not typically or normally associated with the promoter.
Cytokines such as interferon gamma, interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 9, interleukin 12, or interleukin 15 are produced by cells in response to a pathogen infection, and many genes are responsive to stimulation by such cytokines through suitable inducible promoters, for example, and without limitation, promoters that contain one or more gamma-activated sequences (GASs), GAS-related sequences, or STAT-protein-binding sequences. Examples of suitable promoters are well known to those of skill in the art (T. Kisseleva et al. (2002) Gene 285, 1-24). The GAS-containing promoter of the Stratagene PathDetect® GAS vector (Stratagene #219093) is an example of a promoter that can be induced by cytokines such as interferon gamma. A pathogen-induced product-detection domain can be an GAS-containing promoter, GAS-related sequence containing promoter, STAT protein binding sequence-containing promoter, or other suitable promoter as defined supra that is operatively linked to a polynucleotide sequence encoding an effector domain as described herein, the effector domain being one not typically or normally associated with the promoter.
In another preferred embodiment, the pathogen-induced product-detection domain is a dsRNA-inducible promoter that is responsive to dsRNA-stimulated cellular signaling. In one embodiment, the promoter is operatively linked to a polynucleotide sequence encoding an effector domain as described herein, said effector domain being one not typically or normally associated with said promoter. Examples of suitable promoters will be appreciated by one of skill in the art and include the promoters of the following genes: interferon-beta (R. Lin et al. (2000) Molecular and Cellular Biology 20, 6342-6353); RANTES (R. Lin et al. (2000) Molecular and Cellular Biology 20, 6342-6353); and other interferon genes (R. M. Roberts et al. (1998) J. Interferon Cytokine Res. 18, 805-816).
Optionally, a promoter that is a pathogen-induced product-detection domain can be conditionally-regulated. For example, the promoter can include a control region that is responsive to drug stimulation, such as an antibiotic. Examples of drug-inducible promoters include a tetracycline-inducible or doxycycline-inducible promoter (for example, Clontech pTRE2hyg vector), which is stimulated with the appropriate transcription factor (for example, Clontech TetOn); a synthetic receptor recognition element promoter (for example, Stratagene pEGSH vector) which is responsive to a synthetic ecdysone-inducible receptor (for example, as expressed by the Stratagene pERV3 vector); or an IPTG-inducible promoter (for example, Stratagene pOPI3CAT and pOPRSVI/MCS vectors) which is responsive via a Lac repressor protein.
Alternatively, a pathogen-induced product-detection domain can be a 2′,5′-oligoadenylate binding domain, such as, for example, isolated from human Rnase L (NCBI Accession #CAA52920). The 2′,5′-oligoadenylate binding domain of human RNase L is approximately amino acids 1-335 (B. Dong and R. H. Silverman (1997) Journal of Biological Chemistry 272, 22236-22242). Rnase L is expressed in a cell in response to a pathogen infection and it contains a 2′,5′-oligoadenylate binding domain which can be isolated using standard techniques, and used as a pathogen-induced product-detection domain in the invention. Furthermore, a single-chain antibody or other molecular structure that binds to 2′,5′-oligoadenylate can be used as a pathogen-induced product-detection domain.
Further pathogen-induced product-detection domains of the invention include apoptosis-activated molecules, for example, and without limitation, an apoptosis-inducible promoter isolated from one or more of the following genes: DIABLO/Smac (P. G. Ekert et al. (2001) J. Cell Biology 152, 483-490; S. M. Srinivasula et al. (2001) Nature 410, 112-116); Fas/APO-1/CD95 (D. Munsch et al. (2000) J. Biological Chemistry 275, 3867-3872; M. Mueller et al. (1998) J. Exp. Med. 188, 2033-2045); Apaf-1 (A. Fortin et al. (2001) J. Cell Biology 155, 207-216); Bax (E. C. Thomborrow and J. J. Manfredi (2001) J. Biological Chemistry 276, 15598-15608); or other genes whose expression is induced in apoptosis, as will be appreciated by one of skill in the art. Another example of an apoptosis-inducible promoter is the p53-binding-site-containing promoter of the Stratagene PathDetect® p53 vector (Stratagene #219083).
Still other pathogen-induced product-detection domains of the invention include promoters that are activated during an unfolded-protein response or endoplasmic reticulum-associated protein degradation responses, for example and without limitation, a suitable promoter containing an endoplasmic reticulum stress response element (ERSE: C. Patil and P. Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee et al. (2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002) Apoptosis 7, 335-345), ATF6-binding motif (K. Lee et al. (2002) Genes & Development 16, 452-466), or amino-acid response element (AARE: T. Okada et al. (2002) Biochem. J. 366, 585-594), or a promoter from a gene whose expression is induced during unfolded-protein responses or endoplasmic reticulum-associated protein degradation responses, as will be appreciated by one of skill in the art.
Other pathogen-induced product-detection domains of the invention include promoters that are activated during stress responses, for example and without limitation, a promoter containing a heat shock element (HSE: S. Ahn et al. (2001) Genes & Development 15, 2134-2145; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171), a promoter from hsp70 or hsp90 genes, or a promoter from another gene whose expression is induced during stress responses, as will be appreciated by one of skill in the art.
Still other pathogen-induced product-detection domains of the invention include promoters that are activated during inflammatory responses, for example and without limitation, a promoter containing an NF-kappa-B binding site (F. E. Chen and G. Ghosh (1999) Oncogene 18, 6845-6852; H. L. Pahl (1999) Oncogene 18, 6853-6866), the NF-kappa-B-inducible promoter of the Stratagene PathDetect® NF-kappaB vector (Stratagene #219077), or a promoter from another gene whose expression is induced during inflammatory responses, as will be appreciated by one of skill in the art.
Other pathogen-induced product-detection domains can be isolated from molecules that are activated or inhibited during apoptosis or other forms of pathogen-triggered cell death (A. Muller and T. Rudel (2001) Int. J. Med. Microbiol. 291, 197-207; C. A. Benedict et al. (2002) Nature Immunology 3, 1013-1018; V. T. Heussler et al. (2001) International Journal for Parasitology 31, 1166-1176; L.-Y. Gao and Y. A. Kwaik (2000) Microbes and Infection 2, 1705-1719; L.-Y. Gao and Y. A. Kwaik (2000) Trends Microbiol. 8, 306-313; K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70; H. R. Stennicke and G. S. Salvesen (2000) Biochimica et Biophysica Acta 1477, 299-306; S. Nagata (1997) Cell 88, 355-365; Z. Song & H. Steller (1999) Trends Cell Biol. 9, M49-52), for example and without limitation: p53 (Homo sapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM—004324); Bid (Homo sapiens, #NM—001196); Bcl-2 (K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70); inhibitor of apoptosis proteins (IAPs: H. R. Stennicke et al. (2002) TRENDS in Biochemical Sciences 27, 94-101; S. M. Srinivasula et al. (2001) Nature 410, 112-116); mitochondrial cytochrome c (K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70; S. B. Bratton et al. (2001) EMBO Journal 20, 998-1009); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens, #NM—013229, NM—001160; Mus musculus, #NP—033814); Fas ligand (Homo sapiens, #D38122; Mus musculus U58995); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410); tumor necrosis factor alpha (TNF-α: Homo sapiens, #CAA01558, CAB63904, CAB63905; Mus musculus, #CAA68530); TNF receptors (Homo sapiens, #NP—001056; V. Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus, #NM—010175); TRADD (Homo sapiens, #NP—003780, CAC38018); perforin (Homo sapiens, #CAA01809, NP—005032; Mus musculus, #CAA42731, CAA35721, AAB01574); granzyme B (Homo sapiens, #AAH30195, NP—004122; Mus musculus, #AAH02085, NP—038570); Smac/DIABLO (Homo sapiens, #NM—019887); caspases (including but not restricted to Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM—001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); calpains (T. Lu et al., (2002) Biochimica et Biophysica Acta 1590, 16-26); caspase-activated DNase (CAD: Homo sapiens, #AB013918; Mus musculus, #AB009377); or inhibitor of caspase-activated DNase (ICAD: Mus musculus, #AB009375, AB009376). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by natural apoptosis or cell death signaling molecules such as those listed supra.
Other pathogen-detection or pathogen-induced product-detection domains can be isolated from molecules that are activated stimulated or inhibited during interferon-related or cytokine-related responses (T. Kisseleva et al. (2002) Gene 285, 1-24; A. Garcia-Sastre (2002) Microbes and Infection 4, 647-655; C. E. Samuel (2001) Clinical Microbiology Reviews 14, 778-809; S. Landolfo et al. (1995) Pharmacol. Ther. 65, 415-442), for example and without limitation: interferon-alpha (Homo sapiens, #NM—002169, NM—021002, J00207; Mus musculus, #NM—010502, NM—010503, NM—010507, NM—008333, M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM—002176; Mus musculus, #NM—010510); interferon-gamma (Homo sapiens, #NM—000619, J00219; Mus musculus, #M28621); interferon-delta; interferon-tau; interferon-omega (Homo sapiens, #NM—002177); interleukin 1 (IL-1: Homo sapiens, #NM—000575, NM—012275, NM—019618, NM—000576, NM—014439; Mus musculus, #NM—019450, NM—019451, AF230378); interleukin 2 (IL-2: Homo sapiens, #NM—000586); interleukin 3 (IL-3: Homo sapiens, #NM—000588; Mus musculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM—000589, NM—172348; Mus musculus, #NM—021283); interleukin 5 (IL-5: Homo sapiens, #NM—000879; Mus musculus, #NM—010558); interleukin 6 (IL-6: Homo sapiens, #NM—000600; Mus musculus, #NM—031168); interleukin 7 (IL-7: Homo sapiens, #NM—000880, AH006906; Mus musculus, #NM—008371); interleukin 9 (IL-9: Homo sapiens, #NM—000590); interleukin 12 (IL-12: Homo sapiens, #NM—000882, NM—002187; Mus musculus, #NM—008351, NM—008352); interleukin 15 (IL-15: Homo sapiens, #NM—172174, NM—172175, NM—000585; Mus musculus, #NM—008357); cytokine receptors and related signaling molecules (W. E. Paul (ed.), Fundamental immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homo sapiens, #NM—000629; Mus musculus, #NM—010508); interferon type I receptor subunit 2 (IFNAR2: Homo sapiens, #NM—000874; Mus musculus, #NM—010509); janus kinase 1 (JAK1: Homo sapiens, #NP—002218; Mus musculus, #NP—666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP—004963; Mus musculus, #NP—032439, AAN62560); JAK3; Tyk2; signal transducer and activator of transcription 1 (STAT1: Homo sapiens, #NM—007315, NM—139266; Mus musculus, #U06924); signal transducer and activator of transcription 2 (STAT2: Homo sapiens, #NM—005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6; IRF9/interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM—006084; Mus musculus, #NM—008394) interferon regulatory factor 1 (IRF1: Homo sapiens, #NM—002198, P10914; Mus musculus, #NM—008390); interferon regulatory factor 3 (IRF3: Homo sapiens, #NM—001571, Z56281; Mus musculus, #NM—016849, U75839, U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997, NP—036187); interferon regulatory factor 6 (IRF6: Homo sapiens, #AF027292, NM—006147; Mus musculus, #U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036; Mus musculus, #NM—016850, U73037); IRF8; protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); eukaryotic translation initiation factor 2 alpha (eIF-2alpha: Homo sapiens, #NP—004085); p58 (Homo sapiens, #NP—006251); 2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); 2′,5′-oligoadenylate (C. E. Samuel (2001) Clinical Microbiology Reviews 14, 778-809); RNase L (Homo sapiens, #CAA52920); promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Mus musculus, #NP—062629); Mx1 (Homo sapiens, #NM—002462); or Mx2 (Homo sapiens, #NM—002463). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by natural interferon-response-related signaling or cytokine response-related molecules such as those listed supra.
Other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from toll-like receptors, their accessory molecules, or molecules that they activate directly or indirectly, (S. Akira (2003) Current Opinion in Immunology 15, 5-11; T. Vasselon and P. A. Detmers (2002) Infection and Immunity 70, 1033-1041; C. A. Janeway Jr. and R. Medzhitov (2002) Annu. Rev. Immunol. 20, 197-216), including for example and without limitation: toll-like receptor 1, Homo sapiens (NCBI Accession #NP—003254, AAC34137); toll-like receptor 2, Homo sapiens (NCBI Accession #AAH33756, AAM23001, AAC34133); toll-like receptor 3, Homo sapiens (NCBI Accession #AAC34134, NP—003256); toll-like receptor 4, Homo sapiens (NCBI Accession #AAC34135, AAF89753, AAF07823, AAF05316); toll-like receptor 5, Homo sapiens (NCBI Accession #AAC34136, BAB43955); toll-like receptor 6, Homo sapiens (NCBI Accession #NP—006059, BAA78631); toll-like receptor 7, Homo sapiens (NCBI Accession #AAF60188, AAF78035, NP—057646, AAH33651); toll-like receptor 8, Homo sapiens (NCBI Accession #AAF64061, AAF78036); toll-like receptor 9 Homo sapiens (NCBI Accession # AAG01734, AAG01735, AAG01736, BAB19259); toll-like receptor 10, Homo sapiens (NCBI Accession #AAK26744, NP—112218); CD14, Homo sapiens (NCBI Accession #AAH10507, AAL02401, CAD36116); MD-2, Homo sapiens (NCBI Accession #NP—056179, BAA78717, AAH20690); MD-1, Homo sapiens (NCBI Accession #AAC98152, NP—004262); RP105, Homo sapiens (NCBI Accession #BAA12019); toll/IL-1 receptor domain containing adaptor protein (TIRAP), Homo sapiens (NCBI Accession #NP—683708, NP—443119, AAL05627); MyD88, Homo sapiens (NCBI Accession #AAB49967, AAC50954); IL-IR activated kinase 4 (IRAK-4), Homo sapiens (NCBI Accession #CAC60090); TNF-receptor-associated factor 6 (TRAF6), Homo sapiens (NCBI Accession #NP—665802, NP—004611); toll-like receptor 1, Mus musculus (NCBI Accession #AAG35062, AAG37302, NP—109607); toll-like receptor 2, Mus musculus (NCBI Accession #AAD46481, AAF04277, AAD49335, NP—036035, AAF28345); toll-like receptor 3, Mus musculus (NCBI Accession #AAK26117, AAL27007, NP—569054); toll-like receptor 4, Mus musculus (NCBI Accession #AAD29272, AAF04278, AAF05317, NP—067272, AAH29856); toll-like receptor 5, Mus musculus (NCBI Accession #AAF65625, NP—058624); toll-like receptor 6, Mus musculus (NCBI Accession #BAA78632, AAG38563, NP—035734); toll-like receptor 7, Mus musculus (NCBI Accession #AAK62676, NP—573474, AAL73191, AAL73192); toll-like receptor 8, Mus musculus (NCBI Accession #NP—573475, AAK62677); toll-like receptor 9, Mus musculus (NCBI Accession #BAB19260, AAK29625, AAK28488, NP—112455); CD14, Mus musculus (NCBI Accession #CAA32166, BAB68578, NP—033971); MD-2, Mus musculus (NCBI Accession #BAA93619); MD-1, Mus musculus (NCBI Accession #BAA32399); RP105, Mus musculus (NCBI Accession #BAA07043); toll/IL-1 receptor domain containing adaptor protein (TIRAP), Mus musculus (NCBI Accession #AAL05628, NP—473437); MyD88, Mus musculus (NCBI Accession #AAC53013); IL-IR activated kinase 4 (IRAK-4), Mus musculus (NCBI Accession #AAM15773, NP—084202); and TNF-receptor-associated factor 6 (TRAF6), Mus musculus (NCBI Accession #BAA12705, NP—033450). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by toll-like-receptor-pathway-related molecules.
Still other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from nucleotide-binding oligomerization domain (NOD) proteins, or nucleotide-binding-domain (NBD)proteins, or nucleotide-binding-site (NBS)) proteins, or molecules that they activate directly or indirectly, (N. Inohara et al. (2002) Current Opinion in Microbiology 5, 76-80; S. E. Girardin et al. (2002) TRENDS in Microbiology 10, 193-199; J. A. Harton et al. (2002) Journal of Immunology 169, 4088-4093; N. Inohara et al. (2000) Journal of Biological Chemistry 275, 27823-27831), including but not limited to:Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM-021209, AY035391; J.-L. Poyet et al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054, AY084055, AF410154, NM—000246, X74301; M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM—033004, NM—033005, NM—033006, NM—033007, NM—014922); NBS1/NALP2 (Homo sapiens, #AF310106, NM—017852); cryopyrin/CIAS1 (Homo sapiens, #AF410477, AF427617, AH01140, NM—004895); RIP (Homo sapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93, 10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396); Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al. (1998) Journal of Biological Chemistry 273, 18675; M. Thome et al. (1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002) Journal of Biological Chemistry 277, 31871-31876). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by NOD protein pathway-related molecules.
Other pathogen-detection domains or pathogen-induced product-detection domains can also be isolated from pentraxins or molecules that they activate directly or indirectly, (H. Gewurz et al. (1995) Current Opinion in Immunology 7, 54-64), including, but not limited to, C-reactive protein (CRP), Homo sapiens (NCBI Accession #1GNHA, 1GNHB, 1GNHC, 1GNHD, 1GNHE, 1GNHF, 1GNHG, 1GNHH, 1GNHI, 1GNHJ); C-reactive protein (CRP), Mus musculus (NCBI Accession #CAA31928, NP 031794); serum amyloid P component (SAP), Homo sapiens (NCBI Accession #1SACA, 1SACB, 1SACC, 1SACD, 1SACE); and serum amyloid P component (SAP), Mus musculus (NCBI Accession #NP—035448, CAA34774). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by pentraxin pathway-related molecules.
Other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from collectins or molecules that they activate directly or indirectly, (M. Gadjeva et al. (2001) Current Opinion in Immunology 13, 74-78; U. L. Holmskov (2000) APMIS Suppl. 100, 1-59), including for example and without limitation, mannan/mannose binding lectin (MBL), Homo sapiens (NCBI Accession #AAK52907, CAB56120, CAB56044); mannan/mannose binding lectin (MBL), Mus musculus (NCBI Accession #NP—034905, NP—034906); MBL-associated serine protease 1 (MASP1), Homo sapiens (NCBI Accession #NP—001870, NP—624302); MBL-associated serine protease 2 (MASP2), Homo sapiens (NCBI Accession #NP—006601, NP—631947, AAG50274, BAA85659); MBL-associated serine protease 1 (MASP1), Mus musculus (NCBI Accession #XP—193834); MBL-associated serine protease 2 (MASP2), Mus musculus (NCBI Accession #BAA34674, CAB65247, CAB65250); MBL-associated serine protease 3 (MASP3), Mus musculus (NCBI Accession #BAB69688); surfactant protein A (SP-A), Homo sapiens (NCBI Accession #NP—005402, NP—008857); surfactant protein D (SP-D), Homo sapiens (NCBI Accession #CAA46152, NP—003010); surfactant protein D (SP-D), Mus musculus (NCBI Accession #AAF15277); surfactant protein D (SP-D), Bos taurus (NCBI Accession #CAA53510, S33603); conglutinin, Bos taurus (NCBI Accession #CAA50665, BAA03170); collectin-43 (CL-43), Bos taurus (NCBI Accession #CAA53511, P42916, A53570); collectin-L1, Mus musculus (NCBI Accession #BAC53954); and collectin placenta 1 (CL-P1), Homo sapiens (NCBI Accession #AB005145). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by collectin pathway-related molecules.
Still other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from mannose receptors or molecules that they activate directly or indirectly, (L. East and C. M. Isacke (2002) Biochimica et Biophysica Acta 1572, 364-386; S. Zamze et al. (2002) Journal of Biological Chemistry 277, 41613-41623), including for example and without limitation, mannose receptor (MR), Homo sapiens(NCBI Accession #NM—002438); and mannose receptor (MR), Mus musculus (NCBI Accession #CAA78028, NP—032651, NP—032652). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by mannose receptor pathway-related molecules.
Other pathogen-detection domains or pathogen-induced product-detection domains can also be isolated from scavenger receptors or molecules that they activate directly or indirectly, (L. Peiser et al. (2002) Current Opinion in Immunology 14, 123-128; A. Brannstrom et al. (2002) Biochemical and Biophysical Research Communications 290, 1462-1469), including for example and without limitation, scavenger receptor A I (SR-A I), Homo sapiens (NCBI Accession #D90187); scavenger receptor A II (SR-A II), Homo sapiens (NCBI Accession #D90188); scavenger receptor A I (SR-A I), Mus musculus (NCBI Accession #L04274); scavenger receptor A II (SR-A II), Mus musculus (NCBI Accession #L04275); macrophage receptor with collagenous structure (MARCO), Homo sapiens (NCBI Accession #NP—006761); macrophage receptor with collagenous structure (MARCO), Mus musculus (NCBI Accession #NP—034896); scavenger receptor with C-type lectin I (SR-CL I), Homo sapiens (NCBI Accession #BAB39147); scavenger receptor with C-type lectin II (SR-CL II), Homo sapiens (NCBI Accession #BAB39148); and scavenger receptor with C-type lectin (SR-CL), Mus musculus (NCBI Accession #BAB82497). A pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by scavenger-receptor-pathway-related molecules.
Other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from molecules that initiate, signal, or detect immune-related responses (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999); M. T. M. Vossen et al. (2002) Immunogenetics 54, 527-542), for example and without limitation the following molecules or DNA or RNA encoding them: MHC Class I; MHC Class II; antibodies; single-chain antibodies; T cell receptors; Fc receptors; NK cell activation receptors (including but not limited to NKp46, Ly49H, and NKG2D; A. Diefenbach and D. H. Raulet (2003) Current Opinion in Immunology 15, 37-44; A. R. French and W. M. Yokoyama (2003) Current Opinion in Immunology 15, 45-51); NK cell inhibitory receptors; receptor-associated tyrosine kinases; or phospholipase C. A pathogen-detection domain or pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by immune-response-pathway-related molecules.
Other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from molecules that are activated or inhibited during unfolded protein response-related or endoplasmic reticulum-associated protein degradation-related responses (C. Patil and P. Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee et al. (2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002) Apoptosis 7, 335-345), for example and without limitation: BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949, NM—005347; Mus musculus, #NM—022310); PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens, #NP—004827; Mus musculus, #AAD03337, NP—034251); IRE1 alpha (Homo sapiens, #AF059198; Mus musculus, #AB031332, AF071777); IRE1 beta (Homo sapiens, #AB047079); RNA for IRE1 alpha or IRE1 beta (W. Tirasophon et al. (2000) Genes & Development 14, 2725-2736); p58 (Homo sapiens, #NP—006251; W. Yan et al. (2002) Proc. Natl. Acad. Sci. USA 99, 15920-15925); activating transcription factor 4 (ATF4: Homo sapiens, #NM—001675; Mus musculus, #NM—009716); activating transcription factor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM—007348, AF005887, AB015856; Mus musculus, #XM—129579); X-box binding protein 1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM—013842); XBP1 RNA (K. Lee et al. (2002) Genes & Development 16, 452-466; H. Yoshida et al. (2001) Cell 107, 881-891); CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM—004083; Mus musculus, #X67083, NM—007837); site-1 protease (S1P: Homo sapiens, #NM—003791; Mus musculus, #NM—019709); site-2 protease (S2P: Homo sapiens, #NM—015884); presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus, #BC030409, NM—008943, AF149111); TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM—021138, NM—145718, Mus musculus, #XM—203851, XM—130119, L35303); cJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7, 335-345); or eukaryotic translation initiation factor 2 alpha (eIF-2alpha: Homo sapiens, #NP—004085). A pathogen-detection domain or pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by natural unfolded protein response-related or endoplasmic reticulum-associated protein degradation-related molecules such as those listed supra.
Still other pathogen-induced product-detection domains of the invention include a promoter that is activated or inhibited during an unfolded-protein response or endoplasmic-reticulum-associated-protein-degradation response, for example and without limitation, an isolated promoter containing an endoplasmic reticulum stress response element (ERSE: C. Patil and P. Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee et al. (2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002) Apoptosis 7, 335-345), ATF6-binding motif (K. Lee et al. (2002) Genes & Development 16, 452-466), or amino-acid response element (AARE: T. Okada et al. (2002) Biochem. J. 366, 585-594), or a promoter from a gene whose expression is induced or repressed during an unfolded-protein response or endoplasmic-reticulum-associated-protein-degradation response, as will be appreciated by one of skill in the art.
Other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from molecules that are activated or inhibited during a stress or inflammatory response (R. I. Morimoto and M. G. Santoro (1998) Nature Biotech. 16, 833-838; R. I. Morimoto (1998) Genes & Dev. 12, 3788-3796; M. G. Santoro (2000) Biochem. Pharmacol. 59, 55-63; A. De Marco et al. (1998) Eur. J. Biochem. 256, 334-341; C. Conti et al. (1999) Antimicrobial Agents and Chemotherapy 43, 822-829; M. G. Santoro (1996) EXS 77, 337-357; E. A. A. Nollen and R. I. Morimoto (2002) Journal of Cell Science 115, 2809-2816; J. Hiscott et al. (2001) J. Clinical Investigation 107, 143-151; E. N. Hatada et al. (2000) Curr. Opin. Immunol. 12, 52-58; T. Wang et al. (2002) Int. Immunopharmacol. 2, 1509-1520; X. Li and G. R. Stark (2002) Exp. Hematol. 30, 285-296; Z. Sun and R. Andersson (2002) Shock 18, 99-106; H. L. Pahl (1999) Oncogene 18, 6853-6866; F. Mercurio and A. M. Manning Oncogene 18, 6163-6167)), for example and without limitation: heat shock protein 70 or related proteins (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM—016299, NM—005346, NM—005345, NM—002155, NM—021979, AF093759; Mus musculus, #XM—207065, XM—128584, XM—128585, XM—110217, NM—015765, NM—010481, NM—008301, M76613); Hsp90 (Homo sapiens, #M16660, NM—005348, NM—007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM—006145, NM—005880); Hsc70 (Homo sapiens, #AF352832); Hsp47/CBP-2 (Homo sapiens, #D83174); cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110); Bip/GRP78; Hsp60 (Homo sapiens, #NM—002156); Hsp100 (Homo sapiens, #NM—006660); Alpha-A-crystallin (Homo sapiens, #NM—000394); Alpha-B-crystallin (Homo sapiens, #NM—001885); Hsp27-1 (Homo sapiens, #NM—001540); Hsp27-2 (Homo sapiens, #XM—012054); heat shock factor 1 (HSF1: Homo sapiens, #NM—005526, M64673; Mus musculus, #XM—128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131); heat shock factor 2 (HSF2: Homo sapiens, #NM—004506; Mus musculus, #X61754, AH007205, NM—008297); heat shock factor 3 (HSF3: L. Pirkkala et al. (2001) FASEB J. 15, 1.118-1131); heat shock factor 4 (HSF4: Homo sapiens, #NM—001538, D87673, AB029348; Mus musculus, #AF160965, AF160966, AB029349, AB029350); heat shock factor binding protein 1 (HSBP1: Homo sapiens, #NM—001537, BC007515, AF068754); heat shock factor 2 binding protein (HSF2BP: Homo sapiens, #NM—007031); RelA/p65 (Homo sapiens, #NM—021975, Z22948, L19067; Mus musculus, #NM—009045, AF199371); RelB (Homo sapiens, #NM—006509; Mus musculus, #NM—009046, M83380); c-Rel (Homo sapiens, #X75042, NM—002908; Mus musculus, #NM—009044, X15842); p50/p105/NF-kappa B 1 (Homo sapiens, #NM—003998, S76638, AF213884, AH009144; Mus musculus, #NM—008689, AK052726, M57999); p52/p100/NF-kappa B 2 (Homo sapiens, #NM—002502; Mus musculus, #AF155372, AF155373, NM—019408); inhibitors of kappa B (I kappa B: Homo sapiens, #AY033600, NM—020529; S. Ghosh and M. Karin (2002) Cell 109, S81-S96); IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, # AF009225, AF080157); IKK2/I kappa B kinase beta (IKK beta: Homo sapiens, #AF080158; Mus musculus, #AF026524, AF088910); NEMO/I kappa B kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus, #AF069542). A pathogen detection domain or pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by a stress response-related or inflammatory response-related molecule such as those listed supra.
Still other pathogen-induced product-detection domains of the invention include promoters that are activated or inhibited during stress or inflammatory responses, for example and without limitation, a promoter containing a heat shock element (HSE: S. Ahn et al. (2001) Genes & Development 15, 2134-2145; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171) or NF-kappa-B binding site (F. E. Chen and G. Ghosh (1999) Oncogene 18, 6845-6852; H. L. Pahl (1999) Oncogene 18, 6853-6866), a promoter from hsp70 or hsp90 genes, or a promoter from another gene whose expression is induced or repressed during stress or inflammatory responses as will be appreciated by one of skill in the art.
Other pathogen-detection domains or pathogen-induced product-detection domains can be isolated from complement pathway-related molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapter 29; M. K. Pangburn et al. (2000) Journal of Immunology 164, 4742-4751), for example and without limitation: C3 alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF. A pathogen detection domain or pathogen-induced product-detection domain can also be isolated from a molecule that binds to, is activated by, or is inhibited by natural complement pathway-related molecules such as those listed supra.
Effector domains of this invention can mediate, either directly or indirectly, a wide range of effector functions. These include, for example and without limitation, one or more of the following responses: (1) an interferon response; (2) an apoptosis response; (3) stress response; (4) an enhanced immune response; (5) the expression of a double-stranded RNase; (6) inhibition of nuclear localization of targets; (7) inhibition of endosome function or activity; and other anti-pathogen responses.
As used herein, the effector domain is a region of the molecule that includes at least the minimal region necessary to perform the described effector function of the domain. The effector domain can also be encompassed within a larger or smaller region or structure, but it still retains the effector function of the domain.
More particularly, an effector domain as used herein is a molecule that binds to or acts on one or more of the following: a pathogen (for example: a peptide containing amino acids 119-136 of hamster prion protein that binds to and inhibits a pathogenic prion); a pathogen component (for example, a molecule that binds to a viral late domain motif, thereby inhibiting viral budding or release, as described herein); a molecule produced or induced by a pathogen (for example, an RNase III that degrades dsRNA produced in a virus-infected cell, as described herein); a natural anti-pathogen molecule (for example, a molecule that activates caspases in an infected cell, thereby killing said cell and preventing further spread of the infection); a component that is naturally occurring in a cell or organism and that directly or indirectly activates or inhibits an anti-pathogen molecule, or a component that is naturally occurring within a cell or organism and that aids a pathogen or pathogenic effect (for example, a molecule that binds to vacuolar ATPase and inhibits acidification of endosomes in a cell, thereby inhibiting infection of the cell by a virus, as described herein). By binding or acting as described supra and herein, the effector domain exerts an anti-pathogen effect, for example, and without limitation, by performing one or more of the following functions: inhibiting infection of a cell or organism by a pathogen; inhibiting replication of a pathogen; destroying or neutralizing a pathogen; or making a pathogen more vulnerable to other therapeutic anti-pathogen molecules or to natural anti-pathogen molecules. An effector domain can belong to multiple categories described herein.
Effector domains can be isolated from naturally-occurring molecules that normally mediate the function of an effector domain as described herein, such as a cellular protein. Effector domains can be isolated from a wide range of known cellular proteins from a number of different organisms, including for example, humans, non-human primates, rodents, plants, Drosophila, yeast, bacteria and the like, as will be appreciated by one of skill in the art. The effector domain can also be synthetically-derived, such as by chemically modifying a naturally-occurring molecule, or otherwise manipulating a naturally-occurring molecule to enhance, optimize, or modify the effector domain, using standard techniques known to those of skill in the art. Alternatively, an effector domain can be a synthetic product such as a small molecule or a peptidomimetic. Furthermore, an effector domain can be an antibody (including, for example, antibody fragments, such as Fab, Fab′, F(ab′)2, and fragments including either a VL or VH domain, single chain antibodies, bi-specific, chimeric or humanized antibodies), that performs the function of an effector domain.
Effector domains can be isolated from molecules that execute, stimulate, or inhibit apoptosis or other forms of cell death (A. Muller and T. Rudel (2001) Int. J. Med. Microbiol. 291, 197-207; C. A. Benedict et al. (2002) Nature Immunology 3, 1013-1018; V. T. Heussler et al. (2001) International Journal for Parasitology 31, 1166-1176; L.-Y. Gao and Y. A. Kwaik (2000) Microbes and Infection 2, 1705-1719; L.-Y. Gao and Y. A. Kwaik (2000) Trends Microbiol. 8, 306-313; K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70; H. R. Stennicke and G. S. Salvesen (2000) Biochimica et Biophysica Acta 1477, 299-306; S. Nagata (1997) Cell 88, 355-365; Z. Song & H. Steller (1999) Trends Cell Biol. 9, M49-52), for example and without limitation, the following molecules or DNA or RNA encoding them: p53 (Homo sapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM—004324); Bid (Homo sapiens, #NM—001196); Bcl-2 (K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70); inhibitor of apoptosis proteins (IAPs: H. R. Stennicke et al. (2002) TRENDS in Biochemical Sciences 27, 94-101; S. M. Srinivasula et al. (2001) Nature 410, 112-116); mitochondrial cytochrome c (K. C. Zimmermann et al. (2001) Pharmacology & Therapeutics 92, 57-70; S. B. Bratton et al. (2001) EMBO Journal 20, 998-1009); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens, #NM—013229, NM—001160; Mus musculus, #NP—033814); Fas ligand (Homo sapiens, #D38122; Mus musculus U58995); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410); tumor necrosis factor alpha (TNF-a: Homo sapiens, #CAA01558, CAB63904, CAB63905; Mus musculus, #CAA68530); TNF receptors (Homo sapiens, #NP—001056; V. Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus, #NM—010175); TRADD (Homo sapiens, #NP—003780, CAC38018); perforin (Homo sapiens, #CAA01809, NP—005032; Mus musculus, #CAA42731, CAA35721, AAB01574); granzyme B (Homo sapiens, #AAH30195, NP—004122; Mus musculus, #AAH02085, NP—038570); Smac/DIABLO (Homo sapiens, #NM—019887); caspases (including but not restricted to Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM—001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); calpains (T. Lu et al., (2002) Biochimica et Biophysica Acta 1590, 16-26); caspase-activated DNase (CAD: Homo sapiens, #AB013918; Mus musculus, #AB009377); or inhibitor of caspase-activated DNase (ICAD: Mus musculus, #AB009375, AB009376). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural apoptosis or cell death signaling molecules such as those listed supra.
Other effector domains can be isolated from molecules that execute, stimulate, or inhibit interferon-related or cytokine-related responses (T. Kisseleva et al. (2002) Gene 285, 1-24; A. Garcia-Sastre (2002) Microbes and Infection 4, 647-655; C. E. Samuel (2001) Clinical Microbiology Reviews 14, 778-809; S. Landolfo et al. (1995) Pharmacol. Ther. 65, 415-442), for example and without limitation, the following molecules or DNA or RNA encoding them: interferon-alpha (Homo sapiens, #NM—002169, NM—021002, J00207; Mus musculus, #NM—010502, NM—010503, NM—010507, NM—008333, M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM—002176; Mus musculus, #NM—010510); interferon-gamma (Homo sapiens, #NM—000619, J00219; Mus musculus, #M28621); interferon-delta; interferon-tau; interferon-omega (Homo sapiens, #NM—002177); interleukin 1 (IL-1: Homo sapiens, #NM—000575, NM—012275, NM—019618, NM—000576, NM—014439; Mus musculus, #NM—019450, NM—019451, AF230378); interleukin 2 (IL-2: Homo sapiens, #NM—000586); interleukin 3 (IL-3: Homo sapiens, #NM—000588; Mus musculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM—000589, NM—172348; Mus musculus, #NM—021283); interleukin 5 (IL-5: Homo sapiens, #NM—000879; Mus musculus, #NM—010558); interleukin 6 (IL-6: Homo sapiens, #NM—000600; Mus musculus, #NM—031168); interleukin 7 (IL-7: Homo sapiens, #NM—000880, AH006906; Mus musculus, #NM—008371); interleukin 9 (IL-9: Homo sapiens, #NM—000590); interleukin 12 (IL-12: Homo sapiens, #NM—000882, NM—002187; Mus musculus, #NM—008351, NM—008352); interleukin 15 (IL-15: Homo sapiens, #NM—172174, NM—172175, NM—000585; Mus musculus, #NM—008357); cytokine receptors and related signaling molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homo sapiens, #NM—000629; Mus musculus, #NM—010508); interferon type I receptor subunit 2 (IFNAR2: Homo sapiens, #NM—000874; Mus musculus, #NM—010509); janus kinase 1 (JAK1: Homo sapiens, #NP—002218; Mus musculus, #NP—666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP—004963; Mus musculus, #NP—032439, AAN62560); JAK3; Tyk2; signal transducer and activator of transcription 1 (STAT1: Homo sapiens, #NM—007315, NM—139266; Mus musculus, #U06924); signal transducer and activator of transcription 2 (STAT2: Homo sapiens, #NM—005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6; IRF9/interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM—006084; Mus musculus, #NM—008394) interferon regulatory factor 1 (IRF1: Homo sapiens, #NM—002198, P10914; Mus musculus, #NM—008390); interferon regulatory factor 3 (IRF3: Homo sapiens, #NM—001571, Z56281; Mus musculus, #NM—016849, U75839, U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997, NP—036187); interferon regulatory factor 6 (IRF6: Homo sapiens, #AF027292, NM—006147; Mus musculus, #U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036; Mus musculus, #NM—016850, U73037); protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); eukaryotic translation initiation factor 2 alpha (eIF-2alpha: Homo sapiens, #NP—004085); p58 (Homo sapiens, #NP—006251); 2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); 2′,5′-oligoadenylate (C. E. Samuel (2001) Clinical Microbiology Reviews 14, 778-809); RNase L (Homo sapiens, #CAA52920); promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Mus musculus, #NP—062629); Mx1 (Homo sapiens, #NM—002462); or Mx2 (Homo sapiens, #NM—002463). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural interferon-response-related or cytokine-response related molecules such as those listed supra.
Other effector domains can be isolated from molecules that execute, stimulate, or inhibit stress or inflammatory responses (R. I. Morimoto and M. G. Santoro (1998) Nature Biotech. 16, 833-838; R. I. Morimoto (1998) Genes & Dev. 12, 3788-3796; M. G. Santoro (2000) Biochem. Pharmacol. 59, 55-63; A. De Marco et al. (1998) Eur. J. Biochem. 256, 334-341; C. Conti et al. (1999) Antimicrobial Agents and Chemotherapy 43, 822-829; M. G. Santoro (1996) EXS 77, 337-357; E. A. A. Nollen and R. I. Morimoto (2002) Journal of Cell Science 115, 2809-2816; J. Hiscott et al. (2001) J. Clinical Investigation 107, 143-151; E. N. Hatada et al. (2000) Curr. Opin. Immunol. 12, 52-58; T. Wang et al. (2002) Int. Immunopharmacol. 2, 1509-1520; X. Li and G. R. Stark (2002) Exp. Hematol. 30, 285-296; Z. Sun and R. Andersson (2002) Shock 18, 99-106; H. L. Pahl (1999) Oncogene 18, 6853-6866; F. Mercurio and A. M. Manning Oncogene 18, 6163-6167)), for example and without limitation, the following molecules or DNA or RNA encoding them: heat shock protein 70 or related proteins (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM—016299, NM—005346, NM—005345, NM—002155, NM—021979, AF093759; Mus musculus, #XM—207065, XM—128584, XM—128585, XM—110217, NM—015765, NM—010481, NM—008301, M76613); Hsp90 (Homo sapiens, #M16660, NM—005348, NM—007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM—006145, NM—005880); Hsc70 (Homo sapiens, #AF352832); Hsp47/CBP-2 (Homo sapiens, #D83174); cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110); Bip/GRP78; Hsp60 (Homo sapiens, #NM—002156); Hsp100 (Homo sapiens, #NM—006660); Alpha-A-crystallin (Homo sapiens, #NM—000394); Alpha-B-crystallin (Homo sapiens, #NM—001885); Hsp27-1 (Homo sapiens, #NM—001540); Hsp27-2 (Homo sapiens, #XM—012054); heat shock factor 1 (HSF1: Homo sapiens, #NM—005526, M64673; Mus musculus, #XM—128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131); heat shock factor 2 (HSF2: Homo sapiens, #NM—004506; Mus musculus, #X61754, AH007205, NM—008297); heat shock factor 3 (HSF3: L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131); heat shock factor 4 (HSF4: Homo sapiens, #NM—001538, D87673, AB029348; Mus musculus, #AF160965, AF160966, AB029349, AB029350); heat shock factor binding protein 1 (HSBP1: Homo sapiens, #NM—001537, BC007515, AF068754); heat shock factor 2 binding protein (HSF2BP: Homo sapiens, #NM—007031); RelA/p65 (Homo sapiens, #NM—021975, Z22948, L19067; Mus musculus, #NM—009045, AF199371); RelB (Homo sapiens, #NM—006509; Mus musculus, #NM—009046, M83380); c-Rel (Homo sapiens, #X75042, NM—002908; Mus musculus, #NM—009044, X15842); p50/p105/NF-kappa B 1 (Homo sapiens, #NM—003998, S76638, AF213884, AH009144; Mus musculus, #NM—008689, AK052726, M57999); p52/p100/NF-kappa B 2 (Homo sapiens, #NM—002502; Mus musculus, #AF155372, AF155373, NM—019408); inhibitors of kappa B (I kappa B: Homo sapiens, #AY033600, NM—020529; S. Ghosh and M. Karin (2002) Cell 109, S81-S96); IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, # AF009225, AF080157); IKK2/1 kappa B kinase beta (IKK beta: Homo sapiens, #AF080158; Mus musculus, #AF026524, AF088910); NEMO/I kappa B kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus, #AF069542). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural stress-response-related or inflammatory-response-related molecules such as those listed supra.
Other effector domains can be isolated from molecules that execute, stimulate, or inhibit unfolded protein response-related or endoplasmic reticulum-associated protein degradation-related responses (C. Patil and P. Walter (2001) Current Opinion in Cell Biology 13, 349-356; K. Lee et al. (2002) Genes & Development 16, 452-466; S. Oyadomari et al. (2002) Apoptosis 7, 335-345), for example and without limitation, the following molecules or DNA or RNA encoding them: BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949, NM—005347; Mus musculus, #NM—022310); PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens, #NP—004827; Mus musculus, #AAD03337, NP—034251); IRE1 alpha (Homo sapiens, #AF059198; Mus musculus, #AB031332, AF071777); IRE1 beta (Homo sapiens, #AB047079); RNA for IRE1 alpha or IRE1 beta (W. Tirasophon et al. (2000) Genes & Development 14, 2725-2736); p58 (Homo sapiens, #NP—006251; W. Yan et al. (2002) Proc. Natl. Acad. Sci. USA 99, 15920-15925); activating transcription factor 4 (ATF4: Homo sapiens, #NM—001675; Mus musculus, #NM—009716); activating transcription factor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM—007348, AF005887, AB015856; Mus musculus, #XM—129579); X-box binding protein 1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM—013842); XBP1 RNA (K. Lee et al. (2002) Genes & Development 16, 452-466; H. Yoshida et al. (2001) Cell 107, 881-891); CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM—004083; Mus musculus, #X67083, NM—007837); site-1 protease (S1P: Homo sapiens, #NM—003791; Mus musculus, #NM—019709); site-2 protease (S2P: Homo sapiens, #NM—015884); presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus, #BC030409, NM—008943, AF149111); TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM—021138, NM—145718, Mus musculus, #XM—203851, XM—130119, L35303); cJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7, 335-345); or eukaryotic translation initiation factor 2 alpha (eIF-2alpha: Homo sapiens, #NP—004085). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural unfolded protein response-related or endoplasmic reticulum-associated protein degradation-related molecules such as those listed supra.
An effector domain can be any naturally or non-naturally occurring molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen. Such effector domains include, for example and without limitation, an antibody, antibody fragment, single-chain antibody, peptidomimetic, or synthesized molecule. An effector domain can also be an antisense polynucleotide or small interfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl. Acad. Sci. USA 99, 14943-14945) that inhibits expression of a pathogen gene or a host gene that aids a pathogen. An effector domain can also be DNA or RNA that encodes a molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen. In addition, an effector domain can be any molecule that synthesizes a molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen.
Other effector domains can be isolated from complement pathway-related molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapter 29; M. K. Pangburn et al. (2000) Journal of Immunology 164, 4742-4751), for example and without limitation, the following molecules or DNA or RNA encoding them: C3 alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF. An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural complement pathway-related molecules such as those listed supra.
Other effector domains can be isolated from toll-like receptors, their accessory molecules, or molecules that they activate directly or indirectly, (S. Akira (2003) Current Opinion in Immunology 15, 5-11; T. Vasselon and P. A. Detmers (2002) Infection and Immunity 70, 1033-1041; C. A. Janeway Jr. and R. Medzhitov (2002) Annu. Rev. Immunol. 20, 197-216), including for example and without limitation, the following molecules or DNA or RNA encoding them: toll-like receptor 1, Homo sapiens (NCBI Accession #NP—003254, AAC34137); toll-like receptor 2, Homo sapiens (NCBI Accession #AAH33756, AAM23001, AAC34133); toll-like receptor 3, Homo sapiens (NCBI Accession #AAC34134, NP—003256); toll-like receptor 4, Homo sapiens (NCBI Accession #AAC34135, AAF89753, AAF07823, AAF05316); toll-like receptor 5, Homo sapiens (NCBI Accession #AAC34136, BAB43955); toll-like receptor 6, Homo sapiens (NCBI Accession #NP—006059, BAA78631); toll-like receptor 7, Homo sapiens (NCBI Accession #AAF60188, AAF78035, NP—057646, AAH33651); toll-like receptor 8, Homo sapiens (NCBI Accession #AAF64061, AAF78036); toll-like receptor 9 Homo sapiens (NCBI Accession # AAG01734, AAG01735, AAG01736, BAB19259); toll-like receptor 10, Homo sapiens (NCBI Accession #AAK26744, NP—112218); CD 14, Homo sapiens (NCBI Accession #AAH10507, AAL02401, CAD36116); MD-2, Homo sapiens (NCBI Accession #NP—056179, BAA78717, AAH20690); MD-1, Homo sapiens (NCBI Accession #AAC98152, NP—004262); RP105, Homo sapiens (NCBI Accession #BAA12019); toll/IL-1 receptor domain containing adaptor protein (TIRAP), Homo sapiens (NCBI Accession #NP—683708, NP—443119, AAL05627); MyD88, Homo sapiens (NCBI Accession #AAB49967, AAC50954); IL-1R activated kinase 4 (IRAK-4), Homo sapiens (NCBI Accession #CAC60090); TNF-receptor-associated factor 6 (TRAF6), Homo sapiens (NCBI Accession #NP—665802, NP—004611); toll-like receptor 1, Mus musculus (NCBI Accession #AAG35062, AAG37302, NP—109607); toll-like receptor 2, Mus musculus (NCBI Accession #AAD46481, AAF04277, AAD49335, NP—036035, AAF28345); toll-like receptor 3, Mus musculus (NCBI Accession #AAK26117, AAL27007, NP—569054); toll-like receptor 4, Mus musculus (NCBI Accession #AAD29272, AAF04278, AAF05317, NP—067272, AAH29856); toll-like receptor 5, Mus musculus (NCBI Accession #AAF65625, NP—058624); toll-like receptor 6, Mus musculus (NCBI Accession #BAA78632, AAG38563, NP—035734); toll-like receptor 7, Mus musculus (NCBI Accession #AAK62676, NP—573474, AAL73191, AAL73192); toll-like receptor 8, Mus musculus (NCBI Accession #NP—573475, AAK62677); toll-like receptor 9, Mus musculus (NCBI Accession #BAB19260, AAK29625, AAK28488, NP—112455); CD14, Mus musculus (NCBI Accession #CAA32166, BAB68578, NP—033971); MD-2, Mus musculus (NCBI Accession #BAA93619); MD-1, Mus musculus (NCBI Accession #BAA32399); RP105, Mus musculus (NCBI Accession #BAA07043); toll/IL-1 receptor domain containing adaptor protein (TIRAP), Mus musculus (NCBI Accession #AAL05628, NP—473437); MyD88, Mus musculus (NCBI Accession #AAC53013); IL-IR activated kinase 4 (IAK-4), Mus musculus (NCBI Accession #AAM15773, NP—084202); or TNF-receptor-associated factor 6 (TRAF6), Mus musculus (NCBI Accession #BAA12705, NP—033450). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural toll-like-receptor response-related molecules such as those listed supra.
Still other effector domains can be isolated from nucleotide-binding oligomerization domain (NOD), or nucleotide-binding-domain (NBD), or nucleotide-binding-site (NBS), proteins or molecules that they activate directly or indirectly, (N. Inohara et al. (2002) Current Opinion in Microbiology 5, 76-80; S. E. Girardin et al. (2002) TRENDS in Microbiology 10, 193-199; J. A. Harton et al. (2002) Journal of Immunology 169, 4088-4093; N. Inohara et al. (2000) Journal of Biological Chemistry 275, 27823-27831), including for example and without limitation, the following molecules or DNA or RNA encoding them:Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM—021209, AY035391; J.-L. Poyet et al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054, AY084055, AF410154, NM—000246, X74301; M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM—033004, NM—033005, NM—033006, NM—033007, NM—014922); NBS1/NALP2 (Homo sapiens, #AF310106, NM—017852); cryopyrin/CIAS1 (Homo sapiens, #AF410477, AF427617, AH011140, NM—004895); RIP (Homo sapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93, 10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396); Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al. (1998) Journal of Biological Chemistry 273, 18675; M. Thome et al. (1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002) Journal of Biological Chemistry 277, 31871-31876). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural NOD-response-related molecules such as those listed supra.
Effector domains can also be isolated from pentraxins or molecules that they activate directly or indirectly, (H. Gewurz et al. (1995) Current Opinion in Immunology 7, 54-64), including for example and without limitation, the following molecules or DNA or RNA encoding them: C-reactive protein (CRP), Homo sapiens (NCBI Accession #1GNHA, 1GNHB, 1GNHC, 1GNHD, 1GNHE, 1GNHF, 1GNHG, 1GNHH, 1GNHI, 1GNHJ); C-reactive protein (CRP), Mus musculus (NCBI Accession #CAA31928, NP—031794); serum amyloid P component (SAP), Homo sapiens (NCBI Accession #1SACA, 1SACB, 1SACC, 1SACD, 1SACE); and serum amyloid P component (SAP), Mus musculus (NCBI Accession #NP—035448, CAA34774). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural pentraxin-response-related molecules such as those listed supra.
Other effector domains can be isolated from collectins or molecules that they activate directly or indirectly, (M. Gadjeva et al. (2001) Current Opinion in Immunology 13, 74-78; U. L. Holmskov (2000) APMIS Suppl. 100, 1-59), including for example and without limitation, the following molecules or DNA or RNA encoding them: mannan/mannose binding lectin (MBL), Homo sapiens (NCBI Accession #AAK52907, CAB56120, CAB56044); mannan/mannose binding lectin (MBL), Mus musculus (NCBI Accession #NP—034905, NP—034906); MBL-associated serine protease 1 (MASP1), Homo sapiens (NCBI Accession #NP—001870, NP—624302); MBL-associated serine protease 2 (MASP2), Homo sapiens (NCBI Accession #NP—006601, NP—631947, AAG50274, BAA85659); MBL-associated serine protease 1 (MASP1), Mus musculus (NCBI Accession #XP—193834); MBL-associated serine protease 2 (MASP2), Mus musculus (NCBI Accession #BAA34674, CAB65247, CAB65250); MBL-associated serine protease 3 (MASP3), Mus musculus (NCBI Accession #BAB69688); surfactant protein A (SP-A), Homo sapiens (NCBI Accession #NP—005402, NP—008857); surfactant protein D (SP-D), Homo sapiens (NCBI Accession #CAA46152, NP—003010); surfactant protein D (SP-D), Mus musculus (NCBI Accession #AAF15277); surfactant protein D (SP-D), Bos taurus (NCBI Accession #CAA53510, S33603); conglutinin, Bos taurus (NCBI Accession #CAA50665, BAA03170); collectin-43 (CL-43), Bos taurus (NCBI Accession #CAA53511, P42916, A53570); collectin-L1, Mus musculus (NCBI Accession #BAC53954); or collectin placenta 1 (CL-P1), Homo sapiens (NCBI Accession #AB005145). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural collectin response-related molecules such as those listed supra.
Still other effector domains can be isolated from mannose receptors or molecules that they activate directly or indirectly, (L. East and C. M. Isacke (2002) Biochimica et Biophysica Acta 1572, 364-386; S. Zamze et al. (2002) Journal of Biological Chemistry 277, 41613-41623), including for example and without limitation, the following molecules or DNA or RNA encoding them: mannose receptor (MR), Homo sapiens (NCBI Accession #NM—002438); and mannose receptor (MR), Mus musculus (NCBI Accession #CAA78028, NP—032651, NP—032652). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural mannose-receptor-response-related molecules such as those listed supra.
Effector domains can also be isolated from scavenger receptors or molecules that they activate directly or indirectly, (L. Peiser et al. (2002) Current Opinion in Immunology 14, 123-128; A. Brannstrom et al. (2002) Biochemical and Biophysical Research Communications 290, 1462-1469), including for example and without limitation, the following molecules or DNA or RNA encoding them: scavenger receptor A I (SR-A I), Homo sapiens (NCBI Accession #D90187); scavenger receptor A II (SR-A II), Homo sapiens (NCBI Accession #D90188); scavenger receptor A I (SR-A I), Mus musculus (NCBI Accession #L04274); scavenger receptor A II (SR-A II), Mus musculus (NCBI Accession #L04275); macrophage receptor with collagenous structure (MARCO), Homo sapiens (NCBI Accession #NP—006761); macrophage receptor with collagenous structure (MARCO), Mus musculus (NCBI Accession #NP—034896); scavenger receptor with C-type lectin I (SR-CL I), Homo sapiens (NCBI Accession #BAB39147); scavenger receptor with C-type lectin II (SR-CL II), Homo sapiens(NCBI Accession #BAB39148); and scavenger receptor with C-type lectin (SR-CL), Mus musculus (NCBI Accession #BAB82497). An effector domain can also be isolated from a molecule that binds to, stimulates, or inhibits natural scavenger receptor response-related molecules such as those listed supra.
An effector domain can be isolated from a molecule that inhibits transport between the cytoplasm and the nucleus of a cell, including for example and without limitation, the following molecules or DNA or RNA encoding them: importin alpha 1 (Homo sapiens, #NM—002266) with the importin beta binding domain (approximately amino acids 3-99) removed; importin alpha 3 (Homo sapiens, #NM—002268) with the importin beta binding domain (approximately amino acids 3-94) removed; importin alpha 4 (Homo sapiens, #NM—002267) with the importin beta binding domain (approximately amino acids 3-94) removed; importin alpha 5 (Homo sapiens, #U28386) with the importin beta binding domain (approximately amino acids 3-94) removed; importin alpha 6 (Homo sapiens, #NM—002269) with the importin beta binding domain (approximately amino acids 3-94) removed; importin alpha 7 (Homo sapiens, #NM—012316) with the importin beta binding domain (approximately amino acids 3-103) removed; importin alpha with the importin beta binding domain removed as described supra and also with the last two armadillo repeats removed (Y. Miyamoto et al. (2002) EMBO Journal 21, 5833-5842), as will be understood by one of skill in the art; the autoinhibitory domain of an importin alpha mutated to have a higher than normal affinity for wild-type importin alpha (B. Catimel et al. (2001) Journal of Biological Chemistry 276, 34189-34198), as will be understood by one of skill in the art; a modified importin alpha that does not enable nuclear import, but still binds to one or more pathogen nuclear localization signals (NLSs), preferably with a higher affinity than it binds to cellular NLSs, as will be understood by one of skill in the art; the importin beta binding domain of importin alpha 1 (Homo sapiens, #NM—002266, approximately amino acids 1-99); the importin beta binding domain of importin alpha 3 (Homo sapiens, #NM—002268, approximately amino acids 1-94); the importin beta binding domain of importin alpha 4 (Homo sapiens, #NM—002267, approximately amino acids 1-94); the importin beta binding domain of importin alpha 5 (Homo sapiens, #U28386, approximately amino acids 1-94); the importin beta binding domain of importin alpha 6 (Homo sapiens, #NM—002269, approximately amino acids 1-94); the importin beta binding domain of importin alpha 7 (Homo sapiens, #NM—012316, approximately amino acids 1-103); importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind nucleoporins, for example by deleting the region between HEAT-5 and HEAT-6 (approximately amino acids 203-211) and the region between HEAT-6 and HEAT-7 (approximately amino acids 246-252) or by replacing those regions with nonhomologous linker regions (Y. M. Chook and G. Blobel (2001) Current Opinion in Structural Biology 11, 703-715); importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind importin alpha, for example by deleting the acidic loop importin-alpha-binding region spanning from approximately amino acid 333 through approximately amino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229); a defective mutant of an exportin (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594) as will be understood by one of skill in the art; a mutant p10/NTF2 that inhibits import by importin beta 1, for example, p10 D23A (C. M. Lane et al. (2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby et al. (2001) Journal of Biological Chemistry 276, 38820-38829); vesicuovirus matrix protein or a portion thereof that inhibits nuclear import and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular and Cellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) Molecular Cell 6, 1243-1252); a peptide or other molecule that resembles the classical nuclear localization signal of SV40 T antigen (E. Merle et al. (1999) Journal of Cellular Biochemistry 74, 628-637); peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002) Journal of Biological Chemistry 277, 50597-50606); leptomycin B; or a mutant of Ran that interferes with nuclear import or export, for example and without limitation, RanC4A (R. H. Kehlenbach et al. (2001) Journal of Biological Chemistry 276, 14524-14531).
An effector domain can be isolated from any naturally or non-naturally occurring molecule that binds to a pathogen, pathogen component, or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; B. Ossareh-Nazari (2001) Traffic 2, 684-689). Such effector molecules include, for example and without limitation, an antibody, antibody fragment, single-chain antibody, peptidomimetic, or synthesized molecule. An effector molecule can also be DNA or RNA that encodes a molecule that binds to a pathogen, pathogen component, or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell. In addition, an effector molecule can be any molecule that synthesizes a molecule that binds to a pathogen, pathogen component, or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell.
Cellular components that are involved in transport between the cytoplasm and the nucleus of a cell (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; E. Conti and E. Izaurralde (2001) Current Opinion in Cell Biology 13, 310-319) include, for example, importin alpha proteins, importin beta proteins, importin 7, Ran, Nup358 (S. K. Vasu and D. J. Forbes (2001) Current Opinion in Cell Biology 13, 363-375), CAN/Nup214 (L. C. Trotman et al. (2001) Nature Cell Biology 3, 1092-1100; S. K. Vasu and D. J. Forbes (2001) Current Opinion in Cell Biology 13, 363-375), CRM1, CAS, calreticulin, or kinases or phosphatases that regulate nuclear import or export (R. H. Kehlenbach and L. Gerace (2000) Journal of Biological Chemistry 275, 17848-17856). In one embodiment, the effector domain inhibits pathogen transport more efficiently than cellular transport.
An effector domain can be isolated from a molecule that alters the endocytic or phagocytic pathways (for example and without restriction, the properties of endosomes, phagosomes, lysosomes, other intracellular compartments, or vesicular trafficking) to produce an anti-pathogen effect, (L. A. Knodler, J. Celli, and B. B. Finlay (2001) Nat. Rev. Mol. Cell. Biol. 2, 578-588; D. Sacks and A. Sher (2002) Nature Immunology 3, 1041-1047; M. W. Hornef et al. (2002) Nature Immunology 3, 1033-1040; J. Pieters (2001) Current-Opinion in Immunology 13, 37-44), for example and without limitation, the following molecules or DNA or RNA encoding them: dynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736), particularly when overexpressed; cellubrevin (R. A. Fratti et al. (2002) Journal of Biological Chemistry 277, 17320-17326), particularly when overexpressed; Salmonella SpiC protein (NCBI Accession #U51927); a defective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4, 739-750); other vesicular trafficking inhibitors; Nramp1 (P. Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277, 2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D. J. Hackam et al. (1998) J. Exp. Med. 188, 351-364), particularly when overexpressed; NADPH oxidase subunits or cofactors (P. V. Vignais (2002) Cell. Mol. Life Sci. 59, 1428-1459), particularly when overexpressed; NOS2 nitric oxide synthase (J. D. MacMicking et al. (1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248), particularly when overexpressed; human papillomavirus 16 E5 protein (NCBI Accession #W5WLHS); bafilomycin A1; an antibody, single-chain antibody, or other molecule that binds to V-ATPase subunit a (S. B. Sato and S. Toyama (1994) J. Cell. Biol. 127, 39-53), preferably a1 or a2; antisense oligonucleotides that inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154); a peptide composed of approximately the 78 amino-terminal amino acids of vacuolar H+-ATPase subunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277, 38409-38415); A2-cassette mutant of vacuolar H+-ATPase subunit A (N. Hernando et al. (1999) Eur. J. Biochem. 266, 293-301); a defective mutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi et al. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishi et al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol. Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274, 2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765); overexpression of the C and/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724); other defective vacuolar ATPase subunit or portion of a subunit (examples of wild-type human vacuolar ATPase subunits that can be made defective for anti-pathogen effects will be understood by one of skill in the art, and include, without limitation, those vacuolar ATPase subunits with Accession numbers: NM—004231, NM—130463, NM—015994, NM—001694, NM—004047, NM—001696, NM—004691, NM—001695, NM—001693, NM—001690, NM—020632, NM—004888); other vacuolar H+-ATPase inhibitors, particularly inhibitors that alter pH in endosomes, phagosomes, or lysosomes with minimal undesirable effects on cells such as osteoclasts and renal intercalated cells; molecules that inhibit intracellular compartment acidification and can be isolated from intracellular pathogens (for example and without limitation, Mycobacterium spp., Salmonella spp., Yersinia spp., Chlamydia spp., Histoplasma capsulatum (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154), or Toxoplasma gondii); molecules that promote intracellular compartment acidification and can be isolated from intracellular pathogens (for example and without limitation, Coxiella burnetti, Francisella tularensis, Brucella spp. (F. Porte et al. (1999) Infection and Immunity 67, 4041-4047), Leishmania spp., Listeria monocytogenes, Bordetella bronchiseptica, or Legionella pneumophila); or molecules that interfere with vesicular trafficking or other properties of intracellular compartments can be isolated from intracellular pathogens (for example and without limitation, Mycobacterium spp., Salmonella spp., Yersinia spp., Chlamydia spp., Histoplasma capsulatum (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154), Toxoplasma gondii, Coxiella burnetti, Francisella tularensis, Brucella spp. (F. Porte et al. (1999) Infection and Immunity 67, 4041-4047), Leishmania spp., Listeria monocytogenes, Bordetella bronchiseptica, or Legionella pneumophila)
An effector domain can be isolated from a molecule that stimulates, inhibits, or binds to a component of the ubiquitin-proteasome degradative pathway (M. H. Glickman and A. Ciechanover (2002) Physiol. Rev. 82, 373-428; K. M. Sakamoto (2002) Molecular Genetics and Metabolism 77, 44-56) to produce an anti-pathogen effect, for example and without limitation, the following molecules or DNA or RNA encoding them: CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001) EMBO Rep. 2, 1133-1138), particularly when overexpressed; Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442), particularly when overexpressed; molecules that ubiquitinate pathogens, pathogen components, or cellular components that assist pathogens (P. Zhou et al. (2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al. (2002) Biochemical and Biophysical Research Communications 295, 370-375); or inhibitors of ubiquitination or proteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science 292, 1552-1555), for example and without limitation, lactacystin or epoxomicin.
Effector domains can be isolated from molecules that execute, stimulate, or inhibit defensin-related responses (R. I. Lehrer and T. Ganz (2002) Current Opinion in Immunology 14, 96-102; D. Yang et al. (2002) TRENDS in Immunology 23, 291-296; P. A. Raj and A. R. Dentino (2002) FEMS Microbiology Letters 206, 9-18; G. T.-J. Huang et al. (2002) Human Gene Therapy 13, 2017-2025; J. Cohn et al. (2001) Current Opinion in Immunology 13, 55-62), for example and without limitation, the following molecules or DNA or RNA encoding them: alpha defensins, beta defensins, theta defensins, plant defensins, or arthropod defensins. An effector domain can be isolated from a molecule that binds to, stimulates, or inhibits natural defensin-response related molecules such as those listed supra.
Other effector domains can be isolated from molecules that execute, stimulate, or inhibit cathelicidin-related responses (R. I. Lehrer and T. Ganz (2002) Curr. Opin. Hematol. 9, 18-22; B. Ramanathan et al. (2002) Microbes Infect. 4, 361-372; M. Zaiou and R. L. Gallo (2002) J. Mol. Med. 80, 549-561), for example and without limitation, the following molecules or DNA or RNA encoding them: hCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39. An effector domain can be isolated from a molecule that binds to, stimulates, or inhibits natural cathelicidin-response related molecules such as those listed supra.
Still other effector domains can be isolated from molecules that execute, stimulate, or inhibit chemokine-related or thrombocidin-related responses (M. Durr and A. Peschel (2002) Infection and Immunity 70, 6515-6517; Y. Tang et al. (2002) Infection and Immunity 70, 6524-6533; J. Krijgsveld et al. (2000) Journal of Biological Chemistry 275, 20374-20381; A. D. Luster (2002) Current Opinion in Immunology 14, 129-135; M. Mellado et al. (2001) Annu. Rev. Immunol. 19, 397-421), for example and without limitation, the following molecules or DNA or RNA encoding them: CC chemokines, CXC chemokines, C chemokines, CX3C chemokines, CC chemokine receptors, CXC chemokine receptors, C chemokine receptors, CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A, fibrinopeptide B, or thymosin beta 4. An effector domains can be isolated from a molecule that binds to, stimulates, or inhibits natural chemokine-response-related or thrombocidin-response-related molecules such as those listed supra.
An effector domain can be isolated from a molecule that is toxic to an infected host cell or a pathogen cell. In one embodiment, the effector molecule is toxic to an infected host cell is not toxic to uninfected host cells, for example and without limitation, an intracellular bacterial toxin (B. B. Finlay and P. Cossart (1997) Science 276, 718-725; C. Montecucco et al. (1994) FEBS Lett. 346, 92-98; P. O. Falnes et al. (2001) Biochemistry 40, 4349-4358) that has been modified so that it cannot cross cellular plasma membranes, such as the A (21 kDa) fragment of diptheria toxin. An effector domains can be isolated from a molecule that is toxic to a pathogen cell, including but not limited to penicillin, erythromycin, tetracycline, rifampin, amphotericin B, metronidazole, or mefloquine. An effector domains can be isolated from an ATP inhibitor (E. K. Hui and D. P. Nayak (2001) Virology 290, 329-341). An effector molecule can be a toxin that inhibits transcription, translation, replication, oxidative phosphorylation, cytoskeletal processes, or other cell and/or pathogen functions.
An effector domain can be isolated from a molecule that inhibits budding or release of pathogens from an infected cell, for example and without limitation, the following molecules or DNA or RNA encoding them: Hrs, particularly when overexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276, 7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398); defective Vps4 mutants such as K173Q or E228Q, particularly when overexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); small interfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell 107, 55-65); truncated AP-50 consisting of approximately amino acids 121-435, or other defective mutant of AP-50, particularly when overexpressed (B. A. Puffer et al. (1998) Journal of Virology 72, 10218-10221); WW-domain-containing fragment of LDI-1, Nedd4, Yes-associated protein, KIAA0439 gene product, or other defective Nedd4-related proteins, particularly when overexpressed (A. Kikonyogo et al. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consisting of the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late (L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids 1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminal fragment of Tsg101, particularly when overexpressed (D. G. Demirov et al. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J. F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101 (M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBO Journal 21, 2397-2406) with reduced capacity to aid viral budding; a casein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ ID NO: 472)(E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066). An effector domain can be isolated from a molecule that binds to a cellular or pathogen molecule (for example and without limitation, to one or more of the following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28, Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50, Nedd4-related proteins, WW-domain-containing proteins, or L-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in Cell Biology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology 74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76, 11637-11644) that is involved in budding or release of pathogens from an infected cell.
An effector domain can be isolated from a molecule that degrades components of cells or pathogens, for example and without limitation: proteases, including chymotrypsin, trypsin, or elastase; DNases, including caspase-activated DNase (CAD), constitutively active CAD (N. Inohara et al. (1999) Journal of Biological Chemistry 274, 270-274), or restriction enzymes; RNases, including RNase II (Homo sapiens, #AF189011; Escherichia coli, #NP—417062, NC—000913), RNt1p (Saccharomyces cerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), RNase A, or RNase L; glycosidases, including N-glycanase, endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, or beta-galactosidase; or lipases, including to phospholipase A1, phospholipase A2, phospholipase C, or phospholipase D. An effector domain can be encoded by DNA or RNA which encodes a molecule that degrades components of cells or pathogens. An effector domain can be isolated from a molecule that binds to, stimulates, or inhibits a molecule such as those described supra that degrades components of cells or pathogens.
Other effector domain can be isolated from molecules that execute, stimulate, or inhibit immune-related responses (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999)), for example and without limitation, the following molecules or DNA or RNA encoding them: MHC Class I, MHC Class II, antibodies, single-chain antibodies, T cell receptors, Fc receptors, NK cell activation receptors (including but not limited to NKp46, Ly49H, and NKG2D; A. Diefenbach and D. H. Raulet (2003) Current Opinion in Immunology 15, 37-44; A. R. French and W. M. Yokoyama (2003) Current Opinion in Immunology 15, 45-51), NK cell inhibitory receptors, receptor-associated tyrosine kinases, or phospholipase C. An effector domain can be isolated from a molecule that binds to, stimulates, or inhibits natural immune-response related molecules.
A chimeric molecule of the invention that has at least one dsRNA binding domain as described supra, can be bound to, or is associated with, an effector domain that mediates the activation or induction of apoptosis. For example, caspases (also known as pro-caspases) 1 to 14 (Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM—001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; CED-3 caspase, and Caenorhabditis elegans, #AF210702) can be effector domains. Such caspases are widely recognized in the art and include homologs from a variety of organisms, including Homo sapiens, Mus musculus, Drosophila melanogaster and C. elegans. Both a full-length pro-caspase and a fragment of a pro-caspase that contains the active caspase subunits and the activation cleavage sites are suitable for use in the invention, as will be appreciated by one of skill in the art.
Other effector domains that mediate the activation or induction of apoptosis include apoptosis-associated proteins, such as a death effector domain (DED) isolated from FADD, a caspase recruitment domain (CARD) isolated from Apaf-1, or a death domain (DD) isolated from either Fas or TRADD (tumor necrosis factor receptor type 1 (TNFR1)-associated death domain protein). Table 2 provides examples of these effector domain-containing proteins and the approximate amino acid position of the effector domains.
In a preferred embodiment, the chimeric molecule or agent of the invention has one or more dsRNA-binding domains, as described supra, fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more 2′,5′-oligoadenylate-binding domains, as described supra, fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more endoplasmic-reticulum-stress-detection domains from PERK (for example, approximately amino acids 1-542 of human PERK), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more endoplasmic-reticulum-stress-detection domains from IRE1 alpha (for example, approximately amino acids 1-469 of human IRE1 alpha), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more endoplasmic-reticulum-stress-detection domains from IRE1 beta (for example, approximately amino acids 1-451 of human IRE1 beta), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more stress-detection domains from HSF1 (for example, approximately amino acids 125-503 of human HSF1), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod 1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more LPS-binding domains, as described supra, fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example and without limitation, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more apoptosis signal-detection domains from Apaf-1 (for example, approximately amino acids 97-1194 of human Apaf-1), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more apoptosis-signal-detection domains from FADD (for example, approximately amino acids 117-208 of human FADD), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example and without limitation, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more apoptosis-signal-detection domains from caspase 8 (for example, approximately amino acids 1-215 of human caspase 8), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more apoptosis-signal-detection domains from caspase 9 (for example, approximately amino acids 1-92 of human caspase 9), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more apoptosis-signal-detection domains from TNF alpha receptor 1 (for example, the extracellular and transmembrane domain of human TNF-RI), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example and without limitation, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more apoptosis-signal-detection domains from Fas/CD95 (for example, the extracellular and transmembrane domain of human Fas/CD95), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-detection domains from Nod1/CARD4 (for example, approximately amino acids 127-953 of human Nod1/CARD4), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-detection domains from Nod2 (for example, approximately amino acids 251-1040 of human Nod2), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-detection domains from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 126-1024 of human Ipaf-1/CLAN/CARD12), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-detection domains from CIITA (for example, approximately amino acids 341-1130 of CARD-less human CIITA), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-binding domains or pathogen-induced-product-binding domains (for example, a single-chain antibody that binds to one or more pathogens, pathogen components, pathogen-produced products, or pathogen-induced products), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); a protease that is activated by crosslinking; an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more domains that specifically bind to one or more pathogenic forms of prions (for example, a portion of a nonpathogenic prion form (such as approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250) that binds to a pathogenic prion form, or a single-chain antibody that binds to one or more pathogenic forms of prions), fused in frame with or bound to or associated with one or more of the following effector molecules: an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); a protease that is activated by crosslinking; an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more inflammatory-signal-detection domains from IKK gamma (for example, full-length human IKK gamma), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-induced-signal-detection domains from RIP (for example, approximately amino acids 301-671 of human RIP), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-induced-signal-detection domains from Rip2/RICK/CARDIAK (for example, approximately amino acids 301-540 of human Rip2/RICK/CARDIAK), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); or an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP).
In another preferred embodiment, the chimeric molecule or agent of the invention has one or more pathogen-detection domains isolated from toll-like receptors (for example, the extracellular domain of the following human toll-like receptors: TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, or TLR10), fused in frame with or bound to or associated with one or more of the following effector molecules: an apoptosis effector domain as described supra; an effector domain from protein kinase R (for example, approximately amino acids 175-551 or 274-551 of human protein kinase R); an effector domain from RNase L (for example, approximately amino acids 336-741 of human RNase L); an effector domain from PERK (for example, approximately amino acids 543-1115 of human PERK); an effector domain from IRE1 alpha (for example, approximately amino acids 470-977 of human IRE1 alpha); an effector domain from IRE1 beta (for example, approximately amino acids 452-925 of human IRE1 beta); an effector domain from Nod1/CARD4 (for example, approximately amino acids 1-126 of human Nod1/CARD4); an effector domain from Nod2 (for example, approximately amino acids 1-250 of human Nod2); an effector domain from Ipaf-1/CLAN/CARD12 (for example, approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12); an acidic domain effector domain from CIITA (for example, approximately amino acids 1-340 of CARD-less human CIITA); a CARD effector domain from dendritic cell CIITA (for example, approximately amino acids 1-100 of human dendritic cell CIITA); a CARD-acidic-domain effector domain from dendritic cell CIITA (for example, approximately amino acids 1-440 of human dendritic cell CIITA); an effector domain from IKK gamma (for example, full-length human IKK gamma or approximately amino acids 1-200 of human IKK gamma); an effector domain from HSF1 (for example, approximately amino acids 1-227 of human HSF1); an effector domain from RIP (for example, approximately amino acids 1-300 of human RIP); or an effector domain from Rip2/RICK/CARDIAK (for example, approximately amino acids 1-300 of human Rip2/RICK/CARDIAK).
A chimeric molecule or agent of the invention can be a molecule that binds to a pathogen or a product produced or induced by a pathogen and that also binds to a natural effector molecule, thereby activating effector molecules by crosslinking on a polyvalent pathogen/pathogen-produced product/pathogen-induced product and/or promoting an anti-pathogen effect by bringing a pathogen/pathogen-produced product into close proximity with a natural anti-pathogen effector molecule. More specifically, and without restriction, an agent of the invention can be a molecule that binds to a pathogen or product produced or induced by a pathogen and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a protease that is activated by crosslinking; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to dsRNA (for example, by containing lividomycin or by mimicking the dsRNA-binding domain of lividomycin, protein kinase R, or other dsRNA-binding domains as described supra) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to protein kinase R (for example, by binding within the domain from approximately amino acids 174-551 of human protein kinase R) and that also binds to one or more of the following: RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to 2′,5′-oligoadenylate (for example, by mimicking the 2′,5′-oligoadenylate-binding domain from approximately amino acids 1-335 of human RNase L) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to RNase L (for example, by binding within the domain from approximately amino acids 364-741 of human RNase L) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to viral late domains (for example and without restriction, by binding to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, or YXXL, as described supra) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to viral glycoproteins (for example and without restriction, by mimicking the hemagglutinin-binding domain of human NK cell activation receptor NKp46) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to LPS (for example, by mimicking the LPS-binding domain from approximately amino acids 1-199 of human BPI or other LPS-binding domains as described supra) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to peptidoglycan (for example, by mimicking the peptidoglycan-binding domain from the extracellular domain of human TLR2) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to muramyl dipeptide (for example, by mimicking the muramyl-dipeptide-binding domain from approximately amino acids 744-1040 of human Nod2) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to bacterial flagellin (for example, by mimicking the flagellin-binding domain from the extracellular domain of human TLR5) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to a bacterial type III secretion system and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod 1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to CpG DNA (for example, by mimicking the CpG-DNA-binding domain from the extracellular domain of human TLR9) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to zymosan (for example, by mimicking the zymosan-binding domain from the extracellular domain of human TLR2) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to a pathogenic form of a prion (for example, by mimicking a portion of a nonpathogenic prion form (such as approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250), that binds to a pathogenic prion form) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a protease that is activated by crosslinking; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to Apaf-1 (for example, by mimicking the CARD domain from approximately amino acids 1-91 of human caspase 9) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to FADD (for example, by mimicking the DED-containing domain from approximately amino acids 1-215 of human caspase 8) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to TRADD (for example, by mimicking the death domain (DD) from approximately amino acids 117-208 of human FADD) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to Fas/CD95 (for example, by mimicking the death domain (DD) from approximately amino acids 117-208 of human FADD) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to PERK (for example, by binding to the cytoplasmic domain of PERK) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to IRE1 alpha (for example, by binding to the cytoplasmic domain of IRE1 alpha) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to IRE1 beta (for example, by binding to the cytoplasmic domain of IRE1 beta) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to Nod1/CARD4 (for example, by binding to the CARD domain from approximately amino acids 1-126 of human Nod1/CARD4) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to Nod2 (for example, by binding to the CARD-containing domain from approximately amino acids 1-220 of human Nod2) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to Ipaf-1/CLAN/CARD12 (for example, by binding to the CARD domain from approximately amino acids 1-125 of human Ipaf-1/CLAN/CARD12) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to CIITA (for example, by binding to the CARD and/or acidic domains from CIITA isoforms) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to RIP (for example, by binding within the domain from approximately amino acids 1-289 of human RIP) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to Rip2/RICK/CARDIAK (for example, by binding within the domain from approximately amino acids 1-292 of human Rip2/RICK/CARDIAK) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to IKK gamma (for example, by binding within the domain from approximately amino acids 201-419 of human IKK gamma) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod 1); HSF1 (for example, by binding within the domain from approximately amino acids 137-503 of human HSF1); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to HSF1 (for example, by binding within the DNA-binding domain from approximately amino acids 1-120 of human HSF1) and that also binds to one or more of the following: protein kinase R (for example, by binding within the domain from approximately amino acids 1-174 of human protein kinase R); RNase L (for example, by containing or by mimicking a short molecule of 2′,5′-oligoadenylate that binds to RNase L but does not activate it without a secondary crosslinker, which in this case is a pathogen or a product produced or induced by a pathogen); PERK; IRE1 alpha; IRE1 beta; caspase 3; caspase 8 (for example, by mimicking the caspase-8-binding DED domain from approximately amino acids 1-117 of human FADD); caspase 9 (for example, by mimicking the caspase-9-binding CARD domain from approximately amino acids 1-97 of human Apaf-1); Apaf-1; FADD (for example, by mimicking the death domain (DD) from human Fas/CD95 or TRADD); a caspase or apoptosis signaling molecule; Nod1/CARD4 (for example, by binding within the domain from approximately amino acids 126-953 of human Nod1/CARD4); Nod2 (for example, by binding within the domain from approximately amino acids 220-1040 of human Nod2); Ipaf-1/CLAN/CARD12 (for example, by binding within the domain from approximately amino acids 125-1024 of human Ipaf-1/CLAN/CARD12); CIITA (for example, by binding within the nucleotide oligomerization domain (NOD) or leucine-rich-repeat (LRR) domain of a CIITA isoform); RIP (for example, by mimicking the death domain (DD) of Fas/CD95 or TRADD); Rip2/RICK/CARDIAK (for example, by mimicking the CARD domain from approximately amino acids 1-126 of human Nod1); IKK gamma (for example, by binding with the domain from approximately amino acids 201-419 of human IKK gamma); IKK alpha and/or beta (for example, by mimicking the IKK alpha/beta binding domain from approximately amino acids 1-200 of human IKK gamma); a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a heat shock protein as described supra; an E3 ubiquitin ligase as described supra.
A chimeric molecule or agent of the invention can be a molecule that binds to a pathogen or a product produced or induced by a pathogen and that also contains an effector domain, thereby promoting an anti-pathogen effect by bringing a pathogen/pathogen-produced product into close proximity with an anti-pathogen effector domain. More specifically, an agent of the invention can be a molecule (for example and without limitation, a single-chain antibody) that binds to a pathogen or product produced or induced by a pathogen and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to dsRNA (for example, by containing one or more dsRNA-binding domain as described supra) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to viral late domains (for example and without restriction, by binding to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, or YXXL, as described supra) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to viral glycoproteins (for example and without restriction, by containing or mimicking the hemagglutinin-binding domain of human NK cell activation receptor NKp46) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to LPS (for example, by containing or mimicking the LPS-binding domain from approximately amino acids 1-199 of human BPI or other LPS-binding domains as described supra) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to peptidoglycan (for example, by containing or mimicking the peptidoglycan-binding domain from the extracellular domain of human TLR2) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to muramyl dipeptide (for example, by containing or mimicking the muramyl-dipeptide-binding domain from approximately amino acids 744-1040 of human Nod2) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to bacterial flagellin (for example, by containing or mimicking the flagellin-binding domain from the extracellular domain of human TLR5) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to a bacterial type III secretion system and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to CpG DNA (for example, by containing or mimicking the CpG-DNA-binding domain from the extracellular domain of human TLR9) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to zymosan (for example, by containing or mimicking the zymosan-binding domain from the extracellular domain of human TLR2) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to a pathogenic form of a prion (for example, by containing or mimicking a portion of a nonpathogenic prion form (such as approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250) that binds to a pathogenic prion form) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to a pathogen or a product produced or induced by a pathogen and that also contains an effector domain, thereby promoting an anti-pathogen effect by bringing a pathogen/pathogen-produced product into close proximity with an anti-pathogen effector domain. More specifically, an agent of the invention can be a molecule (for example and without limitation, a single-chain antibody) that binds to a pathogen or product produced or induced by a pathogen and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to dsRNA (for example, by containing one or more dsRNA-binding domain as described supra) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to viral late domains (for example and without restriction, by binding to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, or YXXL, as described supra) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to viral glycoproteins (for example and without restriction, by containing or mimicking the hemagglutinin-binding domain of human NK cell activation receptor NKp46) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to LPS (for example, by containing or mimicking the LPS-binding domain from approximately amino acids 1-199 of human BPI or other LPS-binding domains as described supra) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to peptidoglycan (for example, by containing or mimicking the peptidoglycan-binding domain from the extracellular domain of human TLR2) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to muramyl dipeptide (for example, by containing or mimicking the muramyl-dipeptide-binding domain from approximately amino acids 744-1040 of human Nod2) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to bacterial flagellin (for example, by containing or mimicking the flagellin-binding domain from the extracellular domain of human TLR5) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to a bacterial type III secretion system and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to CpG DNA (for example, by containing or mimicking the CpG-DNA-binding domain from the extracellular domain of human TLR9) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to zymosan (for example, by containing or mimicking the zymosan-binding domain from the extracellular domain of human TLR2) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
A chimeric molecule or agent of the invention can be a molecule that binds to a pathogenic form of a prion (for example, by containing or mimicking a portion of a nonpathogenic prion form (such as approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250) that binds to a pathogenic prion form) and that also contains one or more of the following effector domains: a DNase as described supra; an RNase as described supra; a protease as described supra; a glycosidase as described supra; a lipase as described supra; a stress response or heat shock protein as described supra; an E3 ubiquitin ligase as described supra; a molecule that is toxic or inhibitory to a pathogen (including but not limited to defensins as described supra or drosomycin).
In a preferred embodiment, the effector domain is a polynucleotide sequence that encodes for the desired effector domain, and said polynucleotide sequence is operatively linked with a pathogen-detection domain or pathogen-induced-product-detection domain that is a promoter.
A dsRNA-inducible promoter, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Similarly, an apoptosis-inducible promoter, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Furthermore, an unfolded-protein-response-inducible promoter or endoplasmic-reticulum-associated-protein-degradation-response-inducible promoter, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Examples of effector domains which are operatively-linked to these promoters include: a chimeric molecule or agent as described herein, including but not limited to, dsRNA-activated caspase, 2′,5′-oligoadenylate-activated caspase, dsRNA-activated caspase activator, or 2′,5′-oligoadenylate-activated caspase activator; a chimeric transcription factor as described herein; a molecule that contains two or more binding sites for a pathogen, pathogen component, or pathogen product as described herein; an antisense polynucleotide or small interfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl. Acad. Sci. USA 99, 14943-14945) that inhibits expression of a pathogen gene or a host gene that aids a pathogen; a molecule that executes, stimulates, or inhibits stress or inflammatory responses, as described supra (including but not limited to heat shock protein 70 (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM—016299, NM—005346, NM—005345, NM—002155, NM—021979, AF093759; Mus musculus, #XM—207065, XM—128584, XM—128585, XM—110217, NM—015765, NM—010481, NM—008301, M76613), Hsc70 (Homo sapiens, #AF352832), Hsp90 (Homo sapiens, #M16660, NM—005348, NM—007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM—006145, NM—005880), Hsp60 (Homo sapiens, #NM—002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100 (Homo sapiens, #NM—006660), Alpha-A-crystallin (Homo sapiens, #NM—000394), Alpha-B-crystallin (Homo sapiens, #NM—001885), Hsp27-1 (Homo sapiens, #NM—001540), Hsp27-2 (Homo sapiens, #XM—012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heat shock factor 1 (HSF1: Homo sapiens, #NM—005526, M64673; Mus musculus, #XM—128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131), constitutively active HSF1 as will be understood by one of skill in the art, RelA/p65 (Homo sapiens, #NM—021975, Z22948, L19067; Mus musculus, #NM—009045, AF199371), RelB (Homo sapiens, #NM—006509; Mus musculus, #NM—009046, M83380), c-Rel (Homo sapiens, #X75042, NM—002908; Mus musculus, #NM—009044, X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM—003998, S76638, AF213884, AH009144; Mus musculus, #NM—008689, AK052726, M57999), p52/p100/NF-kappa B 2 (Homo sapiens, #NM—002502; Mus musculus, #AF155372, AF155373, NM—019408), inhibitors of kappa B (I kappa B: Homo sapiens, #AY033600, NM—020529; S. Ghosh and M. Karin (2002) Cell 109, S81-S96), IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, #AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homo sapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappa B kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus, #AF069542)); a molecule that executes, stimulates, or inhibits unfolded protein-related or endoplasmic reticulum-associated protein degradation-related responses, as described supra (including but not limited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949, NM—005347; Mus musculus, #NM—022310), PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens, #NP—004827; Mus musculus, #AAD03337, NP—034251), constitutively active PERK as will be understood by one of skill in the art, IRE1 alpha (Homo sapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutively active IRE1 alpha as will be understood by one of skill in the art, IRE1 beta (Homo sapiens, #AB047079), constitutively active IRE1 beta as will be understood by one of skill in the art, activating transcription factor 4 (ATF4: Homo sapiens, #NM—001675; Mus musculus, #NM—009716), activating transcription factor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM—007348, AF005887, AB015856; Mus musculus, #XM—129579), X-box binding protein 1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM—013842), CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM—004083; Mus musculus, #X67083, NM—007837), site-1 protease (S1P: Homo sapiens, #NM—003791; Mus musculus, #NM—019709), site-2 protease (S2P: Homo sapiens, #NM—015884), presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus, #BC030409, NM—008943, AF149111), TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM—021138, NM—145718, Mus musculus, #XM—203851, XM—130119, L35303), or cJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7, 335-345)); a single-chain antibody or other molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen, as described supra; a molecule that executes or stimulates complement pathway-related responses, as described supra, including but not limited to C3 alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes, stimulates, or inhibits toll-like-receptor-related responses, NOD-protein-related responses, (including but not limited to Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM—021209, AY035391; J.-L. Poyet et al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054, AY084055, AF410154, NM—000246, X74301; M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM—033004, NM—033005, NM—033006, NM—033007, NM—014922); NBS1/NALP2 (Homo sapiens, #AF310106, NM—017852); cryopyrin/CIAS1 (Homo sapiens, #AF410477, AF427617, AH011140, NM—004895); RIP (Homo sapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93, 10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396); Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al. (1998) Journal of Biological Chemistry 273, 18675; M. Thome et al. (1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002) Journal of Biological Chemistry 277, 31871-31876)), pentraxin-related responses, collectin-related responses, mannose-receptor-related responses, scavenger-receptor-related responses, or immune-related responses, as described supra; a molecule that inhibits transport between the cytoplasm and the nucleus of a cell, as described supra (including but not limited to importin alpha 1 (Homo sapiens, #NM—002266) with the importin beta binding domain (approximately amino acids 3-99) removed, importin alpha 3 (Homo sapiens, #NM—002268) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 4 (Homo sapiens, #NM—002267) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 6 (Homo sapiens, #NM—002269) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 7 (Homo sapiens, #NM—012316) with the importin beta binding domain (approximately amino acids 3-103) removed, importin alpha with the importin beta binding domain removed as described supra and also with the last two armadillo repeats removed (Y. Miyamoto et al. (2002) EMBO Journal 21, 5833-5842) as will be understood by one of skill in the art, the autoinhibitory domain of an importin alpha mutated to have a higher than normal affinity for wild-type importin alpha (B. Catimel et al. (2001) Journal of Biological Chemistry 276, 34189-34198) as will be understood by one of skill in the art, a modified importin alpha that does not enable nuclear import but still binds to one or more pathogen nuclear localization signals (NLSs) and does so preferably with a higher affinity than it binds to cellular NLSs as will be understood by one of skill in the art, the importin beta binding domain of importin alpha 1 (Homo sapiens, #NM—002266, approximately amino acids 1-99), the importin beta binding domain of importin alpha 3 (Homo sapiens, #NM—002268, approximately amino acids 1-94), the importin beta binding domain of importin alpha 4 (Homo sapiens, #NM—002267, approximately amino acids 1-94), the importin beta binding domain of importin alpha 5 (Homo sapiens, #U28386, approximately amino acids 1-94), the importin beta binding domain of importin alpha 6 (Homo sapiens, #NM—002269, approximately amino acids 1-94), the importin beta binding domain of importin alpha 7 (Homo sapiens, #NM—012316, approximately amino acids 1-103), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind nucleoporins (for example by deleting the region between HEAT-5 and HEAT-6 (approximately amino acids 203-211) and the region between HEAT-6 and HEAT-7 (approximately amino acids 246-252) or by replacing those regions with nonhomologous linker regions (Y. M. Chook and G. Blobel (2001) Current Opinion in Structural Biology 11, 703-715)), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind importin alpha (for example by deleting the acidic loop importin-alpha-binding region spanning from approximately amino acid 333 through approximately amino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229)), a defective mutant of an exportin (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594) as will be understood by one of skill in the art, a mutant p10/NTF2 that inhibits import by importin beta 1 (for example and without limitation, p10 D23A (C. M. Lane et al. (2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby et al. (2001) Journal of Biological Chemistry 276, 38820-38829)), vesicuovirus matrix protein or a portion thereof that inhibits nuclear import and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular and Cellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) Molecular Cell 6, 1243-1252), a peptide that resembles the classical nuclear localization signal of SV40 T antigen (E. Merle et al. (1999) Journal of Cellular Biochemistry 74, 628-637), another nuclear localization signal, peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002) Journal of Biological Chemistry 277, 50597-50606), leptomycin B, a mutant of Ran that interferes with nuclear import or export (for example and without limitation, RanC4A (R. H. Kehlenbach et al. (2001) Journal of Biological Chemistry 276, 14524-14531)), or a molecule that binds to a pathogen or pathogen component or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; B. Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibits pathogenic prions (for example, approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250); a molecule that alters the properties of the endocytic pathway, phagocytic pathway, endosomes, phagosomes, lysosomes, other intracellular compartments, or vesicular trafficking to produce an anti-pathogen effect, as described supra (including but not limited to dynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin (R. A. Fratti et al. (2002) Journal of Biological Chemistry 277, 17320-17326; particularly when overexpressed), Salmonella SpiC protein (NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4, 739-750), other vesicular trafficking inhibitors, Nramp1 (P. Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277, 2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D. J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly when overexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais (2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly when overexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al. (1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly when overexpressed), human papillomavirus 16 E5 protein (NCBI Accession #W5WLHS), bafilomycin A1, a single-chain antibody or other molecule that binds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J. Cell. Biol. 127, 39-53; preferably a1 or a2), antisense oligonucleotides that inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154), a peptide composed of approximately the 78 amino-terminal amino acids of vacuolar H+-ATPase subunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277, 38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N. Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defective mutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi et al. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishi et al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol. Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274, 2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765) as will be understood by one of skill in the art, overexpression of the C and/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724), other defective vacuolar ATPase subunit or portion of a subunit (examples of wild-type human vacuolar ATPase subunits that can be made defective for anti-pathogen effects will be understood by one of skill in the art, and include, without limitation, those vacuolar ATPase subunits with Accession numbers: NM—004231, NM—130463, NM—015994, NM—001694, NM—004047, NM—001696, NM—004691, NM—001695, NM—001693, NM—001690, NM—020632, NM—004888)); a molecule that executes, stimulates, or inhibits ubiquitin proteasome degradative pathway-related responses, as described supra (including but not limited to CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001) EMBO Rep. 2, 1133-1138; particularly when overexpressed), Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442; particularly when overexpressed), molecules that ubiquitinate pathogens or pathogen components or cellular components that assist pathogens (P. Zhou et al. (2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al. (2002) Biochemical and Biophysical Research Communications 295, 370-375), or inhibitors of ubiquitination or proteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science 292, 1552-1555); for example and without limitation, lactacystin or epoxomicin; a molecule that executes, stimulates, or inhibits defensin-related responses, as described supra, including but not limited to alpha defensins, beta defensins, theta defensins, plant defensins, or arthropod defensins; a molecule that executes, stimulates, or inhibits cathelicidin-related responses, as described supra, including but not limited to hCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39; a molecule that executes, stimulates, or inhibits chemokine-related or thrombocidin-related responses, as described supra, including but not limited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines, CC chemokine receptors, CXC chemokine receptors, C chemokine receptors, CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A, fibrinopeptide B, or thymosin beta 4; a molecule that executes, stimulates, or inhibits interferon-related or cytokine-related responses, as described supra (including but not limited to interferon-alpha (Homo sapiens, #NM—002169, NM—021002, J00207; Mus musculus, #NM—010502, NM—010503, NM—010507, NM—008333, M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM—002176; Mus musculus, #NM—010510); interferon-gamma (Homo sapiens, #NM—000619, J00219; Mus musculus, #M28621); interferon-delta; interferon-tau; interferon-omega (Homo sapiens, #NM—002177); interleukin 1 (IL-1: Homo sapiens, #NM—000575, NM—012275, NM—019618, NM—000576, NM—014439; Mus musculus, #NM—019450, NM—019451, AF230378); interleukin 2 (IL-2: Homo sapiens, #NM—000586); interleukin 3 (IL-3: Homo sapiens, #NM—000588; Mus musculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM—000589, NM—172348; Mus musculus, #NM—021283); interleukin 5 (IL-5: Homo sapiens, #NM—000879; Mus musculus, #NM—010558); interleukin 6 (IL-6: Homo sapiens, #NM—000600; Mus musculus, #NM—031168); interleukin 7 (IL-7: Homo sapiens, #NM—000880, AH006906; Mus musculus, #NM—008371); interleukin 9 (IL-9: Homo sapiens, #NM—000590); interleukin 12 (IL-12: Homo sapiens, #NM—000882, NM—002187; Mus musculus, #NM—008351, NM—008352); interleukin 15 (IL-15: Homo sapiens, #NM—172174, NM—172175, NM—000585; Mus musculus, #NM—008357); cytokine receptors and related signaling molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homo sapiens, #NM—000629; Mus musculus, #NM—010508); interferon type I receptor subunit 2 (IFNAR2: Homo sapiens, #NM—000874; Mus musculus, #NM—010509); janus kinase 1 (JAK1: Homo sapiens, #NP—002218; Mus musculus, #NP—666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP—004963; Mus musculus, #NP—032439, AAN62560); JAK3; Tyk2; signal transducer and activator of transcription 1 (STAT1: Homo sapiens, #NM—007315, NM—139266; Mus musculus, #U06924); signal transducer and activator of transcription 2 (STAT2: Homo sapiens, #NM—005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM—006084; Mus musculus, #NM—008394) interferon regulatory factor 1 (IRF1: Homo sapiens, #NM—002198, P10914; Mus musculus, #NM—008390); interferon regulatory factor 3 (IRF3: Homo sapiens, #NM—001571, Z56281; Mus musculus, #NM—016849, U75839, U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997, NP—036187); interferon regulatory factor 6 (IRF6: Homo sapiens, #AF027292, NM—006147; Mus musculus, #U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036; Mus musculus, #NM—016850, U73037); interferon regulatory factor 8 (IRF8); a constitutively active interferon regulatory factor; protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); constitutively active PKR; 2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); constitutively active 2′,5′-oligoadenylate synthetases; RNase L (Homo sapiens, #CAA52920); constitutively active RNase L; promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Mus musculus, #NP—062629); Mx1 (Homo sapiens, #NM—002462); or Mx2 (Homo sapiens, #NM—002463)); a molecule that inhibits budding or release of pathogens from an infected cell, as described supra (including but not limited to Hrs, particularly when overexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276, 7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398); defective Vps4 mutants such as K173Q or E228Q, particularly when overexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); small interfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell 107, 55-65); truncated AP-50 consisting of approximately amino acids 121-435, or other defective mutant of AP-50, particularly when overexpressed (B. A. Puffer et al. (1998) Journal of Virology 72, 10218-10221); WW-domain-containing fragment of LDI-1, Nedd4, Yes-associated protein, KIAA0439 gene product, or other defective Nedd4-related proteins, particularly when overexpressed (A. Kikonyogo et al. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consisting of the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late (L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids 1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminal fragment of Tsg101, particularly when overexpressed (D. G. Demirov et al. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J. F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101 (M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBO Journal 21, 2397-2406) with reduced capacity to aid viral budding; a casein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ ID NO: 472) (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); a molecule that binds to a cellular or pathogen molecule (for example and without limitation, to one or more of the following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28, Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50, Nedd4-related proteins, WW-domain-containing proteins, or L-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in Cell Biology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology 74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76, 11637-11644) that is involved in budding or release of pathogens from an infected cell); a molecule that executes or stimulates apoptosis-related or other cell-death-related responses, as described supra (including but not limited to p53 (Homo sapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM—004324); Bid (Homo sapiens, #NM—001196); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens, #NM—013229, NM—001160; Mus musculus, #NP—033814); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410); TNF receptors (Homo sapiens, #NP—001056; V. Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus, #NM—010175); TRADD (Homo sapiens, #NP—003780, CAC38018); granzyme B (Homo sapiens, #AAH30195, NP—004122; Mus musculus, #AAH02085, NP—038570); constitutively active granzyme B, as will be understood by one of skill in the art; Smac/DIABLO (Homo sapiens, #NM—019887); caspases (including but not restricted to Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM—001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); a constitutively active caspase; calpains (T. Lu et al., (2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule that degrades components of cells or pathogens, as described supra (for example and without limitation: proteases, including chymotrypsin, trypsin, or elastase; DNases, including caspase-activated DNase (CAD), constitutively active CAD (N. Inohara et al. (1999) Journal of Biological Chemistry 274, 270-274), or restriction enzymes; RNases, including RNase III (Homo sapiens, #AF189011; Escherichia coli, #NP—417062, NC—000913), RNt1p (Saccharomyces cerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), RNase A, or RNase L; glycosidases, including N-glycanase, endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, or beta-galactosidase; or lipases, including phospholipase A1, phospholipase A2, phospholipase C, or phospholipase D); a molecule that is toxic to an infected host cell or a pathogen cell, as described supra (including but not limited to an intracellular bacterial toxin (B. B. Finlay and P. Cossart (1997) Science 276, 718-725; C. Montecucco et al. (1994) FEBS Lett. 346, 92-98; P. O. Falnes et al. (2001) Biochemistry 40, 4349-4358) that has been modified so that it cannot cross cellular plasma membranes, such as the A (21 kDa) fragment of diptheria toxin; a molecule that is toxic to a pathogen cell, including but not limited to penicillin, erythromycin, tetracycline, rifampin, amphotericin B, metronidazole, or mefloquine; an ATP inhibitor (E. K. Hui and D. P. Nayak (2001) Virology 290, 329-341); or a toxin that inhibits transcription, translation, replication, oxidative phosphorylation, cytoskeletal processes, or other cell and/or pathogen functions).
An inflammatory response-inducible promoter, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Similarly, a stress/heat shock-inducible promoter, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Likewise, a promoter that can be induced by cytokines such as interferon alpha, interferon beta, or interferon omega, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Additionally, a promoter that can be induced by cytokines such as interferon gamma, interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 9, interleukin 12, or interleukin 15, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Alternatively, a drug-inducible promoter, as described supra, can be operatively linked with a wide variety of effector domains encoded by a polynucleotide sequence, as described supra. Examples of the effector domains that can be operatively linked to these promoters, include: a chimeric molecule or agent as described herein, including but not limited to, dsRNA-activated caspase, 2′,5′-oligoadenylate-activated caspase, dsRNA-activated caspase activator, or 2′,5′-oligoadenylate-activated caspase activator; a chimeric transcription factor as described herein; a molecule that contains two or more binding sites for a pathogen, pathogen component, or pathogen product as described herein; an antisense polynucleotide or small interfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl. Acad. Sci. USA 99, 14943-14945) that inhibits expression of a pathogen gene or a host gene that aids a pathogen; a molecule that executes, stimulates, or inhibits stress or inflammatory responses, as described supra (including but not limited to heat shock protein 70 (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM—016299, NM—005346, NM—005345, NM—002155, NM—021979, AF093759; Mus musculus, #XM—207065, XM—128584, XM—128585, XM—110217, NM—015765, NM—010481, NM—008301, M76613), Hsc70 (Homo sapiens, #AF352832), Hsp90 (Homo sapiens, #M16660, NM—005348, NM—007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM—006145, NM—005880), Hsp60 (Homo sapiens, #NM—002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100 (Homo sapiens, #NM—006660), Alpha-A-crystallin (Homo sapiens, #NM—000394), Alpha-B-crystallin (Homo sapiens, #NM—001885), Hsp27-1 (Homo sapiens, #NM—001540), Hsp27-2 (Homo sapiens, #XM—012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heat shock factor 1 (HSF1: Homo sapiens, #NM—005526, M64673; Mus musculus, #XM—128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131), constitutively active HSF1, RelA/p65 (Homo sapiens, #NM—021975, Z22948, L19067; Mus musculus, #NM—009045, AF199371), RelB (Homo sapiens, #NM—006509; Mus musculus, #NM—009046, M83380), c-Rel (Homo sapiens, #X75042, NM—002908; Mus musculus, #NM—009044, X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM—003998, S76638, AF213884, AH009144; Mus musculus, #NM—008689, AK052726, M57999), p52/p100/NF-kappa B 2 (Homo sapiens, #NM—002502; Mus musculus, #AF155372, AF155373, NM—019408), inhibitors of kappa B (I kappa B: Homo sapiens, #AY033600, NM—020529; S. Ghosh and M. Karin (2002) Cell 109, S81-S96), IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, #AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homo sapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappa B kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus, #AF069542)); a molecule that executes, stimulates, or inhibits unfolded-protein-related or endoplasmic reticulum-associated protein degradation-related responses, as described supra (including but not limited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949, NM—005347; Mus musculus, #NM—022310), PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens, #NP—004827; Mus musculus, #AAD03337, NP—034251), constitutively active PERK, IRE1 alpha (Homo sapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutively active IRE1 alpha as will be understood by one of skill in the art, IRE1 beta (Homo sapiens, #AB047079), constitutively active IRE1 beta, activating transcription factor 4 (ATF4: Homo sapiens, #NM—001675; Mus musculus, #NM—009716), activating transcription factor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM—007348, AF005887, AB015856; Mus musculus, #XM—129579), X-box binding protein 1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM—013842), CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM—004083; Mus musculus, #X67083, NM—007837), site-1 protease (S1P: Homo sapiens, #NM—003791; Mus musculus, #NM—019709), site-2 protease (S2P: Homo sapiens, #NM—015884), presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus, #BC030409, NM—008943, AF149111), TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM—021138, NM—145718, Mus musculus, #XM—203851, XM—130119, L35303), or cJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7, 335-345)); a single-chain antibody or other molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen, as described supra; a molecule that executes or stimulates complement pathway-related responses, as described supra, including but not limited to C3 alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes, stimulates, or inhibits toll-like-receptor-related responses, NOD-protein-related responses, (including but not limited to Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM—021209, AY035391; J.-L. Poyet et al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054, AY084055, AF410154, NM—000246, X74301; M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM—033004, NM—033005, NM—033006, NM—033007, NM—014922); NBS1/NALP2 (Homo sapiens, #AF310106, NM—017852); cryopyrin/CIAS1 (Homo sapiens, #AF410477, AF427617, AH011140, NM—004895); RIP (Homo sapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93, 10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396); Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al. (1998) Journal of Biological Chemistry 273, 18675; M. Thome et al. (1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002) Journal of Biological Chemistry 277, 31871-31876)), pentraxin-related responses, collectin-related responses, mannose-receptor-related responses, scavenger receptor-related responses, or immune-related responses, as described supra; a molecule that inhibits transport between the cytoplasm and the nucleus of a cell, as described supra (including but not limited to importin alpha 1 (Homo sapiens, #NM—002266) with the importin beta binding domain (approximately amino acids 3-99) removed, importin alpha 3 (Homo sapiens, #NM—002268) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 4 (Homo sapiens, #NM—002267) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 6 (Homo sapiens, #NM—002269) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 7 (Homo sapiens, #NM—012316) with the importin beta binding domain (approximately amino acids 3-103) removed, importin alpha with the importin beta binding domain removed as described supra and also with the last two armadillo repeats removed (Y. Miyamoto et al. (2002) EMBO Journal 21, 5833-5842), the autoinhibitory domain of an importin alpha mutated to have a higher than normal affinity for wild-type importin alpha (B. Catimel et al. (2001) Journal of Biological Chemistry 276, 34189-34198), a modified importin alpha that does not enable nuclear import but still binds to one or more pathogen nuclear localization signals (NLSs) and does so preferably with a higher affinity than it binds to cellular NLSs, the importin beta binding domain of importin alpha 1 (Homo sapiens, #NM—002266, approximately amino acids 1-99), the importin beta binding domain of importin alpha 3 (Homo sapiens, #NM—002268, approximately amino acids 1-94), the importin beta binding domain of importin alpha 4 (Homo sapiens, #NM—002267, approximately amino acids 1-94), the importin beta binding domain of importin alpha 5 (Homo sapiens, #U28386, approximately amino acids 1-94), the importin beta binding domain of importin alpha 6 (Homo sapiens, #NM—002269, approximately amino acids 1-94), the importin beta binding domain of importin alpha 7 (Homo sapiens, #NM—012316, approximately amino acids 1-103), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind nucleoporins (for example and without limitation, by deleting the region between HEAT-5 and HEAT-6 (approximately amino acids 203-211) and the region between HEAT-6 and HEAT-7 (approximately amino acids 246-252) or by replacing those regions with nonhomologous linker regions (Y. M. Chook and G. Blobel (2001) Current Opinion in Structural Biology 11, 703-715)), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind importin alpha (for example and without limitation, by deleting the acidic loop importin-alpha-binding region spanning from approximately amino acid 333 through approximately amino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229)), a defective mutant of an exportin (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594), a mutant p10/NTF2 that inhibits import by importin beta 1 (for example and without limitation, p10 D23A (C. M. Lane et al. (2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby et al. (2001) Journal of Biological Chemistry 276, 38820-38829)), vesicuovirus matrix protein or a portion thereof that inhibits nuclear import and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular and Cellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) Molecular Cell 6, 1243-1252), a peptide that resembles the classical nuclear localization signal of SV40 T antigen (E. Merle et al. (1999) Journal of Cellular Biochemistry 74, 628-637), another nuclear localization signal, peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002) Journal of Biological Chemistry 277, 50597-50606), leptomycin B, a mutant of Ran that interferes with nuclear import or export (for example and without limitation, RanC4A (R. H. Kehlenbach et al. (2001) Journal of Biological Chemistry 276, 14524-14531)), or a molecule that binds to a pathogen or pathogen component or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; B. Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibits pathogenic prions (for example and without restriction, approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250); a molecule that alters the properties of the endocytic pathway, phagocytic pathway, endosomes, phagosomes, lysosomes, other intracellular compartments, or vesicular trafficking to produce an anti-pathogen effect, as described supra (including but not limited to dynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin (R. A. Fratti et al. (2002) Journal of Biological Chemistry 277, 17320-17326; particularly when overexpressed), Salmonella SpiC protein (NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4, 739-750), other vesicular trafficking inhibitors, Nramp1 (P. Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277, 2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D. J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly when overexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais (2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly when overexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al. (1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly when overexpressed), human papillomavirus 16 E5 protein (NCBI Accession #W5WLHS), bafilomycin A1, a single-chain antibody or other molecule that binds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J. Cell. Biol. 127, 39-53; preferably a1 or a2), antisense oligonucleotides that inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154), a peptide composed of approximately the 78 amino-terminal amino acids of vacuolar H+-ATPase subunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277, 38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N. Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defective mutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi et al. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishi et al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol. Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274, 2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765), overexpression of the C and/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724), other defective vacuolar ATPase subunit or portion of a subunit (examples of wild-type human vacuolar ATPase subunits that can be made defective for anti-pathogen effects will be understood by one of skill in the art, and include, without limitation, those vacuolar ATPase subunits with Accession numbers: NM—004231, NM—130463, NM—015994, NM—001694, NM—004047, NM—001696, NM—004691, NM—001695, NM—001693, NM—001690, NM—020632, NM—004888)); a molecule that executes, stimulates, or inhibits ubiquitin proteasome degradative pathway-related responses, as described supra (including but not limited to CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001) EMBO Rep. 2, 1133-1138; particularly when overexpressed as will be understood by one of skill in the art), Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442; particularly when overexpressed), molecules that ubiquitinate pathogens or pathogen components or cellular components that assist pathogens (P. Zhou et al. (2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al. (2002) Biochemical and Biophysical Research Communications 295, 370-375), or inhibitors of ubiquitination or proteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science 292, 1552-1555; for example and without limitation, lactacystin or epoxomicin)); a molecule that executes, stimulates, or inhibits defensin-related responses, as described supra, including but not limited to alpha defensins, beta defensins, theta defensins, plant defensins, or arthropod defensins; a molecule that executes, stimulates, or inhibits cathelicidin-related responses, as described supra, including but not limited to hCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39; a molecule that executes, stimulates, or inhibits chemokine-related or thrombocidin-related responses, as described supra, including but not limited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines, CC chemokine receptors, CXC chemokine receptors, C chemokine receptors, CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A, fibrinopeptide B, or thymosin beta 4; a molecule that executes, stimulates, or inhibits interferon-related or cytokine-related responses, as described supra (including but not limited to interferon-alpha (Homo sapiens, #NM—002169, NM—021002, J00207; Mus musculus, #NM—010502, NM—010503, NM—010507, NM—008333, M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM—002176; Mus musculus, #NM—010510); interferon-gamma (Homo sapiens, #NM—000619, J00219; Mus musculus, #M28621); interferon-delta; interferon-tau; interferon-omega (Homo sapiens, #NM—002177); interleukin 1 (IL-1: Homo sapiens, #NM—000575, NM—012275, NM—019618, NM—000576, NM—014439; Mus musculus, #NM—019450, NM—019451, AF230378); interleukin 2 (IL-2: Homo sapiens, #NM—000586); interleukin 3 (IL-3: Homo sapiens, #NM—000588; Mus musculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM—000589, NM—172348; Mus musculus, #NM—021283); interleukin 5 (IL-5: Homo sapiens, #NM—000879; Mus musculus, #NM—010558); interleukin 6 (IL-6: Homo sapiens, #NM—000600; Mus musculus, #NM—031168); interleukin 7 (IL-7: Homo sapiens, #NM—000880, AH006906; Mus musculus, #NM—008371); interleukin 9 (IL-9: Homo sapiens, #NM—000590); interleukin 12 (IL-12: Homo sapiens, #NM—000882, NM—002187; Mus musculus, #NM—008351, NM—008352); interleukin 15 (IL-15: Homo sapiens, #NM—172174, NM—172175, NM—000585; Mus musculus, #NM—008357); cytokine receptors and related signaling molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homo sapiens, #NM—000629; Mus musculus, #NM—010508); interferon type I receptor subunit 2 (IFNAR2: Homo sapiens, #NM—000874; Mus musculus, #NM—010509); janus kinase 1 (JAK1: Homo sapiens, #NP—002218; Mus musculus, #NP—666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP—004963; Mus musculus, #NP—032439, AAN62560); JAK3; Tyk2; signal transducer and activator of transcription 1 (STAT1: Homo sapiens, #NM—007315, NM—139266; Mus musculus, #U06924); signal transducer and activator of transcription 2 (STAT2: Homo sapiens, #NM—005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM—006084; Mus musculus, #NM—008394) interferon regulatory factor 1 (IRF1: Homo sapiens, #NM—002198, P10914; Mus musculus, #NM—008390); interferon regulatory factor 3 (IRF3: Homo sapiens, #NM—001571, Z56281; Mus musculus, #NM—016849, U75839, U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997, NP—036187); interferon regulatory factor 6 (IRF6: Homo sapiens, #AF027292, NM—006147; Mus musculus, #U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036; Mus musculus, #NM—016850, U73037); interferon regulatory factor 8 (IRF8); a constitutively active interferon regulatory factor, as will be understood by one of skill in the art; protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); 2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); RNase L (Homo sapiens, #CAA52920); promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Mus musculus, #NP—062629); Mx1 (Homo sapiens, #NM—002462); or Mx2 (Homo sapiens, #NM—002463)); a molecule that inhibits budding or release of pathogens from an infected cell, as described supra (including but not limited to Hrs, particularly when overexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276, 7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398); defective Vps4 mutants such as K173Q or E228Q, particularly when overexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); small interfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell 107, 55-65); truncated AP-50 consisting of approximately amino acids 121-435, or other defective mutant of AP-50, particularly when overexpressed (B. A. Puffer et al. (1998) Journal of Virology 72, 10218-10221); WW-domain-containing fragment of LDI-1, Nedd4, Yes-associated protein, KIAA0439 gene product, or other defective Nedd4-related proteins, particularly when overexpressed (A. Kikonyogo et al. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consisting of the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late (L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids 1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminal fragment of Tsg101, particularly when overexpressed (D. G. Demirov et al. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J. F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101 (M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBO Journal 21, 2397-2406) with reduced capacity to aid viral budding, as will be understood by one of skill in the art; a casein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ ID NO: 472)(E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); a molecule that binds to a cellular or pathogen molecule (for example and without limitation, to one or more of the following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28, Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50, Nedd4-related proteins, WW-domain-containing proteins, or L-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in Cell Biology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology 74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76, 11637-11644) that is involved in budding or release of pathogens from an infected cell); a molecule that makes a cell more receptive to apoptosis signals, as described supra (including but not limited to p53 (Homo sapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM—004324); Bid (Homo sapiens, #NM—001196); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens, #NM—013229, NM—001160; Mus musculus, #NP—033814); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410); TNF receptors (Homo sapiens, #NP—001056; V. Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus, #NM—010175); TRADD (Homo sapiens, #NP—003780, CAC38018); Smac/DIABLO (Homo sapiens, #NM—019887); caspases (including but not restricted to Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM—001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); calpains (T. Lu et al., (2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule that degrades components of pathogens, as described supra (for example and without limitation: proteases, including chymotrypsin, trypsin, or elastase; DNases, including restriction enzymes; RNases, including RNase III (Homo sapiens, #AF189011; Escherichia coli, #NP 417062, NC—000913), RNt1p (Saccharomyces cerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), or RNase L; glycosidases, including N-glycanase, endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, or beta-galactosidase; or lipases, including phospholipase A1, phospholipase A2, phospholipase C, or phospholipase D); a molecule that inhibits or is toxic to a pathogen cell, as described supra (including but not limited to penicillin, erythromycin, tetracycline, rifampin, amphotericin B, metronidazole, mefloquine, or another molecule that inhibits pathogen functions).
An inducible promoter (for example and without limitation, one of the following promoters as described herein: a dsRNA-inducible promoter; apoptosis-inducible promoter; unfolded protein response-inducible promoter or endoplasmic reticulum-associated protein degradation response-inducible promoter; inflammatory response-inducible promoter; stress/heat shock-inducible promoter; promoter that can be induced by cytokines such as interferon alpha, interferon beta, or interferon omega; promoter that can be induced by cytokines such as interferon gamma, interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 9, interleukin 12, or interleukin 15; or a drug-inducible promoter) can be operatively linked with a polynucleotide sequence encoding an effector molecule that can act within the producing cell, between cells, or on or in other cells. The effector molecule can optionally include a cellular targeting tag or a protein uptake tag as described herein and/or a secretory signal peptide, as will be understood by one of skill in the art. In addition to an optional tag or peptide, the effector molecule can include one or more of the following domains, for example and without limitation: a chimeric molecule or agent as described herein, including but not limited to dsRNA-activated caspase, 2′,5′-oligoadenylate-activated caspase, dsRNA-activated caspase activator, or 2′,5′-oligoadenylate-activated caspase activator; a chimeric transcription factor as described herein; a molecule that contains two or more binding sites for a pathogen, pathogen component, or pathogen product as described herein; a molecule that executes, stimulates, or inhibits stress or inflammatory responses, as described supra (including but not limited to heat shock protein 70 (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM—016299, NM—005346, NM—005345, NM—002155, NM—021979, AF093759; Mus musculus, #XM—207065, XM—128584, XM—128585, XM—110217, NM 015765, NM—010481, NM—008301, M76613), Hsc70 (Homo sapiens, #AF352832), Hsp90 (Homo sapiens, #M16660, NM—005348, NM—007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM—006145, NM—005880), Hsp60 (Homo sapiens, #NM—002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100 (Homo sapiens, #NM—006660), Alpha-A-crystallin (Homo sapiens, #NM—000394), Alpha-B-crystallin (Homo sapiens, #NM—001885), Hsp27-1 (Homo sapiens, #NM—001540), Hsp27-2 (Homo sapiens, #XM—012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heat shock factor 1 (HSF1: Homo sapiens, #NM—005526, M64673; Mus musculus, #XM—128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131), constitutively active HSF1, RelA/p65 (Homo sapiens, #NM—021975, Z22948, L19067; Mus musculus, #NM—009045, AF199371), RelB (Homo sapiens, #NM—006509; Mus musculus, #NM—009046, M83380), c-Rel (Homo sapiens, #X75042, NM—002908; Mus musculus, #NM—009044, X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM—003998, S76638, AF213884, AH009144; Mus musculus, #NM—008689, AK052726, M57999), p52/p100/NF-kappa B 2 (Homo sapiens, #NM—002502; Mus musculus, #AF155372, AF155373, NM—019408), inhibitors of kappa B (I kappa B: Homo sapiens, #AY033600, NM—020529; S. Ghosh and M. Karin (2002) Cell 109, S81-S96), IKK1/I kappa B kinase alpha (1 alpha: Homo sapiens, #AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homo sapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappa B kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus, #AF069542)); a molecule that executes, stimulates, or inhibits unfolded-protein-related or endoplasmic reticulum-associated protein degradation-related responses, as described supra (including but not limited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949, NM—005347; Mus musculus, #NM—022310), PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens, #NP—004827; Mus musculus, #AAD03337, NP—034251), constitutively active PERK, IRE1 alpha (Homo sapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutively active IRE1 alpha, IRE1 beta (Homo sapiens, #AB047079), constitutively active IRE1 beta, activating transcription factor 4 (ATF4: Homo sapiens, #NM—001675; Mus musculus, #NM—009716), activating transcription factor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM—007348, AF005887, AB015856; Mus musculus, #XM—129579), X-box binding protein 1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM—013842), CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM—004083; Mus musculus, #X67083, NM—007837), site-1 protease (S1P: Homo sapiens, #NM—003791; Mus musculus, #NM—019709), site-2 protease (S2P: Homo sapiens, #NM—015884), presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus, #BC030409, NM—008943, AF149111), TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM—021138, NM—145718, Mus musculus, #XM—203851, XM—130119, L35303), or cJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7, 335-345)); a single-chain antibody or other molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen, as described supra; a molecule that executes or stimulates complement pathway-related responses, as described supra, including but not limited to C3 alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes, stimulates, or inhibits toll-like-receptor-related responses, NOD-protein-related responses, (including but not limited to Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM—021209, AY035391; J.-L. Poyet et al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054, AY084055, AF410154, NM—000246, X74301; M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM—033004, NM—033005, NM—033006, NM—033007, NM—014922); NBS1/NALP2 (Homo sapiens, #AF310106, NM—017852); cryopyrin/CIAS1 (Homo sapiens, #AF410477, AF427617, AH011140, NM—004895); RIP (Homo sapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93, 10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396); Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al. (1998) Journal of Biological Chemistry 273, 18675; M. Thome et al. (1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002) Journal of Biological Chemistry 277, 31871-31876)), pentraxin-related responses, collectin-related responses, mannose-receptor-related responses, scavenger receptor-related responses, or immune-related responses, as described supra; a molecule that inhibits transport between the cytoplasm and the nucleus of a cell, as described supra (including but not limited to importin alpha 1 (Homo sapiens, #NM—002266) with the importin beta binding domain (approximately amino acids 3-99) removed, importin alpha 3 (Homo sapiens, #NM—002268) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 4 (Homo sapiens, #NM—002267) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 6 (Homo sapiens, #NM—002269) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 7 (Homo sapiens, #NM—012316) with the importin beta binding domain (approximately amino acids 3-103) removed, importin alpha with the importin beta binding domain removed as described supra and also with the last two armadillo repeats removed (Y. Miyamoto et al. (2002) EMBO Journal 21, 5833-5842), the autoinhibitory domain of an importin alpha mutated to have a higher than normal affinity for wild-type importin alpha (B. Catimel et al. (2001) Journal of Biological Chemistry 276, 34189-34198), a modified importin alpha that does not enable nuclear import but still binds to one or more pathogen nuclear localization signals (NLSs) and does so preferably with a higher affinity than it binds to cellular NLSs, the importin beta binding domain of importin alpha 1 (Homo sapiens, #NM—002266, approximately amino acids 1-99), the importin beta binding domain of importin alpha 3 (Homo sapiens, #NM—002268, approximately amino acids 1-94), the importin beta binding domain of importin alpha 4 (Homo sapiens, #NM—002267, approximately amino acids 1-94), the importin beta binding domain of importin alpha 5 (Homo sapiens, #U28386, approximately amino acids 1-94), the importin beta binding domain of importin alpha 6 (Homo sapiens, #NM—002269, approximately amino acids 1-94), the importin beta binding domain of importin alpha 7 (Homo sapiens, #NM—012316, approximately amino acids 1-103), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind nucleoporins (for example by deleting the region between HEAT-5 and HEAT-6 (approximately amino acids 203-211) and the region between HEAT-6 and HEAT-7 (approximately amino acids 246-252) or by replacing those regions with nonhomologous linker regions (Y. M. Chook and G. Blobel (2001) Current Opinion in Structural Biology 11, 703-715)), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind importin alpha (for example by deleting the acidic loop importin-alpha-binding region spanning from approximately amino acid 333 through approximately amino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229)), a defective mutant of an exportin (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594), a mutant p10/NTF2 that inhibits import by importin beta 1 (for example p10 D23A (C. M. Lane et al. (2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby et al. (2001) Journal of Biological Chemistry 276, 38820-38829)), vesicuovirus matrix protein or a portion thereof that inhibits nuclear import and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular and Cellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) Molecular Cell 6, 1243-1252), a peptide that resembles the classical nuclear localization signal of SV40 T antigen (E. Merle et al. (1999) Journal of Cellular Biochemistry 74, 628-637), another nuclear localization signal, peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002) Journal of Biological Chemistry 277, 50597-50606), leptomycin B, a mutant of Ran that interferes with nuclear import or export (for example RanC4A (R. H. Kehlenbach et al. (2001) Journal of Biological Chemistry 276, 14524-14531)), or a molecule that binds to a pathogen or pathogen component or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; B. Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibits pathogenic prions (for example and without restriction, approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250); a molecule that alters the properties of the endocytic pathway, phagocytic pathway, endosomes, phagosomes, lysosomes, other intracellular compartments, or vesicular trafficking to produce an anti-pathogen effect, as described supra (including but not limited to dynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin (R. A. Fratti et al. (2002) Journal of Biological Chemistry 277, 17320-17326; particularly when overexpressed), Salmonella SpiC protein (NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4, 739-750), other vesicular trafficking inhibitors as will be understood by one of skill in the art, Nramp1 (P. Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277, 2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D. J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly when overexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais (2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly when overexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al. (1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly when overexpressed), human papillomavirus 16 E5 protein (NCBI Accession #W5WLHS), bafilomycin A1, a single-chain antibody or other molecule that binds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J. Cell. Biol. 127, 39-53; preferably a1 or a2), antisense oligonucleotides that inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154), a peptide composed of approximately the 78 amino-terminal amino acids of vacuolar H+-ATPase subunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277, 38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N. Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defective mutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi et al. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishi et al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol. Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274, 2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765), overexpression of the C and/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724), other defective vacuolar ATPase subunit or portion of a subunit (examples of wild-type human vacuolar ATPase subunits that can be made defective for anti-pathogen effects will be understood by one of skill in the art, and include, without limitation, those vacuolar ATPase subunits with Accession numbers: NM—004231, NM—130463, NM—015994, NM—001694, NM—004047, NM—001696, NM—004691, NM—001695, NM—001693, NM—001690, NM—020632, NM—004888)); a molecule that executes, stimulates, or inhibits ubiquitin proteasome degradative pathway-related responses, as described supra (including but not limited to CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001) EMBO Rep. 2, 1133-1138; particularly when overexpressed), Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442; particularly when overexpressed), molecules that ubiquitinate pathogens or pathogen components or cellular components that assist pathogens as will be understood by one of skill in the art (P. Zhou et al. (2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al. (2002) Biochemical and Biophysical Research Communications 295, 370-375), or inhibitors of ubiquitination or proteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science 292, 1552-1555; for example lactacystin or epoxomicin)); a molecule that executes, stimulates, or inhibits defensin-related responses, as described supra, including but not limited to alpha defensins, beta defensins, theta defensins, plant defensins, or arthropod defensins; a molecule that executes, stimulates, or inhibits cathelicidin-related responses, as described supra, including but not limited to hCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39; a molecule that executes, stimulates, or inhibits chemokine-related or thrombocidin-related responses, as described supra, including but not limited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines, CC chemokine receptors, CXC chemokine receptors, C chemokine receptors, CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A, fibrinopeptide B, or thymosin beta 4; a molecule that executes, stimulates, or inhibits interferon-related or cytokine-related responses, as described supra (including but not limited to interferon-alpha (Homo sapiens, #NM—002169, NM—021002, J00207; Mus musculus, #NM—010502, NM—010503, NM—010507, NM—008333, M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM—002176; Mus musculus, #NM—010510); interferon-gamma (Homo sapiens, #NM—000619, J00219; Mus musculus, #M28621); interferon-delta; interferon-tau; interferon-omega (Homo sapiens, #NM—002177); interleukin 1 (IL-1: Homo sapiens, #NM—000575, NM—012275, NM—019618, NM—000576, NM—014439; Mus musculus, #NM—019450, NM—019451, AF230378); interleukin 2 (IL-2: Homo sapiens, #NM—000586); interleukin 3 (IL-3: Homo sapiens, #NM—000588; Mus musculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM—000589, NM—172348; Mus musculus, #NM—021283); interleukin 5 (IL-5: Homo sapiens, #NM—000879; Mus musculus, #NM—010558); interleukin 6 (IL-6: Homo sapiens, #NM—000600; Mus musculus, #NM—031168); interleukin 7 (IL-7: Homo sapiens, #NM—000880, AH006906; Mus musculus, #NM—008371); interleukin 9 (IL-9: Homo sapiens, #NM—000590); interleukin 12 (IL-12: Homo sapiens, #NM—000882, NM—002187; Mus musculus, #NM—008351, NM—008352); interleukin 15 (IL-15: Homo sapiens, #NM—172174, NM—172175, NM—000585; Mus musculus, #NM—008357); cytokine receptors and related signaling molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homo sapiens, #NM—000629; Mus musculus, #NM—010508); interferon type I receptor subunit 2 (IFNAR2: Homo sapiens, #NM—000874; Mus musculus, #NM—010509); janus kinase 1 (JAK1: Homo sapiens, #NP—002218; Mus musculus, #NP—666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP—004963; Mus musculus, #NP—032439, AAN62560); JAK3; Tyk2; signal transducer and activator of transcription 1 (STAT1: Homo sapiens, #NM—007315, NM—139266; Mus musculus, #U06924); signal transducer and activator of transcription 2 (STAT2: Homo sapiens, #NM—005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM—006084; Mus musculus, #NM—008394) interferon regulatory factor 1 (IRF1: Homo sapiens, #NM—002198, P10914; Mus musculus, #NM—008390); interferon regulatory factor 3 (IRF3: Homo sapiens, #NM—001571, Z56281; Mus musculus, #NM—016849, U75839, U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997, NP—036187); interferon regulatory factor 6 (IRF6: Homo sapiens, #AF027292, NM—006147; Mus musculus, #U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036; Mus musculus, #NM—016850, U73037); interferon regulatory factor 8 (IRF8); a constitutively active interferon regulatory factor; protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); 2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); RNase L (Homo sapiens, #CAA52920); ); promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Mus musculus, #NP—062629); Mx1 (Homo sapiens, #NM—002462); or Mx2 (Homo sapiens, #NM—002463)); a molecule that inhibits budding or release of pathogens from an infected cell, as described supra (including but not limited to Hrs, particularly when overexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276, 7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398); defective Vps4 mutants such as K173Q or E228Q, particularly when overexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); small interfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell 107, 55-65); truncated AP-50 consisting of approximately amino acids 121-435, or other defective mutant of AP-50, particularly when overexpressed (B. A. Puffer et al. (1998) Journal of Virology 72, 10218-10221); WW-domain-containing fragment of LDI-1, Nedd4, Yes-associated protein, KIAA0439 gene product, or other defective Nedd4-related proteins, particularly when overexpressed (A. Kikonyogo et al. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consisting of the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late (L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids 1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminal fragment of Tsg101, particularly when overexpressed (D. G. Demirov et al. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J. F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101 (M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBO Journal 21, 2397-2406) with reduced capacity to aid viral budding; a casein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ ID NO: 472)(E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); a molecule that binds to a cellular or pathogen molecule (for example to one or more of the following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28, Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50, Nedd4-related proteins, WW-domain-containing proteins, or L-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in Cell Biology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology 74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76, 11637-11644) that is involved in budding or release of pathogens from an infected cell); a molecule that makes a cell more receptive to apoptosis signals, as described supra (including but not limited to p53 (Homo sapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM—004324); Bid (Homo sapiens, #NM—001196); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens, #NM—013229, NM—001160; Mus musculus, #NP—033814); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410); TNF receptors (Homo sapiens, #NP—001056; V. Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus, #NM—010175); TRADD (Homo sapiens, #NP—003780, CAC38018); Smac/DIABLO (Homo sapiens, #NM—019887); caspases (including but not restricted to Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM—001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); calpains (T. Lu et al., (2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule that degrades components of pathogens, as described supra (for example: proteases, including but not limited to chymotrypsin, trypsin, or elastase; DNases, including but not limited to restriction enzymes; RNases, including but not limited to RNase III (Homo sapiens, #AF189011; Escherichia coli, #NP—417062, NC—000913), RNt1p (Saccharomyces cerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), or RNase L; glycosidases, including but not limited to N-glycanase, endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, or beta-galactosidase; or lipases, including but not limited to phospholipase A1, phospholipase A2, phospholipase C, or phospholipase D); a molecule that inhibits or is toxic to a pathogen cell, as described supra (including but not limited to penicillin, erythromycin, tetracycline, rifampin, amphotericin B, metronidazole, mefloquine, or another molecule that inhibits pathogen functions).
A chimeric molecule or agent of the invention can be a messenger RNA (mRNA) molecule that only encodes a functional anti-pathogen domain or molecular structure if the mRNA is naturally spliced within a cell that is undergoing an unfolded protein response or endoplasmic reticulum-associated protein degradation response. For example and without limitation, the mRNA can include within its protein encoding sequence the 5′ and 3′ splice sites from the intron that is removed from XBP1 mRNA by activated IRE1 alpha (H. Yoshida et al. (2001) Cell 107, 881-891; K. Lee et al. (2002) Genes & Development 16, 452-466; W. Tirasophon et al. (2000) Genes & Development 14, 2725-2736) with nucleotides between the splice sites such that the mRNA encodes an anti-pathogen molecule when the mRNA is spliced by activated IRE1 alpha but only a nonfunctional version of the anti-pathogen molecule with nonsense or frameshift mutations when the mRNA is unspliced, as will be understood by one of skill in the art. The mRNA can encode one or more of the following effector molecules, for example and without limitation: a chimeric molecule or agent as described herein, including but not limited to dsRNA-activated caspase, 2′,5′-oligoadenylate-activated caspase, dsRNA-activated caspase activator, or 2′,5′-oligoadenylate-activated caspase activator; a chimeric transcription factor as described herein; a molecule that contains two or more binding sites for a pathogen, pathogen component, or pathogen product as described herein; an antisense polynucleotide or small interfering RNA (G. M. Barton and R. Medzhitov (2002) Proc. Natl. Acad. Sci. USA 99, 14943-14945) that inhibits expression of a pathogen gene or a host gene that aids a pathogen; a molecule that executes, stimulates, or inhibits stress or inflammatory responses, as described supra (including but not limited to heat shock protein 70 (Hsp70: Homo sapiens, #M11717, M15432, L12723, NM—016299, NM—005346, NM—005345, NM—002155, NM—021979, AF093759; Mus musculus, #XM—207065, XM—128584, XM—128585, XM—110217, NM—015765, NM—010481, NM—008301, M76613), Hsc70 (Homo sapiens, #AF352832), Hsp90 (Homo sapiens, #M16660, NM—005348, NM—007355); Hsp40/Hdj-1 (Homo sapiens, #X62421, NM—006145, NM—005880), Hsp60 (Homo sapiens, #NM—002156), Hsp47/CBP-2 (Homo sapiens, #D83174), Hsp100 (Homo sapiens, #NM—006660), Alpha-A-crystallin (Homo sapiens, #NM—000394), Alpha-B-crystallin (Homo sapiens, #NM—001885), Hsp27-1 (Homo sapiens, #NM—001540), Hsp27-2 (Homo sapiens, #XM—012054), cdc48 (S. Thoms (2002) FEBS Lett. 520, 107-110), heat shock factor 1 (HSF1: Homo sapiens, #NM—005526, M64673; Mus musculus, #XM—128055, X61753, Z49206; A. Mathew et al. (2001) Mol. Cell. Biol. 21, 7163-7171; L. Pirkkala et al. (2001) FASEB J. 15, 1118-1131), constitutively active HSF1, RelA/p65 (Homo sapiens, #NM—021975, Z22948, L119067; Mus musculus, #NM—009045, AF199371), RelB (Homo sapiens, #NM—006509; Mus musculus, #NM—009046 μM83380), c-Rel (Homo sapiens, #X75042, NM—002908; Mus musculus, #NM—009044, X15842), p50/p105/NF-kappa B 1 (Homo sapiens, #NM—003998, S76638, AF213884, AH009144; Mus musculus, #NM—008689, AK052726, M57999), p52/p100/NF-kappa B 2 (Homo sapiens, #NM—002502; Mus musculus, #AF155372, A-F155373, NM—019408), inhibitors of kappa B (I kappa B: Homo sapiens, #AY033600, NM—020529; S. Ghosh and M. Karin (2002) Cell 109, S811-S96), IKK1/I kappa B kinase alpha (IKK alpha: Homo sapiens, #AF009225, AF080157), IKK2/I kappa B kinase beta (IKK beta: Homo sapiens, #AF080158; Mus musculus, #AF026524, AF088910), or NEMO/I kappa B kinase gamma (IKK gamma: Homo sapiens, #AF261086, AF091453; Mus musculus, #AF069542)); a molecule that executes, stimulates, or inhibits unfolded-protein-related or endoplasmic reticulum-associated protein degradation-related responses, as described supra (including but not limited to BiP/GRP78/SHPA5 (Homo sapiens, #AJ271729, AF216292, X87949, NM—005347; Mus musculus, #NM—022310), PKR-like endoplasmic reticulum kinase (PERK: Homo sapiens, #NP—004827; Mus musculus, #AAD03337, NP—034251), constitutively active PERK, IRE1 alpha (Homo sapiens, #AF059198; Mus musculus, #AB031332, AF071777), constitutively active IRE1 alpha, IRE1 beta (Homo sapiens, #AB047079), constitutively active IRE1 beta, activating transcription factor 4 (ATF4: Homo sapiens, #NM—001675; Mus musculus, #NM—009716), activating transcription factor 6 alpha or beta (ATF6 alpha or beta: Homo sapiens, #NM—007348, AF005887, AB015856; Mus musculus, #XM—129579), X-box binding protein 1 (XBP1: Homo sapiens, #AB076383, AB076384; Mus musculus, #AF443192, AF027963, NM 013842), CHOP-10/GADD153/DDIT3 (Homo sapiens, #NM—004083; Mus musculus, #X67083, NM—007837), site-1 protease (S1P: Homo sapiens, #NM—003791; Mus musculus, #NM—019709), site-2 protease (S2P: Homo sapiens, #NM—015884), presenilin-1 (Homo sapiens, #AH004968, AF416717; Mus musculus, #BC030409, NM—008943, AF149111), TNF receptor-associated factor 2 (TRAF2: Homo sapiens, #NM—021138, NM—145718, Mus musculus, #XM—203851, XM—130119, L35303), or cJUN NH2-terminal kinases (JNKs: S. Oyadomari et al. (2002) Apoptosis 7, 335-345)); a single-chain antibody or other molecule that binds to a pathogen, pathogen component, or cellular component that directly or indirectly aids a pathogen, as described supra; a molecule that executes or stimulates complement pathway-related responses, as described supra, including but not limited to C3 alpha, C3 beta, factor B, factor D, properdin, C1q, C1r, C1s, C4, C2, C5, C6, C7, C8, C9, factor I, factor H, C1-INH, C4 bp, S protein, clusterin, carboxypeptidase N, FHL-1, FHR-1, FHR-2, FHR-3, FHR-4, CR1, or DAF; a molecule that executes, stimulates, or inhibits toll-like-receptor-related responses, NOD-protein-related responses, (including but not limited to Nod1/CARD4 (Homo sapiens, #AAD28350, AAD43922; N. Inohara et al. (1999) Journal of Biological Chemistry 274, 14560-14567); Nod2, (Homo sapiens, #AAG33677, AAK70863, AAK70865, AAK70866, AAK70867, AAK70868; Y. Ogura et al. (2001) Journal of Biological Chemistry 276, 4812-4818; N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); Ipaf-1/CLAN/CARD12 (Homo sapiens, #NM—021209, AY035391; J.-L. Poyet et al. (2001) Journal of Biological Chemistry 276, 28309-28313); CIITA (Homo sapiens, #AY084054, AY084055, AF410154, NM—000246, X74301; M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860); NAIP (Homo sapiens, #U21912, U19251); Defcap/NAC/NALP1/CARD7 (Homo sapiens, #NM—033004, NM—033005, NM—033006, NM—033007, NM—014922); NBS1/NALP2 (Homo sapiens, #AF310106, NM—017852); cryopyrin/CIAS1 (Homo sapiens, #AF410477, AF427617, AH011140, NM—004895); RIP (Homo sapiens, #U50062; S. Grimm et al. (1996) Proc. Natl. Acad. Sci. USA 93, 10923-10927; H. Hsu et al. (1996) Immunity 4, 387-396); Rip2/RICK/CARDIAK (Homo sapiens, #AF064824, AF078530; N. Inohara et al. (1998) Journal of Biological Chemistry 273, 18675; M. Thome et al. (1998) Current Biology 8, 885-888); and PKK (A. Muto et al. (2002) Journal of Biological Chemistry 277, 31871-31876)), pentraxin-related responses, collectin-related responses, mannose-receptor-related responses, scavenger receptor-related responses, or immune-related responses, as described supra; a molecule that inhibits transport between the cytoplasm and the nucleus of a cell, as described supra (including but not limited to importin alpha 1 (Homo sapiens, #NM—002266) with the importin beta binding domain (approximately amino acids 3-99) removed, importin alpha 3 (Homo sapiens, #NM—002268) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 4 (Homo sapiens, #NM—002267) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 5 (Homo sapiens, #U28386) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 6 (Homo sapiens, #NM—002269) with the importin beta binding domain (approximately amino acids 3-94) removed, importin alpha 7 (Homo sapiens, #NM—012316) with the importin beta binding domain (approximately amino acids 3-103) removed, importin alpha with the importin beta binding domain removed as described supra and also with the last two armadillo repeats removed (Y. Miyamoto et al. (2002) EMBO Journal 21, 5833-5842), the autoinhibitory domain of an importin alpha mutated to have a higher than normal affinity for wild-type importin alpha (B. Catimel et al. (2001) Journal of Biological Chemistry 276, 34189-34198), a modified importin alpha that does not enable nuclear import but still binds to one or more pathogen nuclear localization signals (NLSs) and does so preferably with a higher affinity than it binds to cellular NLSs as will be understood by one of skill in the art, the importin beta binding domain of importin alpha 1 (Homo sapiens, #NM—002266, approximately amino acids 1-99), the importin beta binding domain of importin alpha 3 (Homo sapiens, #NM—002268, approximately amino acids 1-94), the importin beta binding domain of importin alpha 4 (Homo sapiens, #NM—002267, approximately amino acids 1-94), the importin beta binding domain of importin alpha 5 (Homo sapiens, #U28386, approximately amino acids 1-94), the importin beta binding domain of importin alpha 6 (Homo sapiens, #NM—002269, approximately amino acids 1-94), the importin beta binding domain of importin alpha 7 (Homo sapiens, #NM—012316, approximately amino acids 1-103), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind nucleoporins (for example by deleting the region between HEAT-5 and HEAT-6 (approximately amino acids 203-211) and the region between HEAT-6 and HEAT-7 (approximately amino acids 246-252) or by replacing those regions with nonhomologous linker regions (Y. M. Chook and G. Blobel (2001) Current Opinion in Structural Biology 11, 703-715)), importin beta 1 (Homo sapiens, #NM—002265, #NP—002256) modified to not bind importin alpha (for example by deleting the acidic loop importin-alpha-binding region spanning from approximately amino acid 333 through approximately amino acid 343 (G. Cingolani et al. (1999) Nature 399, 221-229)), a defective mutant of an exportin (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594), a mutant p10/NTF2 that inhibits import by importin beta 1 (for example p10 D23A (C. M. Lane et al. (2000) Journal of Cell Biology 151, 321-331) or N77Y (B. B. Quimby et al. (2001) Journal of Biological Chemistry 276, 38820-38829)), vesicuovirus matrix protein or a portion thereof that inhibits nuclear import and/or nuclear export (J. M. Petersen et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8590-8595; J. M. Petersen et al. (2000) Molecular and Cellular Biology 20, 8590-8601; C. von Kobbe et al. (2000) Molecular Cell 6, 1243-1252), a peptide that resembles the classical nuclear localization signal of SV40 T antigen (E. Merle et al. (1999) Journal of Cellular Biochemistry 74, 628-637), another nuclear localization signal, peptides with FxFG repeats or GLFG repeats (R. Bayliss et al. (2002) Journal of Biological Chemistry 277, 50597-50606), leptomycin B, a mutant of Ran that interferes with nuclear import or export (for example RanC4A (R. H. Kehlenbach et al. (2001) Journal of Biological Chemistry 276, 14524-14531)), or a molecule that binds to a pathogen or pathogen component or cellular component that is involved in transport between the cytoplasm and the nucleus of a cell (I. G. Macara (2001) Microbiology and Molecular Biology Reviews 65, 570-594; B. Ossareh-Nazari (2001) Traffic 2, 684-689)); a molecule that inhibits pathogenic prions (for example and without restriction, approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250); a molecule that alters the properties of the endocytic pathway, phagocytic pathway, endosomes, phagosomes, lysosomes, other intracellular compartments, or vesicular trafficking to produce an anti-pathogen effect, as described supra (including but not limited to dynamin-1 mutant K44A (M. Huber et al. (2001) Traffic 2, 727-736; particularly when overexpressed), cellubrevin (R. A. Fratti et al. (2002) Journal of Biological Chemistry 277, 17320-17326; particularly when overexpressed), Salmonella SpiC protein (NCBI Accession #U51927), a defective mutant of TassC (A. H. Lee et al. (2002) Cell. Microbiol. 4, 739-750), other vesicular trafficking inhibitors as will be understood by one of skill in the art, Nramp1 (P. Cuellar-Mata et al. (2002) Journal of Biological Chemistry 277, 2258-2265; C. Frehel et al. (2002) Cellular Microbiology 4, 541-556; D. J. Hackam et al. (1998) J. Exp. Med. 188, 351-364; particularly when overexpressed), NADPH oxidase subunits or cofactors (P. V. Vignais (2002) Cell. Mol. Life Sci. 59, 1428-1459; particularly when overexpressed), NOS2 nitric oxide synthase (J. D. MacMicking et al. (1997) Proc. Natl. Acad. Sci. USA 94, 5243-5248; particularly when overexpressed), human papillomavirus 16 E5 protein (NCBI Accession #W5WLHS), bafilomycin A1, a single-chain antibody or other molecule that binds to vacuolar ATPase subunit a (S. B. Sato and S. Toyama (1994) J. Cell. Biol. 127, 39-53; preferably a1 or a2,), antisense oligonucleotides that inhibit vacuolar ATPase subunits (J. E. Strasser et al. (1999) Journal of Immunology 162, 6148-6154;), a peptide composed of approximately the 78 amino-terminal amino acids of vacuolar H+-ATPase subunit E (M. Lu et al. (2002) Journal of Biological Chemistry 277, 38409-38415), A2-cassette mutant of vacuolar H+-ATPase subunit A (N. Hernando et al. (1999) Eur. J. Biochem. 266, 293-301), a defective mutant of subunit a1 or a2 of vacuolar H+-ATPase (S. Kawasaki-Nishi et al. (2001) Proc. Natl. Acad. Sci. USA 98, 12397-12402; S. Kawasaki-Nishi et al. (2001) 276, 47411-47420; T. Nishi and M. Forgac (2000) J. Biol. Chem. 275, 6824-6830; S. B. Peng et al. (1999) J. Biol. Chem. 274, 2549-2555; T. Toyomura et al. (2000) J. Biol. Chem. 275, 8760-8765), overexpression of the C and/or H subunits of vacuolar H+-ATPase subunit E (K. K. Curtis and P. M. Kane (2002) Journal of Biological Chemistry 277, 2716-2724), other defective vacuolar ATPase subunit or portion of a subunit (examples of wild-type human vacuolar ATPase subunits that can be made defective for anti-pathogen effects will be understood by one of skill in the art, and include, without limitation, those vacuolar ATPase subunits with Accession numbers: NM—004231, NM—130463, NM—015994, NM—001694, NM—004047, NM—001696, NM—004691, NM—001695, NM—001693, NM—001690, NM—020632, NM—004888)); a molecule that executes, stimulates, or inhibits ubiquitin-proteasome-degradative-pathway-related responses, as described supra (including but not limited to CHIP (D. M. Cyr et al. (2002) Trends Biochem. Sci. 27, 368-375; J. Demand et al. (2001) Curr. Biol. 11, 1569-1577; S. Murata et al. (2001) EMBO Rep. 2, 1133-1138; particularly when overexpressed), Fbx2 (Y. Yoshida et al. (2002) Nature 418, 438-442; particularly when overexpressed), molecules that ubiquitinate pathogens or pathogen components or cellular components that assist pathogens as will be understood by one of skill in the art (P. Zhou et al. (2000) Mol. Cell 6, 751-756; K. M. Sakamoto et al. (2001) Proc. Natl. Acad. Sci. USA 98, 8554-8559; N. Zheng et al. (2000) Cell 102, 533-539; D. Oyake et al. (2002) Biochemical and Biophysical Research Communications 295, 370-375), or inhibitors of ubiquitination or proteasomes (J. Myung et al. (2001) Medicinal Research Reviews 21, 245-273; G. Lennox et al. (1988) Neurosci. Lett. 94, 211-217; N. F. Bence et al. (2001) Science 292, 1552-1555; for example lactacystin or epoxomicin)); a molecule that executes, stimulates, or inhibits defensin-related responses, as described supra, including but not limited to alpha defensins, beta defensins, theta defensins, plant defensins, or arthropod defensins; a molecule that executes, stimulates, or inhibits cathelicidin-related responses, as described supra, including but not limited to hCAP-18/LL-37, CRAMP, Bac4, OaBac5; prophenin-1, protegrin-1, or PR-39; a molecule that executes, stimulates, or inhibits chemokine-related or thrombocidin-related responses, as described supra, including but not limited to CC chemokines, CXC chemokines, C chemokines, CX3C chemokines, CC chemokine receptors, CXC chemokine receptors, C chemokine receptors, CX3C chemokine receptors, JAK proteins, STAT proteins, fibrinopeptide A, fibrinopeptide B, or thymosin beta 4; a molecule that executes, stimulates, or inhibits interferon-related or cytokine-related responses, as described supra (including but not limited to interferon-alpha (Homo sapiens, #NM—002169, NM—021002, J00207; Mus musculus, #NM—010502, NM—010503, NM—010507, NM—008333, M68944, M13710); interferon-beta (Homo sapiens, #M25460, NM—002176; Mus musculus, #NM—010510); interferon-gamma (Homo sapiens, #NM—000619, J00219; Mus musculus, #M28621); interferon-delta; interferon-tau; interferon-omega (Homo sapiens, #NM—002177); interleukin 1 (IL-1: Homo sapiens, #NM—000575, NM—012275, NM—019618, NM—000576, NM—014439; Mus musculus, #NM—019450, NM—019451, AF230378); interleukin 2 (IL-2: Homo sapiens, #NM—000586); interleukin 3 (IL-3: Homo sapiens, #NM—000588; Mus musculus, #A02046); interleukin 4 (IL-4: Homo sapiens, #NM—000589, NM—172348; Mus musculus, #NM—021283); interleukin 5 (IL-5: Homo sapiens, #NM—000879; Mus musculus, #NM—010558); interleukin 6 (IL-6: Homo sapiens, #NM—000600; Mus musculus, #NM—031168); interleukin 7 (IL-7: Homo sapiens, #NM—000880, AH006906; Mus musculus, #NM—008371); interleukin 9 (IL-9: Homo sapiens, #NM—000590); interleukin 12 (IL-12: Homo sapiens, #NM—000882, NM—002187; Mus musculus, #NM—008351, NM—008352); interleukin 15 (IL-15: Homo sapiens, #NM—172174, NM—172175, NM—000585; Mus musculus, #NM—008357); cytokine receptors and related signaling molecules (W. E. Paul (ed.), Fundamental Immunology (4th ed., Lippincott-Raven, Philadelphia, 1999), Chapters 21 and 22); interferon type I receptor subunit 1 (IFNAR1: Homo sapiens, #NM—000629; Mus musculus, #NM—010508); interferon type I receptor subunit 2 (IFNAR2: Homo sapiens, #NM—000874; Mus musculus, #NM—010509); janus kinase 1 (JAK1: Homo sapiens, #NP—002218; Mus musculus, #NP—666257); janus kinase 2 (JAK2: Homo sapiens, #AAC23653, AAC23982, NP—004963; Mus musculus, #NP—032439, AAN62560); JAK3; Tyk2; signal transducer and activator of transcription 1 (STAT1: Homo sapiens, #NM—007315, NM—139266; Mus musculus, #U06924); signal transducer and activator of transcription 2 (STAT2: Homo sapiens, #NM—005419; Mus musculus, AF206162); STAT3; STAT4; STAT5; STAT6; interferon-stimulated gene factor 3 gamma (ISGF3 gamma: Homo sapiens, #Q00978, NM—006084; Mus musculus, #NM—008394) interferon regulatory factor 1 (IRF1: Homo sapiens, #NM—002198, P10914; Mus musculus, #NM—008390); interferon regulatory factor 3 (IRF3: Homo sapiens, #NM—001571, Z56281; Mus musculus, #NM—016849, U75839, U75840); interferon regulatory factor 5 (IRF5: Homo sapiens, #Q13568, U51127; Mus musculus, #AAB81997, NP—036187); interferon regulatory factor 6 (IRF6: Homo sapiens, #AF027292, NM—006147; Mus musculus, #U73029); interferon regulatory factor 7 (IRF7: Homo sapiens, #U53830, U53831, U53832, AF076494, U73036; Mus musculus, #NM—016850, U73037); interferon regulatory factor 8 (IRF8); a constitutively active interferon regulatory factor; protein kinase R (PKR: Homo sapiens, #AAC50768; Mus musculus, #Q03963; S. Nanduri et al. (1998) EMBO J. 17, 5458-5465); constitutively active PKR; 2′,5′-oligoadenylate synthetases (Homo sapiens forms including #P00973, P29728, AAD28543; Mus musculus forms including P11928; S. Y. Desai et al. (1995) J. Biol. Chem. 270, 3454-3461); constitutively active 2′,5′-oligoadenylate synthetases; RNase L (Homo sapiens, #CAA52920); constitutively active RNase L; promyelocytic leukemia protein (PML: W. V. Bonilla et al. (2002) Journal of Virology 76, 3810-3818); p56 or related proteins (J. Guo et al. (2000) EMBO Journal 19, 6891-6899; G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); p200 or related proteins (G. C. Sen (2000) Seminars in Cancer Biology 10, 93-101); ADAR1 (Homo sapiens, #U18121; Mus musculus, #NP—062629); Mx1 (Homo sapiens, #NM—002462); or Mx2 (Homo sapiens, #NM—002463)); a molecule that inhibits budding or release of pathogens from an infected cell, as described supra (including but not limited to Hrs, particularly when overexpressed (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; L. Chin et al. (2001) Journal of Biological Chemistry 276, 7069-7078; C. Raiborg et al. (2002) Nature Cell Biology 4, 394-398); defective Vps4 mutants such as K173Q or E228Q, particularly when overexpressed (J. E. Garrus et al. (2001) Cell 107, 55-65); small interfering RNA that inhibits Tsg101 expression (N. Bishop et al. (2002) Journal of Cell Biology 157, 91-101; J. E. Garrus et al. (2001) Cell 107, 55-65); truncated AP-50 consisting of approximately amino acids 121-435, or other defective mutant of AP-50, particularly when overexpressed (B. A. Puffer et al. (1998) Journal of Virology 72, 10218-10221); WW-domain-containing fragment of LDI-1, Nedd4, Yes-associated protein, KIAA0439 gene product, or other defective Nedd4-related proteins, particularly when overexpressed (A. Kikonyogo et al. (2001) Proc. Natl. Acad. Sci. USA 98, 11199-11204; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); a peptide consisting of the HIV p6 Gag PTAPP-motif-containing late (L) domain (L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729) or other viral late (L) domain containing PTAP, PSAP, PPXY, YPDL, or YXXL motifs (J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; A. Patnaik and J. W. Wills (2002) Journal of Virology 76, 2789-2795); amino acids 1-167 of Tsg101, TSG-5′ fragment of Tsg101, or similar amino-terminal fragment of Tsg101, particularly when overexpressed (D. G. Demirov et al. (2002) Proc. Natl. Acad. Sci. USA 99, 955-9601; E. L. Myers and J. F. Allen (2002) Journal of Virology 76, 11226-11235); a mutant of Tsg101 (M. Babst et al. (2000) Traffic 1, 248-258; L. VerPlank et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7724-7729; J. Martin-Serrano et al. (2001) Nature Medicine 7, 1313-1319; O. Pornillos et al. (2002) EMBO Journal 21, 2397-2406) with reduced capacity to aid viral budding; a casein kinase 2 (CK2) inhibitor, such as the peptide RRADDSDDDDD (SEQ ID NO: 472) (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); or G protein signalling inhibitors (E. K. Hui and D. P. Nayak (2002) Journal of General Virology 83, 3055-3066); a molecule that binds to a cellular or pathogen molecule (for example to one or more of the following molecules: Tsg101, Vps4, casein kinase 2, Hrs, hVps28, Eap30, Eap20, Eap45, Chmp1, Chmp2, Chmp3, Chmp4, Chmp5, Chmp6, AP-50, Nedd4-related proteins, WW-domain-containing proteins, or L-domain-containing proteins; O. Pornillos et al. (2002) TRENDS in Cell Biology 12, 569-579; P. Gomez-Puertas et al. (2000) Journal of Virology 74, 11538-11547; E. Katz et al. (2002) Journal of Virology 76, 11637-11644) that is involved in budding or release of pathogens from an infected cell); a molecule that executes or stimulates apoptosis-related or other cell-death-related responses, as described supra (including but not limited to p53 (Homo sapiens, #AAF36354 through AAF36382; Mus musculus, #AAC05704, AAD39535, AAF43275, AAF43276, AAK53397); Bax (Homo sapiens, #NM—004324); Bid (Homo sapiens, #NM—001196); apoptotic protease activating factor 1 (Apaf-1: Homo sapiens, #NM—013229, NM—001160; Mus musculus, #NP—033814); Fas/CD95 (Homo sapiens, #AAC16236, AAC16237; Mus musculus, #AAG02410); TNF receptors (Homo sapiens, #NP—001056; V. Baud and M. Karin (2001) TRENDS in Cell Biology 11, 372-377; U. Sartorius et al. (2001) Chembiochem 2, 20-29); FLICE-activated death domain (FADD: Homo sapiens, #U24231; Mus musculus, #NM—010175); TRADD (Homo sapiens, #NP—003780, CAC38018); granzyme B (Homo sapiens, #AAH30195, NP—004122; Mus musculus, #AAH02085, NP—038570); constitutively active granzyme B; Smac/DIABLO (Homo sapiens, #NM—019887); caspases (including but not restricted to Caspase 1, Homo sapiens, #NM—001223; Caspase 2, Homo sapiens, #NM—032982, NM 001224, NM—032983, and NM—032984; Caspase 3, Homo sapiens, #U26943; Caspase 4, Homo sapiens, #AAH17839; Caspase 5, Homo sapiens, #NP—004338; Caspase 6, Homo sapiens, #NM—001226 and NM—032992; Caspase 7, Homo sapiens, #XM—053352; Caspase 8, Homo sapiens, #NM—001228; Caspase 9, Homo sapiens, #AB019197; Caspase 10, Homo sapiens, #XP—027991; Caspase 13, Homo sapiens, #AAC28380; Caspase 14, Homo sapiens, #NP—036246; Caspase 1, Mus musculus, #BC008152; Caspase 2, Mus musculus, #NM—007610; Caspase 3, Mus musculus, #NM—009810; Caspase 6, Mus musculus, #BC002022; Caspase 7, Mus musculus, #BC005428; Caspase 8, Mus musculus, #BC006737; Caspase 9, Mus musculus, #NM—015733; Caspase 11, Mus musculus, #NM—007609; Caspase 12, Mus musculus, #NM—009808; Caspase 14, Mus musculus, #AF092997; and CED-3 caspase, Caenorhabditis elegans, #AF210702); a constitutively active caspase; calpains (T. Lu et al., (2002) Biochimica et Biophysica Acta 1590, 16-26)); a molecule that degrades components of cells or pathogens, as described supra (for example: proteases, including but not limited to chymotrypsin, trypsin, or elastase; DNases, including but not limited to caspase-activated DNase (CAD), constitutively active CAD (N. Inohara et al. (1999) Journal of Biological Chemistry 274, 270-274), or restriction enzymes; RNases, including but not limited to RNase III (Homo sapiens, #AF189011; Escherichia coli, #NP—417062, NC—000913), RNt1p (Saccharomyces cerevisiae, #U27016), Pac1, (Schizosaccharomyces pombe, #X54998), RNase A, or RNase L; glycosidases, including but not limited to N-glycanase, endoglycosidase H, O-glycanase, endoglycosidase F2, sialidase, or beta-galactosidase; or lipases, including but not limited to phospholipase A1, phospholipase A2, phospholipase C, or phospholipase D); a molecule that is toxic to an infected host cell or a pathogen cell, as described supra (including but not limited to an intracellular bacterial toxin (B. B. Finlay and P. Cossart (1997) Science 276, 718-725; C. Montecucco et al. (1994) FEBS Lett. 346, 92-98; P. O. Falnes et al. (2001) Biochemistry 40, 4349-4358) that has been modified so that it cannot cross cellular plasma membranes (as will be understood by one of skill in the art), such as the A (21 kDa) fragment of diptheria toxin; a molecule that is toxic to a pathogen cell, including but not limited to penicillin, erythromycin, tetracycline, rifampin, amphotericin B, metronidazole, or mefloquine; an ATP inhibitor (E. K. Hui and D. P. Nayak (2001) Virology 290, 329-341); or a toxin that inhibits transcription, translation, replication, oxidative phosphorylation, cytoskeletal processes, or other cell and/or pathogen functions).
Also included in this invention are chimeric transcriptions factors. The heat shock element (HSE) binding domain is approximately amino acids 13-121 of human heat shock factor 1 (HSF1) (M. Green et al. (1995) Molecular and Cellular Biology 15, 3354-3362; S.-G. Ahn et al. (2001) Genes & Development 15, 2134-2145). One or more copies of this domain can be isolated and linked together, preferably by flexible hydrophilic amino acid sequences in a chimeric transcription factor. In a preferred embodiment, three copies of the HSF1 DNA binding domain, preferably separated by flexible hydrophilic amino acid sequences are present in the chimeric transcription factor.
Interferon-stimulated gene factor 3 gamma (ISGF-3 gamma) induces transcription in response to type-I interferon. The ISGF-3 gamma DNA binding domain is approximately amino acids 1-112. (NCBI Accession #Q00978; H. A. R. Bluyssen, J. E. Durbin, and D. E. Levy (1996) Cytokine & Growth Factor Reviews 7, 11-17; Y. Mamane et al. (1999) Gene 237, 1-14). The ISGF-3 gamma DNA binding domain can be isolated and used in a genetically-engineered chimeric transcription factor, as described below.
Interferon regulatory factor 3 (IRF-3) induces transcription in response to dsRNA. Excluding regions needed for regulation of its activation, the DNA binding domain of IRF-3 is approximately amino acids 1-97 (Y. Mamane et al. (1999) Gene 237, 1-14; R. Lin, Y. Mamane, and J. Hiscott (1999) Molecular and Cellular Biology 19, 2465-2474). The DNA binding domain of IRF-3 can also be isolated and used in a genetically-engineered chimeric transcription factor, as described below.
Interferon regulatory factor 1 (IRF-1) upregulates expression of MHC Class I and functions in other ways to improve immune and antiviral responses. The IRF-1 DNA binding domain is approximately amino acids 1-109 (NCBI Accession # P10914, NP—002189; C. E. Samuel (2001) Clinical Microbiology Reviews 14, 778-809; S. J. P. Gobin et al. (1999) J Immunology 163, 1428-1434; W.-C. Au et al. (1995) Proc. Natl. Acad. Sci. 92, 11657-11661; S. Kirchhoff et al. (2000) Eur. J. Biochem. 267, 6753-6761; Y. Mamane et al. (1999) Gene 237, 1-14). The IRF-1 DNA binding domain can also be isolated and used in a genetically-engineered chimeric transcription factor, as described below.
p53 upregulates apoptosis-related and other genes when activated. The p53 DNA binding domain is approximately amino acids 100-300. (A. Ayed et al. (2001) Nature Structural Biology 8, 756-760; B. F. Mueller-Tiemann et al. (1998) Proc. Natl. Acad. Sci. 95, 6079-6084; M. E. Anderson et al. (1997) Molecular and Cellular Biology 17, 6255-6264; Y. Wang et al. (1995) Molecular and Cellular Biology 15, 2157-2165). In a preferred embodiment, the chimeric transcription factor has four copies of the p53 DNA binding domain, preferably separated by flexible hydrophilic amino acid sequences. The p53 DNA binding domain can be isolated and used in a genetically-engineered chimeric transcription factor, as described below.
XBP1 (K. Lee et al. (2002) Genes & Development 16, 452-466; H. Yoshida et al. (2001) Cell 107, 881-891) and ATF6 (X. Chen et al. (2002) Journal of Biological Chemistry 277, 13045-13052; J. Shi et al. (2002) Developmental Cell 3, 99-111; Y. Wang et al. (2000) Journal of Biological Chemistry 275, 27013-27020) upregulate unfolded-protein-response or endoplasmic-reticulum-associated-protein-degradation-response genes.
CIITA (M. W. Linhoff et al. (2001) Molecular and Cellular Biology 21, 3001-3011; A. Muhlethaler-Mottet et al. (1997) EMBO Journal 16, 2851-2860) upregulates MHC Class II genes when activated. The CARD and/or acidic domains of CIITA isoforms act as transcriptional activators.
NF kappa B upregulates inflammatory-response genes when activated (F. E. Chen and G. Ghosh (1999) Oncogene 18, 6845-6852; H. L. Pahl (1999) Oncogene 18, 6853-6866).
In one embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domain of ISGF-3 gamma is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more transcription activation domains isolated from CIITA; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B; one or more DNA-binding domains isolated from IRF-1.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domain (approximately amino acids 1-97) of IRF-3 is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more transcription activation domains isolated from CIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more DNA-binding domains isolated from p53; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B; one or more DNA-binding domains isolated from IRF-1.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domains of NF kappa B are replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more transcription activation domains isolated from CIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more DNA-binding domains isolated from IRF-3; one or more HSE-binding domains; one or more DNA-binding domains isolated from IRF-1.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domain of ATF6 is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from p53; one or more transcription activation domains isolated from CIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more DNA-binding domains isolated from IRF-3; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B; one or more DNA-binding domains isolated from IRF-1.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domain of p53 is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more transcription activation domains isolated from CIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more DNA-binding domains isolated from IRF-3; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B; one or more DNA-binding domains isolated from IRF-1.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural transcription activation domain of CIITA (the CARD and/or acidic domain) is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more DNA-binding domains isolated from IRF-3; one or more DNA-binding domains isolated from p53; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B; one or more DNA-binding domains isolated from IRF-1.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domain of IRF-1 is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more transcription activation domains isolated from CIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B.
In another embodiment, a chimeric molecule or agent of the invention includes a chimeric transcription factor in which the natural DNA-binding domain (approximately amino acids 13-121) of HSF1 is replaced with one or more of the following: one or more DNA-binding domains isolated from XBP1; one or more DNA-binding domains isolated from ATF6; one or more transcription activation domains isolated from CIITA; one or more DNA-binding domains isolated from ISGF-3 gamma; one or more DNA-binding domains isolated from IRF-3; one or more HSE-binding domains; one or more DNA-binding domains isolated from NF kappa B; one or more DNA-binding domains isolated from IRF-1.
An agent of the invention, as described herein, can comprise at least one pathogen-interacting molecular structure and at least one effector-mediating molecular structure. Alternatively, an agent of the invention can comprise at least one pathogen-induced product-interacting molecular structure and at least one effector-mediating molecular structure.
A pathogen-interacting molecular structure, as used herein, is generally directed to an isolated molecular structure that is capable of recognizing or binding (interacting with) a pathogen, pathogen component or pathogen product. The term pathogen-interacting molecular structure is structure of a molecule that includes at least the minimal region necessary to perform the function of interacting with a pathogen, pathogen component or pathogen product. Isolated pathogen-interacting molecular structures, as used herein, encompass the pathogen-detection domains described supra. Furthermore, a pathogen-interacting molecular structure can be more than or less than a domain of the described proteins or polynucleotide sequences, but still retains the function of interacting with a pathogen, pathogen component or pathogen product.
A pathogen-induced product-interacting molecular structure, as used herein, is generally directed to an isolated molecular structure that is capable of recognizing or binding (interacting with) a pathogen-induced product, as described herein and include, for example and without limitation, cytokines such as an interferons or interleukins, unfolded-protein response or endoplasmic reticulum-associated protein degradation response signaling molecules, stress response or inflammatory response signaling molecules, 2′,5′-oligoadenylate, and apoptosis signaling molecules. The term pathogen-induced product-interacting molecular structure is the structure of a molecule that includes at least the minimal region necessary to perform the function of interacting with a pathogen-induced product. Isolated pathogen-induced product-interacting molecular structures, as used herein, encompass the pathogen-induced product-detection domains described supra. Furthermore, a pathogen-induced product-interacting molecular structure can be more than or less than a domain of the described proteins or polynucleotide sequences, but retains the function of interacting with a pathogen-induced product.
The effector-mediating molecular structure, as used herein, is generally directed to an isolated molecular structure that is capable of mediating a wide range of effector functions, as described supra for an effector domain of a chimeric molecule of the invention. In particular, the effector-mediating molecular structure of this invention can mediate the same responses as an effector domain, for example and without limitation: (1) an interferon response; (2) an apoptosis response; (3) a stress response; (4) an inflammatory response; (5) an enhanced immune response; (6) a degradative response; (7) inhibition of transport between the cytoplasm and the nucleus of a cell; (8) an unfolded-protein response or endoplasmic reticulum-associated protein degradation response; or (9) alteration of the endocytic or phagocytic pathway, all of which are discussed supra.
The molecular structures of the described agent can be isolated from naturally-occurring molecules, such as a cellular protein, that normally recognize a pathogen, pathogen component, pathogen product, or pathogen-induced product, or is a mediator of a wide range of effector function. Molecular structures can be isolated from a wide range of known cellular proteins from a number of different organisms, including for example, humans, non-human primates, rodents, plants, Drosophila, yeast, bacteria and the like, as will be appreciated by one of skill in the art. The molecular structures can also be synthetically-derived, such as by chemically modifying a naturally-occurring molecule, or otherwise manipulating a naturally-occurring molecule to enhance, optimize, or modify the molecular structures, using standard techniques known to those of skill in the art, or alternatively, they can be a synthetic product such as a small molecule or a peptidomimetic. Furthermore, the molecular structures of the agent can be an antibody (including, for example, antibody fragments, such as Fab, Fab′, F(ab′)2, and fragments including either a VL or VH domain, single chain antibodies, bi-specific, chimeric or humanized antibodies), that performs the function of the molecular structure.
More than one detection and/or effector domain can be present in a chimeric molecule. These can be the same or different domains. Similarly, more than one detection and/or effector molecular structures can be present in an agent of the invention.
A chimeric molecule or agent of the invention can be a nonnaturally occurring molecule that contains two or more binding sites for a pathogen or pathogen product. The two or more binding sites promote agglomeration of pathogens or pathogen products and thereby directly or indirectly promote an anti-pathogen effect. For example, a chimeric molecule or agent of the invention can have two or more binding sites for LPS (for example, sites that mimic the LPS-binding domain from approximately amino acids 1-199 of human BPI or other LPS-binding domains as described supra); two or more binding sites for peptidoglycan (for example, sites that mimic the peptidoglycan-binding domain from the extracellular domain of human TLR2); two or more binding sites for muramyl dipeptide (for example, sites that mimic the muramyl-dipeptide-binding domain from approximately amino acids 744-1040 of human Nod2); two or more binding sites for bacterial flagellin (for example, sites that mimic the flagellin-binding domain from the extracellular domain of human TLR5); two or more binding sites for bacterial type III secretion systems; two or more binding sites for CpG DNA (for example, sites that mimic the CpG-DNA-binding domain from the extracellular domain of human TLR9); two or more binding sites for zymosan (for example, sites that mimic the zymosan-binding domain from the extracellular domain of human TLR2); two or more binding sites for a pathogenic form of a prion (for example, sites that mimic a portion of a nonpathogenic prion form that binds to a pathogenic prion form (such as approximately amino acids 119-136 of hamster prion protein; J. Chabry et al. (1999) Journal of Virology 73, 6245-6250)); two or more binding sites for dsRNA (for example, sites that contain lividomycin or that mimic the dsRNA-binding domain of lividomycin, protein kinase R, or other dsRNA-binding domains as described supra); two or more binding sites for viral late domains (for example and without restriction, sites that bind to viral late domain motifs such as PTAP, PSAP, PPXY, YPDL, or YXXL, as described supra); two or more binding sites for viral glycoproteins (for example and without restriction, sites that mimic the hemagglutinin-binding domain of human NK cell activation receptor NKp46).
The chimeric molecules and agents as described herein can be assembled or joined between the domains or molecular structures by, for example, peptide linkage, covalent bonding, artificial linkage, or a flexible linker region normally associated with either domain or molecular structure.
Alternatively, the domains of the chimeric molecules or molecular structures of the agent can be separated. Separate domains or molecular structures are capable of being assembled or joined through several mechanisms, for example and without limitation, through the interaction with another reagent, for example a bi-specific antibody, a chemical cross-linker, or other methods as will be appreciated by one of skill in the art. The separate domains can also be assembled together via non-covalent bonds, such as through electrostatic interactions and the like. Furthermore, the separate domains or molecular structures can mediate their effects either directly or indirectly through such agents as secondary signaling molecules, as will be understood by one of skill in the art.
Attached to the separate domains or separate molecular structures can be further domains or structures that can mediate the joining of the separate domains or structures to form the chimeric molecule or agent, for example, one domain or molecular structure can have one or more streptavidin molecules attached, and the other domain or molecular structure can have one or more biotin molecules attached, thus the specific biotin-streptavidin interaction mediates the forming of a chimeric molecule or agent. Other suitable interaction domains or structures will be recognized by one of skill in the art.
The chimeric molecule or agent can additionally contain cellular targeting tags. For example, tags that direct the chimeric molecule or agent to the cell membrane or cellular organelles, the nucleus, or other varieties of tags. Such tags can be used to mediate crossing of the membrane by the chimeric molecule or agent. Suitable protein uptake tags include, for example and without limitation: (1) poly-arginine and related peptoid tags (L. Chen et al. (2001) Chem. Biol. 8: 1123-1129, P. A. Wender et al. (2000) Proc. Natl. Acad. Sci. 97: 13003-13008); (2) HIV TAT protein, its Protein Transduction Domain (PTD) spanning approximately amino acids 47-57, or synthetic analogs of the PTD (M. Becker-Hapak, S. S. McAllister, and S. F. Dowdy (2001) Methods 24: 247-256, A. Ho et al. (2001) Cancer Res. 61: 474-477); (3) Drosophila Antennapedia protein, the domain spanning approximately amino acids 43-58 also called Helix-3 or Penetratin-1, or synthetic analogs thereof (D. Derossi, G. Chassaing, and A. Prochiantz (1998) Trends Cell Biol. 8: 84-87, A. Prochiantz (1996) Curr. Opin. Neurobiol. 6: 629-63); (4) Herpesvirus VP22 protein, the domain spanning approximately amino acids 159-301, or portions or synthetic analogs thereof (N. Normand, H. van Leeuwen, and P. O'Hare (2001) J. Biol. Chem. 276: 15042-15050, A. Phelan, G. Elliott, and P. O'Hare (1998) Nat. Biotech. 16: 440-443); (5) Membrane-Translocating Sequence (MTS) from Kaposi fibroblast growth factor or related amino acid sequences such as AAVLLPVLLAAP (SEQ ID NO: 473) (M. Rojas, J. P. Donahue, Z. Tan, and Y.-Z. Lin (1998) Nat. Biotech. 16: 370-375, C. Du, S. Yao, M. Rojas, and Y.-Z. Lin (1998) J. Peptide Res. 51: 235-243); (6) Pep-1, MPG, and similar peptides (M. C. Morris et al. (2001) Nat. Biotech. 19: 1173-1176, M. C. Morris et al. (1999) Nuc. Ac. Res. 27: 3510-3517); (7) Transportan, Transportan 2, and similar peptides (M. Pooga et al. (1998) FASEB J. 12: 67-77; M. Pooga et al. (1998) Ann. New York Acad. Sci. 863: 450-453); (8) Amphipathic model peptide and related peptide sequences (A. Scheller et al. (2000) Eur. J. Biochem. 267: 6043-6049, A. Scheller et al. (1999) J. Pept. Sci. 5: 185-194); (9) Tag protein to be delivered with approximately amino acids 1-254 of Bacillus anthracis lethal factor (LF), and administer along with B. anthracis protective antigen (PA) to deliver the tagged protein into cells, or similar methods (S. H. Leppla, N. Arora, and M. Varughese (1999) J. App. Micro. 87: 284, T. J. Goletz et al. (1997) Proc. Natl. Acad. Sci. 94: 12059-12064); and (10) Folic acid (C. P. Leamon and P. S. Low (2001) Drug Discov. Today 6: 44-51, C. P. Leamon, R. B. DePrince, and R. W. Hendren (1999) J. Drug Targeting 7: 157-169). Methods for attaching uptake tags to the proteins employ standard methods and will be recognized by one of skill in the art.
Optionally the chimeric molecule or agent can include one or more binding sites for one or more natural inhibitory or regulatory molecules in order to facilitate the inhibitory or regulatory molecule(s) to regulate the activity of the chimeric molecule or agent, and prevent toxicity in uninfected cells. For example and without restriction, the chimeric molecule or agent can include one or more binding sites for one of more of the following: the natural P58 inhibitor of protein kinase R and PERK (W. Yan et al. (2002) Proc. Natl. Acad. Sci. USA 99, 15920-15925); the natural RLI inhibitor of RNase L (C. Bisbal et al. (1995) Journal of Biological Chemistry 270, 13308-13317); the natural XIAP inhibitor of caspase 9 (S. M. Srinivasula et al. (2001) Nature 410, 112-116); or the natural HSBP1 inhibitor of HSF1 (R. I. Morimoto (1998) Genes & Development 12, 3788-3796).
The chimeric molecule and its individual domains, and the agent and its individual molecular structures, can be of a variety of compounds or substances, for example, protein, DNA, RNA, single chain antibodies, small molecule drugs, pro-drugs, or peptidomimetics. A DNA or RNA encoding a molecule of interest can, optionally, be operatively-linked to a promoter. Furthermore, said promoter can be conditionally regulated.
The chimeric molecule or agent can be administered to a cell or organism before (prophylactically) or after infection (therapeutically).
The composition of the present invention can be administered by any known route of administration. For example, the route of administration can be intravenous, intramuscular, intraarterial, intraperitoneal, intrasternal, subcutaneous, intraocular, inhalation, orally and by intraarticular injection or infusion.
The composition of the present invention can be, for example, solid (or semi-solid, such as, creams or a gelatin-type substance), liquid, or aerosol. Examples of solid compositions include pills, creams, and implantable dosage units. The pills can be administered orally, the creams can be administered topically. The implantable dosage unit can be administered locally, or implanted for systemic release of the chimeric molecules or agents, for example subcutaneously. Examples of liquid composition include formulations adapted for injection subcutaneously, intravenously, intraarterially, and formulations for topical and administration. Examples of aersol formulation include inhaler formulation for administration to the lungs.
Pharmaceutical compositions for parenteral injection comprise pharmaceutically acceptable sterile aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, as well as sterile powders for reconstitution into sterile injectable solutions, or dispersions, just prior to use. Examples of suitable aqueous and nonaqueous carriers, diluents, solvents or vehicles include water, ethanol, polyols (e.g., glycerol, propylene glycol, polyethylene glycol and the like), carboxymethylcellulose and suitable mixtures thereof, vegetable oils (e.g., olive oil) and injectable organic esters such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials such as lecithin, by the maintenance of the required particle size in the case of dispersions and by the use of surfactants. These compositions can also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents such as paraben, chlorobutanol, phenol sorbic acid and the like. It can also be desirable to include isotonic agents such as sugars, sodium chloride and the like. Prolonged absorption of the injectable pharmaceutical form can be brought about by the inclusion of agents, such as aluminum monostearate and gelatin, which delay absorption. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-polyglycolide, poly(orthoesters) and poly(anhydrides). Depending upon the ratio of drug to polymer and the nature of the particular polmer employed, the rate of drug release can be controlled. Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissues. The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable media just prior to use.
The compositions of the present invention can include pharmaceutically-acceptable salts of the compositions described herein, e.g., which can be derived from inorganic or organic acids. A “pharmaceutically-acceptable salt” is meant to describe those salts which are, within the scope of sound medical judgement, suitable for use in contact with the tissues of animals, preferably mammals, without undue toxicity, irritation, allergic response and the like and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well-known in the art. For example, S. M. Berge, et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences (1977) 66:1 et seq. Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the polypeptide) that are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, tartaric, mandelic and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine and the like. The salts can be prepared in situ during the final isolation and purification of the compounds of the invention or separately by reacting a free base function with a suitable organic acid. Representative acid addition salts include, but are not limited to acetate, adipate, alginate, citrate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, camphorate, camphorsufonate, digluconate, glycerophosphate, hemisulfate, heptonoate, hexanoate, fumarate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxymethanesulfonate (isethionate), lactate, maleate, methanesulfonate, nicotinate, 2-naphthalenesulfonate, oxalate, pamoate, pectinate, persulfate, 3-phenylpropionate, picrate, pivalate, propionate, succinate, tartate, thiocyanate, phosphate, glutamate, bicarbonate, p-toluenesulfonate and undecanoate. Also, the basic nitrogen-containing groups can be quaternized with such agents as lower alkyl halides such as methyl, ethyl, propyl, and butyl chlorides, bromides and iodides; dialkyl sulfates like dimethyl, diethyl, dibutyl, and diamyl sulfates; long chain halides such as decyl, lauryl, myristyl and stearyl chlorides, bromides and iodides; arylalkyl halides like benzyl and phenethyl bromides and others. Water or oil-soluble or dispersible products are thereby obtained. Examples of acids which can be employed to form pharmaceutically acceptable acid addition salts include such inorganic acids as hydrochloric acid, hydrobromic acid, sulphuric acid and phosphoric acid and such organic acids as oxalic acid, maleic acid, succinic acid and citric acid.
As used herein, the terms “pharmaceutically acceptable,” “physiologically tolerable” and grammatical variations thereof as they refer to compositions, carriers, diluents and reagents, are used interchangeably and represent materials that are capable of administration to or upon an animal, preferably a mammal, with a minimum of undesirable physiological effects such as nausea, dizziness, gastric upset and the like. The preparation of a pharmacological composition that contains active ingredients dissolved or dispersed therein is well understood in the art and need not be limited based on formulation. Typically such compositions are prepared as injectables either as liquid solutions or suspensions, however, solid forms suitable for solution, or suspensions, in liquid prior to use can also be prepared. The preparation can also be emulsified.
The active ingredient can be mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient and in amounts suitable for use in the therapeutic methods described herein. Suitable excipients include, for example, water, saline, dextrose, glycerol, ethanol or the like and combinations thereof. In addition, if desired, the composition can contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents and the like which enhance the effectiveness of the active ingredient.
Use of timed release or sustained release delivery systems are also included in the invention. A sustained-release matrix, as used herein, is a matrix made of materials, usually polymers, which are degradable by enzymatic or acid/base hydrolysis or by dissolution. Once inserted into the body, the matrix is acted upon by enzymes and body fluids. The sustained-release matrix desirably is chosen from biocompatible materials such as liposomes, polylactides (polylactic acid), polyglycolide (polymer of glycolic acid), polylactide co-glycolide (co-polymers of lactic acid and glycolic acid) polyanhydrides, poly(ortho)esters, polyproteins, hyaluronic acid, collagen, chondroitin sulfate, carboxylic acids, fatty acids, phospholipids, polysaccharides, nucleic acids, polyamino acids, amino acids such as phenylalanine, tyrosine, isoleucine, polynucleotides, polyvinyl propylene, polyvinylpyrrolidone and silicone. A preferred biodegradable matrix is a matrix of one of either polylactide, polyglycolide, or polylactide co-glycolide (co-polymers of lactic acid and glycolic acid).
The chimeric molecules and agents described herein can be administered individually, in combinations with each other, or in combination with other treatments, as will be apparent to one of skill in the art. The individual domains of the chimeric molecules, or individual molecular structures of the agent described herein, can be administered separately or simultaneously to the cell or organism. Formation of the chimeric molecules or agent of the invention, from separate domains or molecular structures, can occur prior to administering to the cell or organism (ex vivo or in vitro assembly), or the separate domains or molecular structures can be administered to the cell or organism separately and allowed to assemble as chimeric molecules, or as the agent of the invention, in the cell or organism (in vivo assembly).
Furthermore, one or more chimeric molecules and/or agents of the invention can be administered to a cell or organism to treat or prevent an infection by one or more pathogens. To minimize undesirable effects, one or more pathogen detector or pathogen-induced product detector molecules can optionally be administered together with one or more effector molecules, such that detection of a pathogen or pathogen-induced product by the detector molecule(s) directly or indirectly stimulates, activates, facilitates, or upregulates the effector molecule(s). For example and without limitation: one or more detector molecules can be joined to one or more effector molecules such that binding to a pathogen or pathogen-induced product activates or facilitates the function of the effector molecule(s); a detector molecule can be a genetic promoter which is operatively linked to a gene that encodes an effector molecule; a pathogen or pathogen-induced product can affect a detector molecule, which then stimulates, activates, facilitates, or upregulates the effector molecule(s); a pathogen or pathogen-induced product can affect a detector molecule, which then acts via one or more naturally occurring molecules to stimulate, activate, facilitate, or upregulate the effector molecule(s); the detector and effector molecules can be the same molecule, for example and without limitation, a molecule that binds to one or more pathogens or pathogen components, thereby interfering with the pathogens or pathogen components; the detector and/or effector molecules can bind to or interact with one or more naturally occurring molecules, thereby making use of the pathogen-detection, pathogen-induced-product-detection, or anti-pathogen properties of said naturally occurring molecules.
As will be appreciated by one of skill in the art, the chimeric molecule, agent, domains of the chimeric molecule, or molecular structures of the agent, can be administered alone or as admixtures with conventional excipients, as described supra, and which do not deleteriously react with the chimeric molecule or agent. Such preparations can be mixed with auxilliary agents such a lubricants, preservatives, stablilizers, wetting agents, emulsifiers, buffers, coloring, and/or aromatic substances and the like, which also do not deleteriously react with the chimeric molecules or agents of the invention. Furthermore, the preparations can also be combined with other active substances to reduce metabolic degradation, as desired.
The dosage and frequency (single or multiple dosages) administered to the cell or organism can vary depending on a variety of factors, including the type of pathogen, duration of pathogen infection, extent of disease associated with pathogen infection, weight and health of the recipient and the route of administration of the composition. Those skilled in the art will be readily able to determine suitable dosages and frequencies using standard techniques.
As used herein, the term “therapeutically effective amount” means the total amount of each active component of the composition or method that is sufficient to show a meaningful benefit to the recipient, i.e., treatment, healing, prevention or amelioration of the relevant disease or disorder, or an increase in rate of treatment, healing, prevention or amelioration of such diseases or disorders. When applied to a combination, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
Other methods of treatment include gene therapy. Gene transfer methods for gene therapy fall into three broad categories: physical (e.g., electroporation, direct gene transfer and particle bombardment), chemical (e.g., lipid-based carriers, or other non-viral vectors) and biological (e.g., virus-derived vector and receptor uptake). For example, non-viral vectors can be used which include liposomes coated with DNA. Such liposome/DNA complexes can be directly injected intravenously into the patient. Additionally, vectors or the “naked” DNA of the gene can be directly injected into the desired organ, tissue or tumor for targeted delivery of the therapeutic DNA.
Gene therapy methodologies can also be described by delivery site. Fundamental ways to deliver genes include ex vivo gene transfer, in vivo gene transfer, and in vitro gene transfer. In ex vivo gene transfer, cells are taken from the patient and grown in cell culture. The DNA is transfected into the cells, the transfected cells are expanded in number and then reimplanted in the patient. In in vitro gene transfer, the transformed cells are cells growing in culture, such as tissue culture cells, and not particular cells from a particular patient. These “laboratory cells” are transfected, the transfected cells are selected and expanded for either implantation into a patient or for other uses.
In vivo gene transfer involves introducing the DNA into the cells of the patient when the cells are within the patient. Methods include using virally-mediated gene transfer using a noninfectious virus to deliver the gene in the patient or injecting naked DNA into a site in the patient and the DNA is taken up by a percentage of cells in which the gene product protein is expressed. Additionally, other methods such as use of a “gene gun,” can be used for in vitro insertion of the DNA or regulatory sequences controlling production of the chimeric protein or agent described herein.
Chemical methods of gene therapy can involve a lipid based compound, not necessarily a liposome, to transfer the DNA across the cell membrane. Lipofectins or cytofectins, lipid-based positive ions that bind to negatively charged DNA, make a complex that can cross the cell membrane and provide the DNA into the interior of the cell. Another chemical method uses receptor-based endocytosis, which involves binding a specific ligand to a cell surface receptor and enveloping and transporting it across the cell membrane. The ligand binds to the DNA and the whole complex is transported into the cell. The ligand gene complex is injected into the blood stream and then target cells that have the receptor will specifically bind the ligand and transport the ligand-DNA complex into the cell.
Many gene therapy methodologies employ viral vectors to insert genes into cells. For example, altered retrovirus vectors have been used in ex vivo methods to introduce genes into peripheral and tumor-infiltrating lymphocytes, hepatocytes, epidermal cells, myocytes, or other somatic cells. These altered cells are then introduced into the patient to provide the gene product from the inserted DNA.
Viral vectors have also been used to insert genes into cells using in vivo protocols. To direct the tissue-specific expression of foreign genes, cis-acting regulatory elements or promoters that are known to be tissue-specific can be used. Alternatively, this can be achieved using in situ delivery of DNA or viral vectors to specific anatomical sites in vivo. For example, gene transfer to blood vessels in vivo was achieved by implanting in vitro transduced endothelial cells in chosen sites on arterial walls. The virus infected surrounding cells which also expressed the gene product. A viral vector can be delivered directly to the in vivo site, by a catheter for example, thus allowing only certain areas to be infected by the virus, and providing long-term, site specific gene expression.
Viral vectors that have been used for gene therapy protocols include but are not limited to, retroviruses, other RNA viruses such as poliovirus or Sindbis virus, adenovirus, adeno-associated virus, herpes viruses, SV40, vaccinia and other DNA viruses. Replication-defective murine retroviral vectors are the most widely utilized gene transfer vectors. Retroviral vector systems exploit the fact that a minimal vector containing the 5′ and 3′ LTRs and the packaging signal are sufficient to allow vector packaging, infection and integration into target cells providing that the viral structural proteins are supplied in trans in the packaging cell line. Fundamental advantages of retroviral vectors for gene transfer include efficient infection and gene expression in most cell types, precise single copy vector integration into target cell chromosomal DNA, and ease of manipulation of the retroviral genome.
Mechanical methods of DNA delivery include fusogenic lipid vesicles such as liposomes or other vesicles for membrane fusion, lipid particles of DNA incorporating cationic lipid such as lipofectin, polylysine-mediated transfer of DNA, direct injection of DNA, such as microinjection of DNA into germ or somatic cells, pneumatically delivered DNA-coated particles, such as the gold particles used in a “gene gun,” and inorganic chemical approaches such as calcium phosphate transfection. Particle-mediated gene transfer methods were first used in transforming plant tissue. With a particle bombardment device, or “gene gun,” a motive force is generated to accelerate DNA-coated high density particles (such as gold or tungsten) to a high velocity that allows penetration of the target organs, tissues or cells. Particle bombardment can be used in in vitro systems, or with ex vivo or in vivo techniques to introduce DNA into cells, tissues or organs. Another method, ligand-mediated gene therapy, involves complexing the DNA with specific ligands to form ligand-DNA conjugates, to direct the DNA to a specific cell or tissue.
The DNA of the plasmid may or may not integrate into the genome of the cells. Non-integration of the transfected DNA would allow the transfection and expression of gene product proteins in terminally differentiated, non-proliferative tissues for a prolonged period of time without fear of mutational insertions, deletions, or alterations in the cellular or mitochondrial genome. Long-term, but not necessarily permanent, transfer of therapeutic genes into specific cells can provide treatments for genetic diseases or for prophylactic use. The DNA could be re-injected periodically to maintain the gene product level without mutations occurring in the genomes of the recipient cells. Non-integration of exogenous DNA can allow for the presence of several different exogenous DNA constructs within one cell with all of the constructs expressing various gene products.
Electroporation for gene transfer uses an electrical current to make cells or tissues susceptible to electroporation-mediated mediated gene transfer. A brief electric impulse with a given field strength is used to increase the permeability of a membrane in such a way that DNA molecules can penetrate into the cells. This technique can be used in in vitro systems, or with ex vivo or in vivo techniques to introduce DNA into cells, tissues or organs.
Carrier mediated gene transfer in vivo can be used to transfect foreign DNA into cells. The carrier-DNA complex can be conveniently introduced into body fluids or the bloodstream and then site-specifically directed to the target organ or tissue in the body. Both liposomes and polycations, such as polylysine, lipofectins or cytofectins, can be used. Liposomes can be developed which are cell-specific or organ-specific and thus the foreign DNA carried by the liposome will be taken up by target cells. Injection of immunoliposomes that are targeted to a specific receptor on certain cells can be used as a convenient method of inserting the DNA into the cells bearing the receptor. Another carrier system that has been used is the asialoglycoportein/polylysine conjugate system for carrying DNA to hepatocytes for in vivo gene transfer.
The transfected DNA can also be complexed with other kinds of carriers so that the DNA is carried to the recipient cell and then resides in the cytoplasm or in the nucleoplasm. DNA can be coupled to carrier nuclear proteins in specifically engineered vesicle complexes and carried directly into the nucleus.
Chimeric molecules or agents of the invention can optionally be targeted to certain cells within an organism, for example and without restriction by using a liposome vector, viral vector, or other delivery vector that targets a ligand specifically expressed on said cells, or by using a cell-type-specific promoter operatively linked to a polynucleotide sequence encoding a chimeric molecule or agent of the invention, as will be readily appreciated by one of skill in the art.
The concentration, dose, and duration of treatment with chimeric molecules or agents of the invention can be controlled to maximize the therapeutic benefit while minimizing toxicity or undesirable side-effects. Methods of achieving such control will be readily appreciated by one of skill in the art and include, without restriction, the administered dose of chimeric molecules or agents of the invention, frequency of administration, number of adminstrations, inducible promoters, molecular structures to control rates of metabolism by the liver and excretion by the kidneys, mRNA stability signals, ubiquitination signals or other protein stability signals, and delivery vector.
Suitable recipients of the agents described herein include animals, specifically mammals, such as humans, non-human primates, rodents, cattle, and the like. Also included are avian species, fish, plants, insects and prokaryotes, as will be readily appreciated by one of skill in the art.
Furthermore, it is preferred that these chimeric molecules and agents have minimum toxic side-effects. Even more preferred, the chimeric molecules and agents of the invention have no toxic side-effects. Minimum toxic side-effects can be assessed by those of skill in art. Tolerable toxic side-effects allow the recipient to receive treatment that is effective in preventing or treating a pathogen infection, but which does not cause irreparable or intolerable injury to the recipient. Preferably, the recipient cell or organism exhibits or suffers no deleterious toxic side-effects from administration of the treatment, while sufficiently treating or preventing a pathogen infection.
Optionally, chimeric molecules or agents of the invention can be administered together with stimuli that induce latent viruses to upregulate viral gene expression, thereby enhancing the effect of the chimeric molecules or agents on infected cells, as will be readily appreciated by one of skill in the art.
It is also considered that some of the chimeric molecules and agents described herein can treat illnesses other than pathogen infections and that similar therapeutic agents can be designed that will treat additional illnesses other than pathogen infections. Illnesses that can be treated by chimeric molecules or agents described herein, or by similar therapeutic agents, include, for example and without restriction, the following: cancer, such as lymphomas, carcinomas and sarcomas; autoimmune diseases, such as rheumatoid arthritis, lupus, transplant rejection, and multiple sclerosis; inflammatory disorders such as those associated with hypersensitivity or Crohn's disease (N. Inohara et al. (2003) Journal of Biological Chemistry, PMID: 12514169); primary immunodeficiency diseases; neural disorders such as ischemic neuron injury (W. Paschen and J. Doutheil (1999) J. Cereb. Blood Flow Metab. 19, 1-18), Alzheimer's disease (K. Imaizumi et al. (2001) Biochimica et Biophysica Acta 1536, 85-96; T. Kudo et al. (2002) Ann. N.Y. Acad. Sci. 977, 349-355), Huntington's disease, and Parkinson's disease; diabetes (S. Oyadomari et al. (2002) Apoptosis 7, 335-345); cystic fibrosis (M. H. Glickman and A. Ciechanover (2002) Physiol. Rev. 82, 373-428; K. M. Sakamoto (2002) Molecular Genetics and Metabolism 77, 44-56); atherosclerosis (C. Patterson and D. Cyr (2002) Circulation 106, 2741-2746); and the like. For example, detection domains of chimeric molecules or agents can detect apoptosis signals, endoplasmic reticulum stress signals, inflammatory response signals, protein aggregation, cell-cycle-control signals, specific illness-associated molecular epitopes, or other signals associated with illnesses such as those listed supra. Effector domains of said chimeric molecules or agents can be stimulated or induced by said detection domains to affect apoptosis pathways, inflammatory-response pathways, unfolded-protein response-pathways, endoplasmic-reticulum-associated-protein degradation-response pathways, ubiquitin-proteasome pathways, stress-response pathways, or other pathways such that the illness is slowed, alleviated, cured, or prevented.
Chimeric molecules or agents of the invention can be used to detect pathogens, pathogen components, pathogen products, or other molecules. For example and without restriction, chimeric molecules having a caspase effector domain and a detector domain that recognizes a polyvalent pathogen, pathogen component, pathogen product, cancer antigen, other antigen, or other molecule can be used to detect said pathogen, pathogen component, pathogen product, cancer antigen, other antigen, or molecule in a sample. Colorimetric, fluorometric, and other assays for caspase activity (for example, those from R&D Systems) are well known to those of skill in the art. An increase in caspase activity of the chimeric molecules or agents indicates that said pathogen, pathogen component, pathogen product, cancer antigen, other antigen, or molecule is present in a sample and can optionally be used to determine the concentration of said pathogen, pathogen component, pathogen product, cancer antigen, other antigen, or molecule in said sample, as will be readily appreciated by one of skill in the art. Optionally, another effector domain such as a kinase that activates upon crosslinking can be used with a suitable assay, as will be readily appreciated by one of skill in the art.
The present invention is further illustrated by the following examples, which more specifically illustrate the invention.
Materials: dsRNA-Activated Caspases
Plasmids encoding human procaspase 3 (NCBI Accession #U26943) and amino acids 1-125 of human FADD (#U24231) were provided by D. M. Spencer, Baylor College of Medicine. A plasmid encoding human protein kinase R (#U50648) was provided by E. F. Meurs, Institut Pasteur. The mammalian expression vector pTRE2hyg, HeLa Tet-On™ human cell line, doxycycline, and tetracycline-free fetal bovine serum were obtained from Clontech. The pCR®2.1-TOPO vector was supplied by Invitrogen. PCR primers, LIPOFECTIN® reagent, and PLUS reagent were obtained from Gibco BRL/Life Technologies/Invitrogen. Polyclonal goat IgG antibodies specific for human caspase 3 were from R&D Systems, and HRP-conjugated rabbit antibodies specific for goat IgG (H+L) were from Zymed. Polyclonal rabbit IgG antibodies specific for human FADD were from Upstate Biotechnology, and HRP-conjugated goat antibodies specific for rabbit IgG were from Santa Cruz Biotechnology. CellTiter 96® AQueous One Solution was obtained from Promega. Poly(I)•poly(C) double-stranded RNA was from Amersham Pharmacia.
Synthesis of dsRNA-Activated Caspases: PCR Product 7
Synthesis of dsRNA-Activated Caspases: PCR Product 8
Synthesis of dsRNA-Activated Caspase Activators: PCR Product 9
Synthesis of dsRNA-Activated Caspase Activators: PCR Product 10
Cloning of PCR Products 7 through 10
PCR products 7, 8, 9, and 10 were gel purified and inserted into the Invitrogen pCR®2.1-TOPO vector following the manufacturer's protocol. The inserts are sequenced on both strands by the Nucleic Acid/Protein Research Core Facility at the Children's Hospital of Philadelphia. The pCR®2.1-TOPO vectors containing PCR products 7 through 10 were digested by BamH I and Mlu I restriction enzymes, and the fragments corresponding to PCR products 7 through 10 were gel purified. The pTRE2hyg vector, shown schematically in
Cell Transfections with dsRNA-Activated Caspases and dsRNA-Activated Caspases Acitvators
The Clontech Tet-On HeLa human cell line contains the rtTA regulatory protein necessary for the proper functioning of the tetracycline or doxycycline-inducible promoters. Cells were maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% tetracycline-free fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250 ng/ml amphotericin B, and 100 μg/ml G418.
As shown in
The pools of hygromycin-resistant cells that resulted from each transfection are presumably genetically heterogeneous, with different cells having different copy numbers of the inserted vector or having the vector inserted into different regions of the cellular genome. Therefore, genetically homogeneous clonal cell populations were isolated. Limiting dilutions of the pools of transfected cells are used to deposit approximately 1 cell per well into 96-well plates, and the cells are allowed to multiply. Wells that appear to have received more than one initial cell were disregarded. The resulting clonal cell populations were designated HeLa 7-x, 8-x, 9Ax, or 10-x; the first number indicates which PCR product from
Protein Expression in Transfected Cells
Western blots were used to analyze the cell clones. PKR-Caspase-3 fusion proteins (deriving from PCR 7 and 8) were detected using caspase-3-specific polyclonal goat IgG antibodies from R&D Systems, and PKR-FADD fusion proteins (deriving from PCR 9 and 10) were detected using FADD-specific polyclonal rabbit IgG antibodies from Upstate Biotechnology. Cells were cultured for two days either with or without doxycyline, and the proteins extracted from the cells and analyzed by Western blot following the manufacturers' protocol.
The Western blot in
The Western blot in
The Western blot in
The Western blot in
Doxycycline Concentration Dependent Expression in Transfected Cells
The Western blot in
Toxicity Assays
The toxicity of the transfected genes was assayed as follows. Cells were added to 96-well plates at an initial density of 5×104 cells/ml and with 100 μl of medium per well. Different expression levels of the transfected genes were induced by adding 0, 0.01, 0.1, 1, or 10 μg/ml doxycycline. The cell numbers were estimated after three days using Promega CellTiter 96® AQueous One Solution, which is bioreduced by live cells into a colored formazan product. The manufacturer's recommended protocol was followed. After subtracting the background absorbance found in wells with medium but no cells, the absorbance at 492 nm is approximately linear with the number of live cells. All assays were performed in quadruplicate to reduce statistical variations.
dsRNA-dependent Apoptosis
Cells were tested with poly(I)•poly(C) dsRNA to determine if apoptosis was induced as expected. Cells were cultured either with or without 10 μg/ml doxycycline for two days. Then the dsRNA was transfected into the cells at a concentration of approximately 7.5 μg/ml using the LIPOFECTIN® and PLUS reagents from Invitrogen and following Invitrogen's recommended protocol for transfecting HeLa cells. Control cells were transfected using the same protocol but without any dsRNA. Cells that had previously been cultured with doxycycline remained in doxycycline, and cells that had not previously been cultured in doxycycline were not treated with doxycycline. Approximately 20 hours after the dsRNA transfections, the cells were photographed using a CCD camera attached to a 400× inverted phase-contrast microscope. Healthy cells tend to spread out, whereas apoptotic cells round up and appear to have bright granulated interiors.
The photographs in
The photographs in
The photographs in
Materials: Interferon-Inducible Defense Genes
Plasmids encoding human Hdj-1 (NCBI Accession #X62421) and human Hsp70 (#M11717 M15432) were provided by R. I. Morimoto, Northwestern University. A plasmid encoding human Hsp90 (#M16660) was provided by R. D. Mosser, Biotechnology Research Institute, National Research Council of Canada. The vector pISRE-Luc was obtained from Stratagene. The mammalian expression vector pCMV/Bsd and cloning vector pCR®2.1-TOPO were obtained from Invitrogen. PCR primers, LIPOFECTIN® reagent, and PLUS reagent were obtained from Gibco BRL/Life Technologies/Invitrogen. The H1-HeLa human cell line (CRL-1958) was obtained from ATCC. Human interferon-alpha is from Sigma.
Synthesis of Interferon-Inducible Defense Genes
Using the strategy shown in
Using the strategy shown in
Synthesis of Interferon-Inducible Defense Genes: Hdj-1
Using the strategy shown in
Synthesis of Interferon-Inducible Defense Gene: Hsp70
Using the strategy shown in
Synthesis of Interferon-Inducible Defense Gene: Hsp90
Using the strategy shown in
Synthesis of Interferon-Inducible Defense Gene: Control Gene
Using the strategy shown in
DNA Gel Electrophoresis Analyses of Interferon-Inducible Defense Genes
The DNA electrophoresis gel photographs in
The DNA electrophoresis gel photograph in
Cell Transfections with Interferon-Inducible Defense Genes
H1-HeLa cells are maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, and 250 ng/ml amphotericin B.
The interferon-inducible expression vectors for Hdj-1, Hsp70, Hsp90, and luciferase are linearized and transfected into the H1-HeLa cells. The transfections use LIPOFECTIN® and PLUS reagents from Invitrogen and follow Invitrogen's recommended protocol for HeLa cells. One day after the transfection, blasticidin is added to the cell culture medium to kill any cells that have not been stably transfected with the vectors, and the cells are permanently kept in blasticidin as a precaution against the possibility that the cells might lose the transfected genes.
The pools of blasticidin-resistant cells that result from each transfection are presumably genetically heterogeneous, with different cells having different copy numbers of the inserted vector or having the vector inserted into different regions of the cellular genome. Therefore, genetically homogeneous clonal cell populations are isolated. Limiting dilutions of the pools of transfected cells are used to deposit approximately 1 cell per well into 96-well plates, and the cells are allowed to multiply. Wells that appear to have received more than one initial cell are disregarded.
Protein Expression of Interferon-Inducible Defense Genes in Transfected Cells
Western blots are used to analyze the cell clones. Cells are cultured for one day either with or without human interferon-alpha, and then proteins are extracted from the cells and analyzed by Western blot with antibodies specific for human Hdj-1, Hsp70, or Hsp90. Cells induced with interferon express more of the heat shock protein with which they were transfected than cells that have not been induced or control untransfected H1-HeLa cells.
dsRNA-activated Caspase Protects H1-HeLa Cells from Rhinovirus
Materials and Methods
H1-HeLa cells (ATCC CRL-1958) were chosen because of their particular susceptibility to rhinovirus. Cells were maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% tetracycline-free fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, and 250 ng/ml amphotericin B. The vector pTetOn encodes the rtTA regulatory protein necessary for the proper functioning of tetracycline or doxycycline-inducible promoters; it was obtained from BD Bioscences Clontech and prepared and linearized following the manufacturer's directions.
H1-HeLa cells were co-transfected with 5 μg each of linearized pTetOn and the linearized pTRE2hyg-derived vector that contained PCR 8. The transfections used LIPOFECTIN® and PLUS reagents from Invitrogen and follow Invitrogen's recommended protocol for HeLa cells. One day after the transfection, 600 μg/ml G418 and 400 μg/ml hygromycin were added to the cell culture medium to kill any cells that had not been stably transfected with the vectors, and the cells were subsequently kept in 800 μg/ml G418 and 400 μg/ml hygromycin as a precaution against the possibility that the cells might lose the transfected genes. The resulting transfected cells were designated 8S or 8 simultaneous.
Results and Discussion
The Western blot in
To demonstrate the effectiveness of the dsRNA-activated caspase against virus, cells were infected with human rhinovirus 14 (ATCC VR-284), as shown in
dsRNA-activated Caspases in Human Embyonic Kidney 293 Cells
Materials and Methods
The 293 TetOn™ cell line (BD Biosciences Clontech) contained the rtTA regulatory protein necessary for the proper functioning of the tetracycline or doxycycline-inducible promoters. Cells were maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% tetracycline-free fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250 ng/ml amphotericin B, and 100 μg/ml G418.
The linearized pTRE2hyg-derived vectors with inserted PCR 7, 8, 9, or 10 were transfected into the 293 Tet-On™ cells. The transfections used LIPOFECTIN® and PLUS reagents from Invitrogen and followed Invitrogen's recommended protocol for HeLa cells. One day after the transfection, 100 μg/ml hygromycin was added to the cell culture medium to kill any cells that had not been stably transfected with the vectors, and the cells were subsequently kept in 100 μg/ml G418 and 200 μg/ml hygromycin as a precaution against the possibility that the cells might lose the transfected genes.
The pools of hygromycin-resistant cells that result from each transfection were presumably genetically heterogeneous, with different cells having different copy numbers of the inserted vector or having the vector inserted into different regions of the cellular genome. Therefore, genetically homogeneous clonal cell populations were isolated. Limiting dilutions of the pools of transfected cells were used to deposit approximately 1 cell per well into 96-well plates, and the cells were allowed to multiply. Wells that appeared to have received more than one initial cell were disregarded. The resulting clonal cell populations were designated 293 7-x, 8-x, 9-x, or 10-x; the first number after the cell line name indicates which PCR product was transfected into the cells, and the x is replaced with the cell clone number. For example, cell line 293 7-3 indicates PCR product 7, cell clone 3.
Western blots were used to analyze the cell clones. PKR-caspase 3 fusion proteins (deriving from PCR 7 and 8) were detected using caspase-3-specific polyclonal goat IgG antibodies from R&D Systems, and PKR-FADD fusion proteins (deriving from PCR 9 and 10) were detected using FADD-specific polyclonal rabbit IgG antibodies from Upstate Biotechnology. Cells were cultured for two days either with or without doxycycline, and then proteins were extracted from the cells and analyzed by Western blot following the manufacturers' protocols.
Results and Discussion
The Western blot in
The Western blot in
The Western blot in
This demonstrates that 293 cells can be induced to express PCR 7, 8, 9, or 10 for two days and illustrates that the corresponding proteins have limited or no toxicity to uninfected cells.
Other Pathogen-activated Apoptosis Treatments
Materials and Methods
A plasmid encoding human procaspase 3 (NCBI Accession #U26943) was provided by D. M. Spencer, Baylor College of Medicine. A plasmid encoding human protein kinase R (#U50648) was from E. F. Meurs, Institut Pasteur. A plasmid encoding human RNase L (#CAA52920) was provided by R. Silverman, Cleveland Clinic Foundation. A plasmid encoding human Apaf-1 (#NM—013229, NM—001160) was donated by Y. Shi, Princeton University. A plasmid encoding human BPI (#NM—001725) was provided by L. J. Beamer, University of Missouri-Columbia. The mammalian expression vector pTRE2hyg, 293 Tet-On™ human cell line, doxycycline, and tetracycline-free fetal bovine serum were obtained from BD Biosciences Clontech. The pCR®2.1-TOPO vector was supplied by Invitrogen. PCR primers, Lipofectamine™ 2000 reagent, LIPOFECTIN® reagent, and PLUS reagent were obtained from Gibco BRL/Life Technologies/Invitrogen. Polyclonal goat IgG antibodies specific for human caspase 3 come from R&D Systems. Polyclonal rabbit antibodies specific for human BPI were from Cell Sciences, Inc. Antibodies specific for human Apaf-1 were from Exalpha Biologicals (polyclonal rabbit IgG) and Santa Cruz Biotechnology (polyclonal goat IgG). Secondary anti-goat and anti-rabbit antibodies were from Santa Cruz Biotechnology and Zymed.
Results and Discussion
PCR products 25, 26, 27, 28, and 29 were gel purified and inserted into the Invitrogen pCR®2.1-TOPO vector following the manufacturer's protocol. The inserts were sequenced on both strands by the Nucleic Acid/Protein Research Core Facility at the Children's Hospital of Philadelphia. The pCR®2.1-TOPO vectors containing PCR products 25 through 29 were digested by BamH I and Mlu I restriction enzymes, and the fragments corresponding to PCR products 25 through 29 were gel purified. The pTRE2hyg vector, shown schematically in
The 293 Tet-On™ human cell line contains the rtTA regulatory protein necessary for the proper functioning of the tetracycline or doxycycline-inducible promoters. Cells were maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% tetracycline-free fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250 ng/ml amphotericin B, and 100 μg/ml G418.
The linearized pTRE2hyg-derived vectors with inserted PCR 25, 26, 27, 28, or 29 were transfected into the 293 Tet-On™ cells. The transfections use Lipofectamine™ 2000 reagent from Invitrogen and follow Invitrogen's recommended protocol for 293 cells. One day after the transfection, 200 μg/ml hygromycin was added to the cell culture medium to kill any cells that had not been stably transfected with the vectors, and the cells were permanently kept in this concentration of hygromycin as a precaution against the possibility that the cells might lose the transfected genes.
The pools of hygromycin-resistant cells that result from each transfection were presumably genetically heterogeneous, with different cells having different copy numbers of the inserted vector or having the vector inserted into different regions of the cellular genome. Therefore, genetically homogeneous clonal cell populations were isolated. Limiting dilutions of the pools of transfected cells were used to deposit approximately 1 cell per well into 96-well plates, and the cells were allowed to multiply. Wells that appeared to have received more than one initial cell were disregarded. The resulting clonal cell populations were designated 293 25-x, 26-x, 27-x, 28-x, or 29-x; the first number after the cell line name indicates which PCR product from
Western blots were used to analyze the cell clones. Antibodies listed above in the Materials and Methods section were used to detect fusion proteins containing regions of caspase 3, Apaf-1, and/or BPI. Cells were cultured for two days either with or without doxycycline, and then proteins were extracted from the cells and analyzed by Western blot following the manufacturers' protocols.
Anti-pathogen Treatments that Involve Heat Shock Proteins, Import Inhibitors, or dsRNase
Plasmids encoding human importin α1 (NCBI Accession #NM—002266), importin α4 (#NM—002267), and importin α6 (#NM—002269) were provided by B. R. Cullen, Duke University. A plasmid encoding Escherichia coli (E. coli) RNase III (#NP—417062, NC—000913) was from A. W. Nicholson, Wayne State University. A plasmid encoding the human papillomavirus 16 (HPV-16) E5 protein (#W5WLHS) was provided by D. J. McCance, University of Rochester. A plasmid encoding the Salmonella enterica SpiC protein (#U51927) was donated by E. A. Groisman, Washington University in St. Louis. Rat IgG1 monoclonal antibodies specific for the hemagglutinin (HA) epitope were provided by Roche. Monoclonal mouse antibodies specific for human Hdj-1 (also known as Hsp40) and human Hsp70 were from Stressgen. Rat antibodies specific for human Hsp90 were provided by Calbiochem. Secondary anti-mouse and anti-rat antibodies were from Santa Cruz Biotechnology and Zymed.
PCR products 30, 31, 32, 33, 34, 35, 36, 37, and 38 were gel purified and inserted into the Invitrogen pCR®2.1-TOPO vector following the manufacturer's protocol. The inserts were sequenced on both strands by the Nucleic Acid/Protein Research Core Facility at the Children's Hospital of Philadelphia.
The pCR®2.1-TOPO vectors containing PCR products 30, 32, 33, 34, 35, 36, and 37 were digested by BamH I and Mlu I restriction enzymes, and the fragments corresponding to the PCR products were gel purified. The pTRE2hyg vector was also digested by BamH I and Mlu I, and the larger resulting fragment was gel purified. Then the digested PCR products were ligated into the digested vector to create expression vectors for PCR 30, 32, 33, 34, 35, 36, and 37.
The pCR®2.1-TOPO vectors containing PCR products 31 and 38 were digested by Mlu I and Not I restriction enzymes, and the fragments corresponding to the PCR products were gel purified. The pTRE2hyg vector was also digested by Mlu I and Not I, and the larger resulting fragment was gel purified. Then the digested PCR products were ligated into the digested vector to create expression vectors for PCR 31 and 38.
The expression vectors include a doxycycline or tetracycline-inducible promoter for the inserted gene, as well as a hygromycin resistance gene for selection of transfected cells. The inserted region of the new vectors was sequenced on both strands by the Nucleic Acid/Protein Research Core Facility at the Children's Hospital of Philadelphia. All of the vectors with the inserted genes were linearized for transfection using the Fsp I restriction enzyme (except the vector with PCR 37, which was linearized with Apa I) and purified with the Zymo Research DNA Clean & Concentrator kit. The prepared vectors are shown in the DNA gel electrophoresis photo in
The 293 Tet-On™ human cell line contains the rtTA regulatory protein necessary for the proper functioning of the tetracycline or doxycycline-inducible promoters. Cells were maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% tetracycline-free fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, 250 ng/ml amphotericin B, and 100 μg/ml G418.
The linearized pTRE2hyg-derived vectors with inserted PCR 30, 31, 32, 33, 34, 35, 36, 37, or 38 were transfected into the 293 Tet-On™ cells. The transfections use Lipofectamine™ 2000 reagent from Invitrogen and follow Invitrogen's recommended protocol for 293 cells. One day after the transfection, 200 μg/ml hygromycin was added to the cell culture medium to kill any cells that have not been stably transfected with the vectors, and the cells were permanently kept in this concentration of hygromycin as a precaution against the possibility that the cells might lose the transfected genes.
The pools of hygromycin-resistant cells that result from each of these transfections were presumably genetically heterogeneous, with different cells having different copy numbers of the inserted vector or having the vector inserted into different regions of the cellular genome. Therefore, genetically homogeneous clonal cell populations were isolated. Limiting dilutions of the pools of transfected cells were used to deposit approximately 1 cell per well into 96-well plates, and the cells were allowed to multiply. Wells that appear to have received more than one initial cell were disregarded. The resulting clonal cell populations were designated 293 30-x, 31-x, 32-x, 33-x, 34-x, 35-x, 36-x, 37-x, or 38-x; the first number indicates which PCR product was transfected into the cells, and the x is replaced with the cell clone number. For example, cell line 293 30-3 indicates PCR product 30, cell clone 3.
H1-HeLa cells were maintained using standard tissue culture practices, humidified incubators at 37° C. and 5% CO2, and DMEM culture medium containing 10% fetal bovine serum, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 4 mM L-glutamine, 100 units/ml penicillin G, 100 μg/ml streptomycin, and 250 ng/ml amphotericin B.
The new expression vectors derived from pCMV/Bsd/ISRE were linearized with the Apa I restriction enzyme, purified with the Zymo Research DNA Clean & Concentrator kit, and transfected into the H1-HeLa cells. The transfections use LIPOFECTIN® and PLUS reagents from Invitrogen and follow Invitrogen's recommended protocol for HeLa cells. One day after the transfection, 4 μg/ml blasticidin was added to the cell culture medium to kill any cells that have not been stably transfected with the vectors, and the cells were permanently kept in blasticidin as a precaution against the possibility that the cells might lose the transfected genes.
The pools of blasticidin-resistant cells that result from each of these transfections were presumably genetically heterogeneous, with different cells having different copy numbers of the inserted vector or having the vector inserted into different regions of the cellular genome. Therefore, genetically homogeneous clonal cell populations were isolated. Limiting dilutions of the pools of transfected cells were used to deposit approximately 1 cell per well into 96-well plates, and the cells were allowed to multiply. Wells that appear to have received more than one initial cell were disregarded.
Production and Testing of Anti-pathogen Proteins that can be Transduced into Cells in vitro or in vivo
Materials
The vector pET100/D-TOPO®, E. coli strain BL21(DE)pLysS, Ni-NTA purification kit with anti-Xpress™ antibodies, EKMax™ enterokinase, and EK-Away™ resin are obtained from Invitrogen. The vector pCMV.IRES.AEQ was provided by D. Button, Stanford University, and the vector pEGFP-IRES-puro is from Clontech.
Methods
The expression vector is transformed into a suitable expression system, as will be understood by one of skill in the art, which in the illustrated example is the E. coli strain BL21(DE)pLysS. After approximately 6-24 hours, the tagged expressed protein is harvested from the expression system using the Invitrogen Ni-NTA purification kit and following either the manufacturer's directions or the protocol in M. Becker-Hapak, S. S. McAllister, and S. F. Dowdy (2001) Methods 24, 247-256. Protocols for either denatured protein or soluble protein product can be followed. If desired, Invitrogen EKMax™ enterokinase and EK-Away™ resin are used as per the manufacturer's directions to remove the six-histidine and Xpress™ tags and re-purify the protein.
The relevant teachings of all the references, patents and patent applications cited herein are incorporated herein by reference in their entirety.
While this invention has been particularly described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.
This application is a Divisional of U.S. application Ser. No. 10/361,208, filed on Feb. 7, 2003, now U.S. Pat. No. 7,125,839, issued Oct. 24, 2006, which claims the benefit of U.S. Provisional Application No. 60/355,359, filed Feb. 7, 2002, U.S. Provisional Application No. 60/355,022, filed Feb. 7, 2002, and U.S. Provisional Application No. 60/432,386, filed Dec. 10, 2002. The entire teachings of the above applications are incorporated herein by reference.
The invention was supported, in whole or in part, by contract number F19628-00-C-0002 from the United States Air Force. The Government has certain rights in the invention.
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| Number | Date | Country | |
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| Parent | 10361208 | Feb 2003 | US |
| Child | 11503416 | US |
