Patent Application
20130202598
The present invention relates to activatable toxin complexes which include a cleavable inhibitory peptide, and use thereof for treating infections and malignant diseases.
Engineered proteins combining several functional protein domains have been proposed as therapeutic agents to address major medical challenges, in particular, for selective killing of diseased cells, such as cancer cells and cells infected by bacteria or viruses, and for generation of protective immune responses. One such type of multi-domain protein, referred as a “sitoxin” (for “signal-regulated cleavage-mediated toxin”), comprises a toxin effector domain, a domain including an intracellular signaling moiety, and an intervening domain positioned between the aforementioned domains, which includes a cleavage site for a predetermined protease expressed within a target cell (Varshaysky, 1995).
A diphtheria toxin-based sitoxin containing a signal for N-end-rule-mediated degradation upstream of a cleavage site for the HIV type 1 protease has been disclosed, and reportedly exhibited a substantial increase in toxicity via inhibition of cellular protein synthesis following in vitro cleavage by the viral protease, although such toxins were unable to selectively eradicate HIV-1-infected cells (Falnes et al., 1999).
The term “zymogenization” has been used to describe modification of an enzyme so as to convert a constitutively active enzyme to a protease-activatable form. Modified forms of bovine RNase A have been disclosed, in which the enzyme was modified so as to expose its natively conformed active site only upon proteolytic cleavage mediated by proteases of Plasmodium falciparum, HIV or HCV, which elicited significant enhancement of in vitro RNase activity (Plainkum et al., 2003; Johnson et al., 2006; Turcotte and Raines, 2008).
An engineered form of Vip2, an actin modifying vegetative insecticidal protein produced by the bacterium Bacillus cereus, has been disclosed in which a propeptide was fused to the C-terminus of Vip2, so as to form a Vip2 proenzyme with significantly reduced enzymatic activity, while having the ability to express as a transgene in corn plants. According to the disclosure, the proenzyme was activated extracellularly within the digestive tract of the pest western corn rootworm, and resulted in the killing of rootworm larvae (Jucovic et al., 2008).
Pseudomonas aeruginosa exotoxin A (PE; also referred to as Pseudomonas exotoxin or ETA) is a three-domain bacterial toxin that kills mammalian cells by gaining entry to the cytosol and inactivating protein synthesis. PE is composed of three major domains and one minor domain. Domain 1a (amino acid residues 1-252) is the cell-binding domain; domain 2 (amino acid residues 253-364) is the translocation domain that enables PE to reach the cytosol, and domain 3 (amino acid residues 395-613) has ADP-ribosyl transferase activity that inactivates translation elongation factor 2 and thus causes cell death. The pathway of toxin entry to mammalian cells includes the steps: 1) binding to a surface receptor, mediated by the binding of PE domain 1 to the alpha 2-macroglobulin receptor/low density lipoprotein receptor-related protein (LRP) which is ubiquitously expressed in most tissues and cell types (Gu et al., 1996); 2) internalization via coated pits and endosomes, and 3) proteolytic cleavage between Arg-279 and Gly-280 within domain 2 and reduction of disulfide bonds, which is mediated by the cellular protease furin, and generates the active C-terminal fragment (residues 280-613) (FitzGerald and Pastan, 1991). At the final step 4), the enzymatically active C-terminal fragment is translocated by retrograde transport through the trans-Golgi network, then backward through the Golgi apparatus to the endoplasmic reticulum and from there to the cytosol. Once in the cytosol, this fragment inhibits protein synthesis by ADP ribosylation of elongation factor 2 (Iglewski and Kabat, 1975).
Diphtheria toxin (DT), produced by Corynebacterium diphtheriae, kills mammalian cells via a mechanism similar to that of PE, namely, by gaining entry to the cytosol and inactivating protein synthesis by ADP ribosylating elongation factor 2. X-ray crystallographic analysis demonstrated that DT is composed of three structural domains: the amino terminal catalytic (C) domain (also referred as “DTA”) the translocation domain (T) and the carboxy-terminal receptor binding (R) domain. DT is cleaved at the surface of sensitive eukaryotic cells by the enzyme furin, and following binding to its receptor (the heparin binding epidermal growth factor-like precursor), the di-chain protein that is linked by a single disulfide bond is internalized into clathrin coated pits and reaches the lumen of a developing endosome. Upon acidification, the T domain facilitates the translocation of the catalytic domain directly across the endosomal membrane and into the host cell cytoplasm (Rafts and Murphy, 2004; Deng and Barbieri, 2008).
A large group of toxins naturally found in plants are classified as ribosome-inactivating proteins (RIPs), which are polynucleotide adenosine glycosidases that cleave the glycosidic bond of an adenosine base in an evolutionarily conserved sequence (GAGA) in the alpha-sarcin/ricin loop (SRL) of 28S rRNA of eukaryotic ribosomes. This depurination reaction prevents binding of elongation factor 2 to the eukaryotic ribosome, and results in protein synthesis inhibition. RIPS include ricin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1, and alpha-luffin (for a review see for example, Peumans et al, 2001). RIPs are sub-classified according to their molecular structure as: Type I, consisting of a single polypeptide chain corresponding to an N-glycosidase domain; Type II, consisting of two polypeptide chains in disulphide linkage, corresponding to an N-terminal N-glycosidase domain and a C-terminal lectin domain, which are synthesized from a single precursor that undergoes post-translational processing; or Type III (or alternately termed two-chain Type I), consisting of two polypeptide chains, corresponding to segments of an N-glycosidase domain, held together by non-covalent interactions which are synthesized from a single precursor that undergoes post-translational processing.
Ricin toxin (RT) from Ricinus communis is a type II RIP consisting of the catalytic A chain covalently linked to the lectin domain B chain, the latter of which binds to galactose residues on the surface of eukaryotic cells and stimulates receptor-mediated endocytosis of the toxin molecule (Stirpe and Battelli, 2006). Cell-bound ricin is taken up by endocytosis, following which most of the toxin molecules are recycled back to the cell surface or transported to the lysosomes and degraded. A small fraction is translocated by retrograde transport to the trans-Golgi network, backward through the Golgi apparatus to the endoplasmic reticulum and from there to the cytosol (Olsnes, 2004).
Maize RIP is a Type III RIP produced as an inactive precursor proenzyme (pro-RIP) having a 25-amino acid internal inactivation region on the protein surface. During germination, proteolytic removal of this internal inactivation region generates the active heterodimeric maize RIP (Walsh et al., 1991; Bass et al., 1992). HIV-activated toxins designed on the basis of maize RIP have been disclosed (Law et al., 2010). According to this disclosure, replacement of the first and last 10 residues of the internal inactivation region with two HIV-PR recognition sequences, and fusion of an 11 amino acid transduction peptide derived from the HIV-1 Tat protein to the N-termini of the modified RIPs resulted in the generation of pro-RIPs which were efficiently cleaved in-vitro by recombinant HIV-PR or in-vivo (in HIV infected cells) by virally encoded protease. Upon treatment of infected cells, the N-glycosidase and anti-viral activities of the modified cleavable RIPs were found to be higher than these of an uncleavable-nonactivated pro-RIP and resembled these of an activated mutant in which the inhibitory region was genetically removed.
The mammalian defensins are a family of small cationic peptides characterized by their β-sheet-dominant structure stabilized by two or three intramolecular disulfide bonds (Ganz, (2003) Nat. Rev. Immunol. 3, 710-720). They are further subdivided into three subfamilies: α-defensins; β-defensins; and θ-defensins. Six human α-defensin peptides (each composed of 29-35 amino acid residues) have been identified from five genes, namely HNP (human neutrophil peptide)-1 to -4, HD-5, and HD-6 (Ericksen et al., Antimicrob Agents Chemother. 2005; 49:269-75). HNP-1-4 are expressed primarily by granulocytes and certain lymphocyte populations (Ganz et al., (1985) J. Clin. Invest. 76, 1427-1435; Agerberth et al., (2000) Blood 96, 3086-3093). The amino acid sequences of HNP-1-3 are identical except for the first N-terminal residue. The α-defensins have been identified as natural peptide antibiotics which display microbicidal activity against numerous bacteria, fungi, and viruses (Lehrer et al., (1993) Annu. Rev. Immunol. 11, 105-128).
HNP-1, HNP-2 and HNP-3 have been disclosed to have neutralizing activity against lethal factor (LF), the major toxin of B. anthracis (Kim et al., Proc Natl Acad Sci USA. 2005 Mar. 29; 102(13)). HNP-1, HNP-2 and HNP-3 have further been disclosed to neutralize toxins of the mono-ADP-ribosyltransferase family, particularly diphtheria toxin and Pseudomonas exotoxin A (Kim et al Biochem J (2006) 399, 225-229). HNP-1, HNP-3, and enteric human defensin-5 (HD-5) have been disclosed to inhibit the activity of Clostridium difficile toxin B.
The conserved C-terminus of the ribosome stalk proteins P1 and P2 has been disclosed to interact with both ricin and Shiga-like toxin 1. This interaction is reportedly required for efficient ribosome binding and cytotoxicity. In addition, a synthetic peptide corresponding to the sequence of the conserved C terminus of P1 and P2 was shown to inhibit the ribosome-inactivating function of SLT-1 (Vater et al., 1995; Chiou et al., 2008; McCluskey et al., 2008). The crystal structure of a similar peptide in complex with the type I RTP trichosanthin has been disclosed (Too et al., 2009).
Hepatitis C virus (HCV) is a small, enveloped RNA virus belonging to the Hepacivirus genus of the Flaviviridae family, which is recognized as a major cause of chronic liver disease and affects approximately 200 million people worldwide. Persistent infection is associated with the development of chronic hepatitis, hepatic steatosis, cirrhosis, and hepatocellular carcinoma. A protective vaccine for HCV is not yet available, and the currently favored treatment, which is a combination of pegylated α-interferon and ribavirin, fails to eliminate infection in nearly 50% of infected subjects.
The HCV genome encodes one large open reading frame that is translated as a polyprotein and proteolytically processed to yield the viral structural and non-structural (NS) proteins. The envelope glycoproteins E1 and E2 and the core protein are the structural proteins, which together form the viral particle. The non-structural proteins include the p7 ion channel, the NS2-3 protease, the NS3 serine protease/RNA helicase and its co-factor NS4A, the NS4B and NS5A proteins and the NS5B RNA-dependent RNA polymerase (RdRp) (Moradpour et al., 2007; Suzuki et al., 2007). HCV polyprotein processing involves the NS2-3 autoprotease, which cleaves in cis at the NS2-3 junction, and the NS3-4A serine protease, which cleaves at four downstream NS protein junctions, respectively termed NS3/4A; NS4A/4B; NS/4B/5A, AND NS5A/5B. NS3 has been extensively studied and shown to possess multiple enzymatic activities that are essential for HCV replication. The N-terminus, in complex with its co-factor NS4A, primarily functions as a serine protease, which cleaves the viral polyprotein precursor downstream to NS3. The remaining ⅔ of the protein has helicase and NTPase activities (Bartenschlager, 1999).
WO 2006/109196 discloses a method to identify a compound that inhibits HCV replication comprising: contacting a genetically modified mouse with a compound and analyzing the expression of NS3 protease activity, whereby a compound that inhibits expression of NS3 is indicative that said compound inhibits HCV replication.
WO 2009/022236 discloses compositions that comprise an isolated nucleic acid encoding a chimeric hepatitis C virus NS3/4A polypeptide or a fragment thereof, which comprises a sequence that encodes an antigen, preferably a non-HCV epitope, wherein the nucleic acid encoding the antigen can be inserted within the NS3/4A nucleic acid or attached thereto. Further disclosed is a composition comprising a recombinant peptide immunogen comprising an antigen, such as an antigen comprising an epitope from a plant, virus, bacteria, or a cancer cell; and a heterologous HCV NS3 protease cleavage site. According to the disclosure, NS3/4A is used as a carrier or adjuvant to provide T helper cells access to a fused antigen, thereby enhancing the immune response to the fused antigen, and the antigen may be inter alia a toxin.
WO 2008/052490 discloses a chimeric peptide containing at least one segment which inhibits the activation of the NS3 protease of a Flaviviridae family virus, and a cell penetrating segment which can inhibit or attenuate infection by the virus. Further disclosed are pharmaceutical compounds containing the chimeric peptides and use thereof for prevention and/or treatment of Flaviviridae virus infections.
WO 2004/005473 discloses an immunogenic fusion protein comprising (a) a modified NS3 polypeptide comprising at least one amino acid substitution to the HCV NS3 region, such that protease activity is inhibited, and (b) at least one polypeptide derived from a region of the HCV polyprotein other than the NS3 region. According to the disclosure, compositions of the invention may include a carrier or an adjuvant inter alia a detoxified mutant of a bacterial ADP-ribosylating toxin such as a cholera toxin.
WO 2003/064453 discloses active inhibitors, termed “trojan inhibitors” (TI) and the use thereof in the form of specifically shaped trojan proteasome-inhibitors (TPI) or trojan assembling-inhibitors (TAI), such as proteasome- and assembling-inhibitors which are initially inactive and are only activated in the target cell by means of a specific protease for the target cell. According to the disclosure, said inhibitor can be used in the treatment of viral infections, whereby a virus-specific protease is expressed, particularly in HIV-infections and AIDS-therapy, and in the therapy of tumoral diseases, whereby the tumor cells are characterized by a specific protease.
WO 2002/087500 discloses a synthetic prototoxophore, which is a relatively non-toxic compound that includes a toxin moiety, such as an antimetabolite or a DNA intercalating agent, and a substrate domain for a viral enzyme, which upon binding of a viral enzyme to the substrate domain, the catalytic activity of the viral enzyme converts the prototoxophore to a toxophore, which is toxic to a cell. Further disclosed are methods of using a prototoxophore to reduce or inhibit viral infectivity, and to ameliorate the severity of a viral infection.
WO 2005/090393 discloses a composition comprising a first effector component of a multimeric bacterial protein toxin, the first effector component comprising at least a first monomer and a second monomer, wherein said first and second monomers form a heterooligomer, wherein said first and second monomers are different, and each of said first and second monomers are modified by at least two of the following methods: (a) substitution of a native cell-recognition domain for a non-native cell-recognition domain; (b) substitution of a native proteolytic activation site for a non-native proteolytic activation site; (c) modification of said first monomer to generate a first modified monomer, whereby said first modified monomer can pair only with said second monomer; (d) modification of said first monomer and said second monomer, whereby a second effector component can bind only at a site formed by the interaction of said first monomer and said second monomer molecule; or (e) a combination thereof.
According to the disclosure, the bacterial protein toxin may be inter alia cholera toxin or Shiga toxin; (b) may comprise substitution of a native furin cleavage site by a serine protease cleavage site; and the composition may be used for treating a viral infection inter alia HCV.
WO 2000/062067 discloses a fusion molecule comprising at least one protein transduction domain (PTD) and at least one linked molecule, inter alia an anti-infective drug.
WO 1999/029721 discloses an anti-pathogen system comprising a fusion protein comprising a covalently linked protein transduction domain and a cytotoxic domain (i.e. a caspase), wherein the cytotoxic domain further comprises at least one pathogen-specific protease cleavage site, wherein the pathogen may be inter alia HCV.
U.S. Pat. No. 7,247,715 discloses a purified and isolated nucleic acid sequence having a nucleotide sequence encoding an A chain of a ricin-like toxin, a B chain of a ricin-like toxin and a heterologous linker amino acid sequence linking the A and B chains, the heterologous linker sequence containing a cleavage recognition site for a protease, inter alia a viral protease, wherein the cleavage recognition site is recognized by the viral protease inter alia hepatitis C virus.
There remains an unmet need for therapeutic agents which are effective for the treatment of debilitating diseases, including viral infections such as HCV.
The inventors of the present invention disclose herein a therapeutic approach for eradicating diseased cells, including cells infected by intracellular pathogens such as viruses, as well as cancerous cells. The invention provides multi-segment fusion proteins, which include a highly toxic catalytic domain based on a naturally occurring toxin, such as that of a plant or bacterial species, and a cleavable inhibitory peptide which “disarms” the activity of the catalytic domain until the inhibitory peptide is released, preferably at the infection or disease site. The inhibitory peptide is rendered cleavable due to the presence of a protease cleavage recognition site within the fusion protein, with the cleavage site being the target of a protease specifically expressed in the diseased cells. When the fusion protein comes into contact with the protease, such as a virus-encoded protease, enzymatic release of the inhibitory peptide occurs and “arms” the fusion protein into the active toxic state.
Specifically, the multi-segment fusion protein comprises the following segments from the amino terminus to the carboxy terminus in the following order: a cell binding domain; a cell translocation domain; a toxin catalytic domain; a protease enzyme cleavage recognition site; an inhibitory peptide; and at least one linker, wherein the at least one linker is located between the protease enzyme cleavage recognition site and the inhibitory peptide.
The invention is based, in part, on the finding that hepatitis C virus (HCV) NS3 protease-activated chimeric toxins comprising cell binding and translocation domains from Pseudomonas exotoxin A, and a catalytic toxin domain of either diphtheria toxin or ricin A in fusion with a cleavable inhibitor peptide, exhibit a significant increase in enzymatic activity following NS3-mediated cleavage, and exhibit high levels of cytotoxicity, both in NS3-transfected cells and in HCV-infected cells. The fusion proteins disclosed herein comprise toxin enzymatic domains which have been “zymogenized”, and thus are also referred to herein as “zymogenized toxins” or “zymoxins”.
Without being bound by any theory or mechanism of action, the efficacy of the invention disclosed herein is due to the selective activation of the fusion protein in vivo. Since the inhibitory peptide may only be released within infected cells which express the virally encoded protease, the invention disclosed herein is effective for selective killing of infected cells, and for blocking multiplication and spread of the infectious organism.
The present invention is particularly advantageous for eradicating intracellular viral infections which do not involve display of viral antigens on the outer surface of infected cells, and are thus not amenable to treatment with agents which include targeting and binding moieties, such as antibodies, directed to cell surface-displayed viral antigens. Such infections, including those caused by hepatitis B and hepatitis C viruses, are generally characterized by the arrangement of viral proteins on internal cell membranes and budding of viral particles from cells, in the absence of any trace of viral infection on the outer cell membrane.
However, the invention may also be used to provide agents for treating viral infections which do involve display of viral antigens on the outer surface of infected cells, such as HIV infection.
After 9 hours, cells were treated with 1 μg/ml of tetracycline (+TET) or left untreated (NO TET). After 2 hours, serial dilutions of the toxins “PE-DTA-cleavage site-defensin” or “PE-DTA-mutated cleavage site-defensin” were added to the cells and incubation was continued for an additional 72 hours (presence of tetracycline was kept in the growth media of induced cells). The relative fraction of viable cells was determined using an enzymatic MTT assay. A representative graph of three independent experiments is shown. Each point represents the mean±SD of a set of data determined in triplicate.
The present invention provides toxin fusion proteins and conjugate proteins which are selective and activatable in vivo due to the presence of a cleavable inhibitory peptide which prevents toxic effects until cleaved by a protease. The inhibitory peptide included in the protein is selected and positioned so as to specifically inhibit the activity of the catalytic toxic domain and not the other functional domains. The protein is further engineered so as to contain a protease enzyme cleavage recognition site, which is the substrate of a specific protease expressed in diseased cells, such as the NS3 protease expressed in HCV infected cells. Upon contact with the relevant protease at the disease site, such as within virus-infected cells, the protein is acted upon by the protease so as to release the inhibitory peptide, thus activating the protein into its active toxic state.
In a first aspect, the invention provides a multi-domain toxin protein conjugate, the conjugate comprising: a cell binding domain; a cell translocation domain; a toxin catalytic domain; a protease enzyme cleavage recognition site; an inhibitory peptide (protease inhibitory peptide); and at least one linker, wherein the at least one linker is located between the protease enzyme cleavage recognition site and the inhibitory peptide.
In another aspect, the invention provides a toxin fusion protein, the fusion protein comprising: a first segment comprising a cell binding domain; a second segment comprising a cell translocation domain; a third segment comprising a toxin catalytic domain; a fourth segment comprising a protease enzyme cleavage recognition site; a fifth segment comprising an inhibitory peptide; and at least one linker, wherein the at least one linker is located between the fourth segment comprising the protease enzyme cleavage recognition site and the fifth segment comprising the inhibitory peptide. In a particular embodiment, the protein conjugate comprises a fusion protein. In a particular embodiment, the protein conjugate comprises covalent linkages between the domains.
In a particular embodiment, the protein conjugate comprises non-covalent linkages between the domains. In a particular embodiment, the protein conjugate comprises a combination of covalent and non-covalent linkages between or among the domains.
In a particular embodiment, the cell binding domain comprises at least one of: a cell binding domain of a bacterial, plant or fungal toxin; a cell-penetrating peptide (CPP); an antibody; a cell surface receptor ligand, or a combination thereof. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the cell binding domain comprises a cell binding domain of a bacterial or plant toxin. In a particular embodiment, the toxin is selected from the group consisting of Pseudomonas exotoxin, diphtheria toxin, cholera toxin; tetanus toxin, botulinum toxin, Clostridium difficile toxin, anthrax toxin, verotoxin, pertussis toxin, ricin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1, and alpha-luffin. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the cell binding domain comprises a cell binding domain from a toxin selected from the group consisting of Pseudomonas exotoxin and diphtheria toxin. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the cell binding domain comprises a cell-penetrating peptide. In a particular embodiment, the cell-penetrating peptide is selected from the group consisting of a polyarginine, such as RRRRRRRRR (SEQ ID NO:74); TAT49-57 (RKKRRQRRR; SEQ ID NO:75); TAT (GRKKRRQRRRPPQ; SEQ ID NO:76), Pep-1 (KETWWETWWTEWSQPKKKRKV; SEQ ID NO:77) Antennapedia cell-penetrating peptide (RQIKIWFQNRRMKWKK; SEQ ID NO:78), transportan (GWTLNSAGYLLGKINLKALAALAKKIL; SEQ ID NO:79) and a nuclear localization sequence (NLS), such as VQRKRQKLMP (SEQ ID NO:80), SKKKKIKV (SEQ ID NO:81) or GRKRKKRT (SEQ ID NO:82).
In a particular embodiment, the cell binding domain comprises an antibody specific for an antigen expressed on the surface of a diseased cell. In a particular embodiment, the cell binding domain comprises an antibody specific for an antigen encoded by an intracellular pathogen. In a particular embodiment, the diseased cell is selected from the group consisting of a pathogen-infected cell and a cancerous cell. In a particular embodiment, the pathogen is selected from the group consisting of a virus, a bacteria and a fungus. In a particular embodiment, the diseased cell is selected from the group consisting of a virus-infected cell, a bacteria-infected cell and a fungus-infected cell.
In a particular embodiment, the pathogen is a virus. In a particular embodiment, the virus is selected from the group consisting of a retrovirus, a paramyxovirus, a orthomyxovirus, an arenavirus, a filovirus, a coronavirus and a rhabdovirus. In a particular embodiment, the virus is selected from a human immunodeficiency virus (HIV), such as HIV-1; a hepatitis virus, such as HBV or HCV; a herpes simplex virus, such as HSV-1 or HSV-2; an influenza virus such as influenza A virus, influenza B virus or influenza C virus; cytomegalovirus (CMV); respiratory syncytial virus (RSV); measles virus; polio virus and smallpox virus. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the virus is HCV.
In a particular embodiment, the cell binding domain comprises an antibody such as a monoclonal antibody or an antigen-binding fragment thereof. In a particular embodiment, the fragment is selected from the group consisting of Fab, F(ab)2, scFv, dsFv, sc-dsFv and Fv.
In a particular embodiment, the antigen expressed on the surface of a diseased cell is a viral antigen. In a particular embodiment, the viral antigen is selected from the group consisting of HIV gp120 and HIV gp41.
In a particular embodiment, the antigen encoded by a pathogen is a virus-encoded antigen. In a particular embodiment, the virus-encoded antigen is selected from the group consisting of HCV NS3; HCV NS4B; HCV NS5A; HCV NS5B; HBV core protein (HBcAg); HIV gp120 and HIV gp41. [OK—WE ARE PROVIDING POSSIBILITIES FOR THE CASES OF “antigen expressed on the surface of a diseased cell” AND “antigen encoded by an intracellular pathogen” SPECIFIED ABOVE.
In a particular embodiment, the antigen is a tumor-specific antigen.
In a particular embodiment, the cell binding domain specifically binds the asialoglycoprotein receptor. In a particular embodiment, the cell binding domain comprises carbohydrate residues.
In a particular embodiment, the cell translocation domain comprises a cell translocation domain of a plant, bacterial or fungal toxin. In a particular embodiment, the cell translocation domain comprises a cell translocation domain of a toxin selected from the group consisting of Pseudomonas exotoxin diphtheria toxin, anthrax toxin, botulinum toxin and Clostridium difficile toxin. In a particular embodiment, the cell translocation domain comprises the cell translocation of Pseudomonas exotoxin or diphtheria toxin. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the cell translocation domain comprises a cell-penetrating peptide. In a particular embodiment, the cell-penetrating peptide is selected from the group consisting of a polyarginine, such as RRRRRRRRR (SEQ ID NO:74); TAT49-57 (RKKRRQRRR; SEQ ID NO:75); TAT (GRKKRRQRRRPPQ; SEQ ID NO:76), Pep-1 (KETWWETWWTEWSQPKKKRKV; SEQ ID NO:77) Antennapedia cell-penetrating peptide (RQIKIWFQNRRMKWKK; SEQ ID NO:78), transportan (GWTLNSAGYLLGKINLKALAALAKKIL; SEQ ID NO:79) and a nuclear localization sequence (NLS), such as VQRKRQKLMP (SEQ ID NO:80), SKKKKIKV (SEQ ID NO:81) or GRKRKKRT (SEQ ID NO:82).
In a particular embodiment, the cell translocation domain comprises a transduction domain of a viral protein. In a particular embodiment, the cell translocation domain comprises an HIV TAT protein transduction domain.
In a particular embodiment, the cell binding domain and the cell translocation domain are derived from Pseudomonas exotoxin. In a particular embodiment, the cell binding domain and the cell translocation domain comprise a single domain. In a particular embodiment, the cell binding domain and the cell translocation domain are derived from heterologous toxins. In a particular embodiment, the cell binding domain and the cell translocation domain are derived from a single toxin.
In a particular embodiment, the toxin catalytic domain comprises a catalytic domain from a plant, bacterial or fungal toxin. In a particular embodiment, the toxin catalytic domain is from a toxin selected from the group consisting of Pseudomonas exotoxin, diphtheria toxin, tetanus toxin, botulinum toxin, Clostridium difficile toxin, anthrax toxin, verotoxin, pertussis toxin, ricin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, mosquitocidal toxin from Bacillus sphaericus SSII-1 (MTX); luffaculin 1, and alpha-luffin. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the toxin catalytic domain is derived from a toxin selected from the group consisting of diphtheria toxin, ricin and Pseudomonas exotoxin. Each possibility corresponds to a separate embodiment of the invention. In a particular embodiment, the cell binding domain and the toxin catalytic domain are from heterologous toxins.
In a particular embodiment, the cell binding domain and the cell translocation domain are both derived from Pseudomonas exotoxin, and the toxin catalytic domain is from diphtheria toxin or ricin. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the protease enzyme cleavage recognition site comprises a cleavage recognition site of a protease enzyme specifically expressed in a diseased cell but not in a healthy cell. In a particular embodiment, a diseased cell expressed a protease unique to the disease. In a particular embodiment, proteases within a healthy cell do not cleave the protease enzyme cleavage recognition site. In a particular embodiment, the diseased cell is a pathogen-infected cell or a cancerous cell. In a particular embodiment, the pathogen encodes the protease enzyme. Particular embodiments of the pathogen are as hereinbefore described. In a particular embodiment, the protease enzyme cleavage recognition site is a substrate of a viral protease enzyme. In a particular embodiment, the viral protease enzyme is selected from the group consisting of HCV NS3 protease; HIV protease; CMV protease; and HSV protease. In a particular embodiment, the protease enzyme cleavage recognition site comprises an HCV NS3 target site. In a particular embodiment, the HCV NS3 target site is at an NS protein junction selected from the group consisting of NS3/4A; NS4A/4B; NS4B/5A and NS5A/5B.
In a particular embodiment, the protease enzyme cleavage recognition site comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:1-18. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the protease enzyme cleavage recognition site comprises SEQ ID NO:1.
In a particular embodiment, the protease enzyme cleavage recognition site comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:19-38. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the protease enzyme cleavage recognition site comprises SEQ ID NO:19.
In other embodiments, the protease enzyme cleavage recognition site comprises a CMV protease enzyme cleavage recognition site selected from SEQ ID NO:39 and SEQ ID NO:40. In other embodiments, the protease enzyme cleavage recognition site comprises an HSV-1 protease enzyme cleavage recognition site selected from SEQ ID NO:41 and SEQ ID NO:42.
In other embodiments, the protease enzyme cleavage recognition site comprises an HIV protease enzyme cleavage recognition site selected from SEQ ID NO:43; SEQ ID NO:44; SEQ ID NO:45; SEQ ID NO:46; SEQ ID NO:47; SEQ ID NO:48; SEQ ID NO:49; SEQ ID NO:50; SEQ ID NO:51; SEQ ID NO:52; SEQ ID NO:53; SEQ ID NO:54; SEQ ID NO:55; and SEQ ID NO:56. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the inhibitory peptide specifically inhibits a catalytic domain that has ADP-ribosyl transferase activity. In a particular embodiment, the inhibitory peptide specifically inhibits a catalytic domain that has N-glycosidase activity. In a particular embodiment, the inhibitory peptide comprises an autoinhibiting fragment of a toxin that has ADP-ribosyl transferase activity. In a particular embodiment, the inhibitory peptide comprises an autoinhibiting fragment of a toxin that has N-glycosidase activity.
In a particular embodiment, the inhibitory peptide comprises a defensin peptide or a fragment thereof. In a particular embodiment, the inhibitory peptide comprises a ribosomal protein or a fragment thereof. In a particular embodiment, the inhibitory peptide is a fragment of a human defensin peptide or a fragment of a ribosomal stalk protein. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the human defensin peptide is a human alpha defensin peptide selected from the group consisting of HNP-1; HNP-2; HNP-3; HNP-4; HD-5 and HD-6. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the human defensin peptide is human HNP-1.
In a particular embodiment, the inhibitory peptide is a fragment of a ribosomal stalk protein selected from the group consisting of ribosomal stalk protein P1 and ribosomal stalk protein P2.
In a particular embodiment, the inhibitory peptide comprises an autoinhibiting fragment of a toxin selected from the group consisting mosquitocidal toxin (MTX; SEQ ID NO:119) from Bacillus sphaericus SSII-1 and maize RIP (SEQ ID NO:120). In a particular embodiment, the inhibitory peptide comprises FILDLDYNQDFDMFAPNGEIPN (SEQ ID NO:121).
Bacillus
sphaericus
In a particular embodiment, the inhibitory peptide comprises a peptide selected from the group consisting of SEQ ID NO:57 (ACYCRIPACIAGERRYGTCIYQGRLWAFCC) and EESEESDDDMGFGLFD (SEQ ID NO:58). In a particular embodiment, the inhibitory peptide is selected from the group consisting of SEQ ID NO:57, SEQ ID NO:58 and SEQ ID NO:59 (EESEESDDDMGFGLFDTGGEESEESDDDMGFGLFD).
In a particular embodiment, the inhibitory peptide comprises a human alpha defensin peptide or a fragment thereof, and the catalytic domain comprises a catalytic domain from a toxin that has ADP-ribosyl transferase activity. In a particular embodiment, the inhibitory peptide comprises a human alpha defensin peptide or a fragment thereof; and the catalytic domain has ADP-ribosyl transferase activity. In a particular embodiment, the inhibitory peptide comprises a fragment of a human alpha defensin peptide selected from the group consisting of HNP-1, HNP-2 and HNP-3; and the catalytic domain is from a toxin selected from the group consisting of: Pseudomonas exotoxin, diphtheria toxin, Clostridium difficile toxin and anthrax toxin. Each possibility corresponds to a separate embodiment of the invention.
In a particular embodiment, the inhibitory peptide comprises a ribosomal stalk protein or a fragment thereof and the catalytic domain is from a toxin that has N-glycosidase activity. In a particular embodiment, the inhibitory peptide comprises a ribosomal stalk protein or a fragment thereof; and the catalytic domain has N-glycosidase activity. In a particular embodiment, the inhibitory peptide comprises a fragment of a ribosomal stalk protein selected from the group consisting of ribosomal stalk protein P1 and ribosomal stalk protein P2; and the catalytic domain is from a toxin selected from the group consisting of ricin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1 and alpha-luffin. Each possibility corresponds to a separate embodiment of the invention.
In one embodiment, the at least one linker comprises from about 2 to about 50 amino acid residues. In a particular embodiment, the at least one linker comprises from about 2 to about 20 amino acid residues. In a particular embodiment, the at least one linker comprises a plurality of amino acid residues selected from the group consisting of glycine, serine histidine and a combination thereof. In another embodiment, the linker is a single amino acid.
In a particular embodiment, the linker comprises an amino acid sequence selected from the group consisting of GGGGSGGGSGSGGSG (SEQ ID NO:60); GSGS (SEQ ID NO:61); SSGS (SEQ ID NO:62); and GGGGS (SEQ ID NO:63).
In a particular embodiment, the inhibitory peptide of the protein conjugate is flanked by linkers. In a particular embodiment, the inhibitory peptide flanked by linkers is C-terminal to the protease enzyme cleavage recognition site in the protein conjugate. In a particular embodiment of the protein conjugate, the inhibitory peptide is C-terminal to the catalytic domain. In a particular embodiment of the protein conjugate, the protease enzyme cleavage recognition site and the inhibitory peptide are C-terminal to the catalytic domain.
In a particular embodiment, the inhibitory peptide in the protein conjugate is N-terminal to the catalytic domain. In a particular embodiment, the inhibitory peptide is directly linked or linked via a linker to the N-terminal of the catalytic domain. In a particular embodiment, the protease enzyme cleavage recognition site and the inhibitory peptide in the protein conjugate are N-terminal to the catalytic domain. In a particular embodiment, the protease enzyme cleavage recognition site and the inhibitory peptide are linked to the N-terminal of the catalytic domain.
In a particular embodiment of the fusion protein, the fifth segment comprising the inhibitory peptide is flanked by linkers. In a particular embodiment of the fusion protein, the fifth segment flanked by linkers is C-terminal to the fourth segment comprising the protease enzyme cleavage recognition site.
In a particular embodiment of the fusion protein, the fourth and fifth segments are C-terminal to the third segment. In a particular embodiment of the fusion protein, the fourth and fifth segments are N-terminal to the third segment.
In a particular embodiment of the fusion protein, the first through fifth segments are arranged in the order of N-terminal to C-terminal. In a particular embodiment of the fusion protein, the first through fifth segments are arranged in the order of C-terminal to N-terminal.
In a particular embodiment, the fusion protein comprises an amino acid sequence selected from the group consisting of SEQ ID NO:64; SEQ ID NO:65; SEQ ID NO:66; SEQ ID NO:67; and SEQ ID NO:68.
In a particular embodiment, the fusion protein is encoded by a nucleic acid sequence selected from the group consisting of SEQ ID NO:69; SEQ ID NO:70; SEQ ID NO:71; SEQ ID NO:72; and SEQ ID NO:73 (encoding SEQ ID NOS:64-68, respectively).
In particular embodiments, there is provided a pharmaceutical composition comprising a multi-domain toxin protein conjugate or toxin fusion protein as disclosed herein; and a pharmaceutically acceptable carrier.
In another aspect, the invention provides a method for treating a disease, the method comprising administering to a subject in need thereof a therapeutically effective amount of a multi-domain toxin protein conjugate, or a toxin fusion protein, or a pharmaceutical composition, as disclosed herein.
In another aspect, the invention provides a multi-domain toxin protein conjugate or toxin fusion protein as disclosed herein for treating a disease.
In particular embodiments, the disease is selected from an infectious disease and cancer.
In particular embodiments, the infectious disease is caused by a pathogen selected from the group consisting of a virus, a bacteria and a fungus. In particular embodiments, the pathogen is characterized by having a protease (the nucleic acid encoding the protease and/or the actual protein) that is not expressed endogenically by a healthy cell.
Particular embodiments of the virus are as hereinbefore described.
In a particular embodiment, the virus is HCV.
In particular embodiments, the multi-domain toxin protein conjugate or toxin fusion protein is administered as a single dose or over a period of time in multiple doses.
In particular embodiments, the multi-domain toxin protein conjugate or toxin fusion protein is formulated for administration by a route selected from parenteral (for example for infusion, bolus injection or direct injection to an organ or infection site); and oral.
Other objects, features and advantages of the present invention will become clear from the following description and examples.
The term “protein conjugate” as used herein refers to a polypeptide structure comprising a plurality of segments or domains in association through covalent bonds, non-covalent bonds or a combination thereof. The segments and domains may be from heterologous proteins, or from the same protein.
The term “protein domain” as used herein refers to a polypeptide unit that is a structural and/or functional unit of a larger protein, either as found in nature, such as a multi-domain bacterial or plant toxin, or a recombinantly engineered multi-domain protein. Reference to a protein domain includes both the situation when the protein domain is contained within the larger protein and when it is separate therefrom.
The term “segment” as used herein refers to a peptide or polypeptide fragment of a larger protein, which may or may not be distinguished on the basis of structural and/or functional characteristics. Reference to a segment includes both the situation when the segment is contained within the larger protein and when it is separate therefrom.
The term “fusion protein” as used herein refers to a multi-segment continuous polypeptide, wherein at least some of the segments are derived from heterologous proteins.
The term “heterologous” in reference to portions of a larger protein molecule indicates that the larger polypeptide comprises two or more subsequences that are not found in the same relationship in nature. For example, a fusion protein may comprise the heterologous segments of a cell binding domain from a first bacterial toxin e.g. Pseudomonas exotoxin, and a catalytic domain from a different second bacterial toxin e.g. diphtheria toxin. In general, heterologous protein segments are joined together to form a fusion protein using recombinant engineering techniques, in which nucleic acid molecules encoding the corresponding heterologous protein segments are produced, ligated together into a plasmid with appropriate regulatory elements and expressed in a recombinant organism. Similarly, “heterologous” nucleic acid molecules in reference to portions of a larger nucleic acid molecule means that the larger nucleic acid comprises two or more subsequences that are not found in the same relationship in nature.
The term “linker” as used herein refers to an internal amino acid sequence or a single amino acid which is covalently linked between two distinct segments of a fusion protein or domains of a fusion protein or protein conjugate. In general, a linker has no functional activity of its own and preferably does not interfere with the activity of any of the functional units of the protein, but serves to provide a spatial separation between such segments or domains so as to reduce or avoid steric hindrance between or among them.
The term “inhibitory peptide” as used herein refers to a peptide or protein which reversibly inhibits the activity of a catalytic domain of a catalytic protein, for example, by physically blocking the active site, by physically blocking an allosteric site, by providing a physical barrier which prevents interaction of the catalytic domain with its substrate, or by destabilizing the catalytic domain in any manner.
As used herein, the singular forms “a”, “an” and “the” include plural forms unless the context clearly dictates otherwise.
Protein Conjugates and Fusion Proteins
The protein conjugates and fusion proteins of the invention comprise a plurality of functional domains which respectively confer upon the protein the ability to bind to a cell, translocate across the cell membrane, and exert a toxic effect by catalyzing an enzymatic activity. In addition, the proteins comprise an inhibitory peptide which neutralizes the activity of the toxic domain until and unless cleaved by a specific protease.
The functional domains of the proteins of the invention include domains from plant, bacterial or fungal protein toxins. As used herein, “plant toxins”, “bacterial toxins” and “fungal toxins” respectively refer any toxin produced by a plant, bacteria or fungus. The toxin domains may be wild-type proteins or recombinant proteins. Further, such toxins include those which are variously classified according to their mechanism of action and/or structural organization, for example ADP-ribosylating toxins such as Pseudomonas exotoxin and diphtheria toxin; N-glycosidase containing ribosome inactivating toxins (RIPs) such as ricin, abrin, and Shiga-like toxin 1, including those variously classified as Type I, Type II and Type III RIPs; and binary bacterial toxins to refer to those which comprise separate cell binding and catalytic domains, including for example, anthrax toxin, pertussis toxins, cholera toxin, E. coli heat-labile enterotoxin, Shiga toxin, pertussis toxin, Clostridium perfringens iota toxin, Clostridium spiroforme toxin, Clostridium difficile toxin, Clostridium botulinum C2 toxin, and Bacillus cereus vegetative insecticidal protein.
The proteins of the invention may include domains from different i.e. heterologous toxins which are joined together by chemical conjugation (and/or non-covalent interactions), or often preferably those which are expressed as recombinant fusion proteins. In addition, the cell binding domain of the protein disclosed herein may include a cell binding domain of a toxin, and additionally or alternately comprise a cell targeting antibody of a cell surface receptor ligand. All of these types of moieties may be found together in a single fusion protein or protein conjugate, and may further include various modifications.
As used herein the term “cell binding domain” refers to a protein domain which has affinity for a receptor expressed on a target cell. The cell binding domain of the protein of the invention may be a cell binding domain of a toxin; or may alternately or in addition comprise an antibody or a cell surface receptor ligand.
A cell binding domain of a toxin may be a separate functional domain, as in the case of bacterial binary toxins, or it may be a toxin which comprises as single chain which possesses cell binding and catalytic properties.
Cell binding domains of toxins include for example, domain Ia of Pseudomonas exotoxin; the R domain of diphtheria toxin; the B chain of ricin; anthrax protective antigen; the B chain of cholera toxin; the B chain of tetanus toxin; the heavy chain of botulinum toxin, the B chain of Clostridium difficile toxin; and anthrax protective antigen. Additional possibilities include cell binding domains of verotoxin, pertussis toxin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1, and alpha-luffin.
A “cell translocation domain” refers to a protein domain which causes or facilitates transport of a protein according to the invention across a cell membrane and into the cytosol. The cell translocation domain may be that of a plant, bacterial or fungal toxin, such as a cell translocation domain of Pseudomonas exotoxin diphtheria toxin, anthrax toxin, botulinum toxin or Clostridium difficile toxin; or may be from a viral protein, such as the HIV TAT protein transduction domain.
The cell binding domain and/or the cell translocation domain may comprise a cell-penetrating peptide, which is any short peptide that promotes and facilitates transport of a protein across the plasma membrane and into a cell. Cell-penetrating peptides are reviewed for example in Sawant et al Mol Biosyste., 2010, 6,628-640.
Non limiting examples of cell-penetrating peptides include various polyarginines, such as R8; TAT49-57 (RKKRRQRRR); TAT (GRKKRRQRRRPPQ), Pep-1 (KETWWETWWTEWSQPKKKRKV) Antennapedia cell-penetrating peptide, also referred to as “penetratin” (RQIKIWFQNRRMKWKK), transportan (GWTLNSAGYLLGKINLKALAALAKKIL).
Various nuclear localization sequences (NLS) may also serve as cell-penetrating peptides, such as the sequence PKKKRKV (SEQ ID NO: 124) from the SV40 Large T-antigen (see for example, Kalderon et al., (1984) Cell 39 (3 Pt 2): 499-509); the NLS of nucleoplasmin (KR[PAATKKAGQA]KKKK (SEQ ID NOs: 125-127); see for example, Dingwall et al., (September 1988). J Cell Biol. 107 (3): 841-9); the acidic M9 domain of hnRNP A1; the sequence KIPIK (SEQ ID NO: 128) in yeast transcription repressor Matα2, and the complex signals of U snRNPs.
A “toxin catalytic domain” refers to a protein domain derived from a toxin which exerts a toxic effect on a cell by catalyzing a enzymatic reaction which is detrimental to the cell. Toxin catalytic domains include Pseudomonas exotoxin domain 3; diphtheria toxin domain C; the A chain of tetanus toxin; the A chain of cholera toxin; Clostridium botulinum C2 subunit A; Clostridium difficile toxin subunit A; lethal factor of anthrax toxin; Shiga toxin subunit A; pertussis toxin Sl subunit; the A chain of ricin; and corresponding domains of verotoxin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1, and alpha-luffin
It is to be understood that a toxin catalytic domain may be from a toxin having only a catalytic i.e. A chain, such as for example the plant toxins trichosanthin, MMC and pokeweed antiviral proteins, d wheat germ inhibitor, and the fungal toxins alpha-sarcin, restrictocin, mitogillin, neomycin and phenomycin.
It is to be understood that a toxin domain for use in the invention, such as a cell binding domain or a catalytic domain, may be altered relative to that of the native toxin domain. Such alterations may include for example truncation or chemical modification. For example, a toxin catalytic domain may be truncated to contain only that portion of the native chain which is necessary for exerting its cytotoxic effect. For example, the first 30 amino acids of the ricin A chain may be removed resulting in a truncated A chain which retains toxic activity. A truncated domain may be prepared by expression of a truncated gene or by proteolytic degradation. Similarly, a protein of the invention may contain only a portion of a toxin cell binding domain that is necessary or sufficient for cell binding; and only a portion of a toxin cell translocation domain that is necessary or sufficient for transport into the cell cytoplasm.
In addition, domains may be modified by having a different glycosylation state relative to the native toxin domain. Thus, a domain may be glycosylated or non-glycosylated. Glycosylated proteins may be obtained by expression in the appropriate host cell capable of glycosylation. Non-glycosylated proteins may be obtained by expression in nonglycosylating host cells or by treatment to remove or destroy the all or some of the carbohydrate moieties.
A sequence containing a cleavage recognition site for a viral, fungal, parasitic or cancer associated protease may be selected based on the pathogen-infected or malignant diseased cell which is to be targeted by the protein of the invention. The cleavage recognition site may be selected from sequences known to encode a cleavage recognition site for a viral, bacterial, fungal or cancer associated protease. Sequences encoding cleavage recognition sites may be identified by testing the expression product of the sequence for susceptibility to cleavage by a viral, bacterial, fungal or cancer associated protease. A polypeptide containing the suspected cleavage recognition site may be incubated with a protease and the amount of cleavage product determined (Dilannit, 1990, J. Biol. Chem. 285: 17345-17354 (1990)).
Substrates and cleavage recognition sequence of HCV NS3 are disclosed in WO 2009/022236 and referenced disclosed therein.
Substrates of proteases from human cytomegalovirus, human herpes virus, varicalla zoster virus and infectious laryngotracheitis virus, and enzymatic activity assay methodologies, are disclosed for example in Liu F. & Roizman, B. (J. Virol. 65:5149-5156 (1991)) and Welch, A. R. (Proc. Natl. Acad. Sci. USA 88:10792-10796 (1991)).
Substrates of Epstein-Barr virus protease, and enzymatic activity assay methodology is disclosed for example in Welch, A. R. (Proc. Natl. Acad. Sci. USA 88:10792-10796 (1991)).
Substrates of poliovirus protease, and enzymatic activity assay methodology is disclosed for example in Weidner, J. R. et al. (Arch. Biochem. Biophys. 286:402-408 (1991)).
Substrates of proteases associated with Candida yeasts, and enzymatic activity, including that of aspartic proteinases associated specifically with numerous virulent strains including Candida albicans, Candida tropicalis, and Candida parapsilosis is disclosed for example in Abad-Zapatero, C. et al., Protein Sci. 5:640-652 (1996); Cutfield, S. M. et al., Biochemistry 35:398-410 (1995); Ruchel, R. et al, Zentralbl. Bakteriol. Mikrobiol Hyg. I Abt. Orig. A. 255:537-548 (1983); Remold, H. et al., Biochim. Biophys. Acta 167:399-406 (1968)).
The fusion proteins and complexes of the invention further include an inhibitory peptide which specifically inhibits the catalytic domain. The inhibitory peptide may specifically inhibit a catalytic domain that has ADP-ribosyl transferase activity, for example a catalytic domain of Pseudomonas exotoxin, diphtheria toxin, or Clostridium difficile toxin. Alternately, the inhibitory peptide may specifically inhibit a catalytic domain that has N-glycosidase activity, for example a catalytic domain of RIP toxin such as ricin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1 or alpha-luffin.
In additional embodiment, the inhibitory peptide may correspond to an autoinhibiting fragment of a toxin that has ADP-ribosyl transferase activity, or a toxin that has N-glycosidase activity. Toxins that contain autoinhibitory fragments include for example, mosquitocidal toxin (MTX) from Bacillus sphaericus SSII-1 and maize RIP
A defensin peptide or a fragment thereof may serve as the inhibitory peptide, when the fusion protein or conjugate includes a catalytic domain that has ADP-ribosyl transferase activity. The defensin peptide may be a human alpha defensin peptide, such as HNP-1; HNP-2; HNP-3; HNP-4; HD-5 or HD-6. In a particular embodiment, the human defensin peptide is human HNP-1. Human alpha defensin peptides are disclosed for example, in Ericksen et al., Antimicrob Agents Chemother. 2005; 49:269-75; Ganz et al., J Clin Invest. 1985; 76:1427-35; Valore et al., Blood. 1992; 79:1538-44; and Mallow et al., J Biol Chem. 1996; 271:4038-45.
In a particular embodiment, the inhibitory peptide comprises a fragment of a human alpha defensin peptide selected from HNP-1, HNP-2 and HNP-3; and the catalytic domain is from a toxin selected from Pseudomonas exotoxin, diphtheria toxin, Clostridium difficile toxin and anthrax toxin.
A ribosomal protein or a fragment thereof may serve as the inhibitory peptide when the fusion protein or conjugate includes a catalytic domain that has N-glycosidase activity. For example, the inhibitory peptide may be a fragment of a ribosomal stalk protein selected from ribosomal stalk protein P1 and ribosomal stalk protein P2. The interaction between ribosomal stalk proteins P1 and P2 and ricin toxin is disclosed for example, in Chiou et al., Mol Microbiol 2008, December 70(6), 1441-1452.
In a particular embodiment, the inhibitory peptide comprises a fragment of a ribosomal stalk protein selected ribosomal stalk protein P1 and ribosomal stalk protein P2; and the catalytic domain is from a toxin selected from ricin, abrin, Shiga-like toxin 1 (SLT-1), modecin, volkensin, visumin, trichosanthin, maize RIP, luffaculin 1 and alpha-luffin.
For preparing recombinant proteins, a nucleic acid can be amplified from cDNA or genomic DNA using appropriate oligonucleotide primers and standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. It will be appreciated that cDNA may be prepared from mRNA, by isolating total cellular mRNA by a variety of techniques. cDNA is then synthesized from the mRNA using reverse transcriptase (for example, Moloney MLV reverse transcriptase, or AMV reverse transcriptase. Such methods may be used to obtain the coding sequences of toxins or domains thereof from plants, bacteria or fungi.
Sequences encoding toxin domains may be obtained by selective amplification of a coding region, using sets of degenerative primers or probes for selectively amplifying the coding region in a genomic or cDNA library. Appropriate primers may be selected from the nucleic acid sequence the toxin domains of interest. It is also possible to design synthetic oligonucleotide primers from the nucleotide sequences for use in PCR. Suitable primers may be selected from the sequences encoding regions of toxin proteins which are highly conserved.
The nucleic acid molecule of the invention may also be prepared by site directed mutagenesis. Site directed mutagenesis may be accomplished by DNA amplification of mutagenic primers in combination with flanking primers.
The nucleic acid molecule of the invention may also be prepared by total gene synthesis assembled from synthesized oligonucleotides, as is known in the art.
The nucleic acid molecule of the invention may also encode a fusion protein. A sequence encoding a heterologous linker sequence and encoding a cleavage recognition site for a disease-specific protease may be cloned from a cDNA or genomic library or chemically synthesized based on the known sequence of such cleavage sites. The linker sequence may then be fused in frame with the sequences encoding domains of a toxin for expression as a fusion protein. It will be appreciated that a nucleic acid molecule encoding a fusion protein may contain a sequence encoding different functional domains e.g. cell binding and catalytic, from the same toxin or from different toxins. For example, the cell binding domain may be derived from Pseudomonas exotoxin, and the catalytic domain may be derived from ricin. A protein may also be prepared by chemical conjugation of the various domains or segments and linker sequence using conventional coupling agents for covalent attachment.
A nucleic acid molecule may comprise, as operatively linked elements, a transcriptional promoter; a nucleic acid sequence encoding a secretion signal peptide; a transcriptional termination signal; a selectable marker and a nucleic acid sequence encoding the recombinant toxic protein of the invention. The term “operatively linked” as used herein indicates that the segments are arranged so that they function in their intended purposes, e.g. transcription begins in the promoter, proceeds through the coding regions and halts at the terminator. The nucleic acid molecules may also include sequences such that homologous recombination occurs between the vector and the genomic DNA of the yeast.
Nucleic acid molecules encoding the protein comprising the domains of interest may be incorporated in a known manner into an appropriate expression vector which ensures good expression of the protein. Possible expression vectors include cosmids, plasmids, or modified viruses (e.g. replication defective retroviruses, adenoviruses and adeno-associated viruses), so long as the vector is compatible with the host cell used. The expression vectors are “suitable for transformation of a host cell”, which means that the expression vectors contain a nucleic acid molecule of the invention and regulatory sequences selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid molecule. Operatively linked is intended to mean that the nucleic acid is linked to regulatory sequences in a manner which allows expression of the nucleic acid.
The invention therefore contemplates a recombinant expression vector of the invention containing a nucleic acid molecule of the invention, or a fragment thereof, and the necessary regulatory sequences for the transcription and translation of the inserted protein sequence.
Suitable regulatory sequences may be derived from a variety of sources, including bacterial, fungal, yeast, viral, mammalian, or insect genes (For example, see the regulatory sequences described in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Selection of appropriate regulatory sequences is dependent on the host cell chosen, and may be readily accomplished by one of ordinary skill in the art. Examples of such regulatory sequences include: a transcriptional promoter and enhancer or RNA polymerase binding sequence, a ribosomal binding sequence, including a translation initiation signal. Additionally, depending on the host cell chosen and the vector employed, other sequences, such as an origin of replication, additional DNA restriction sites, enhancers, and sequences conferring inducibility of transcription may be incorporated into the expression vector. It will also be appreciated that the necessary regulatory sequences may be supplied by the native toxins and/or flanking regions.
The recombinant expression vectors of the invention may also contain a selectable marker gene which facilitates the selection of host cells transformed or transfected with a recombinant molecule of the invention. Examples of selectable marker genes are genes encoding a protein such as G418 and hygromycin which confer resistance to certain drugs, beta-galactosidase, chloramphenicol acetyltransferase, firefly luciferase, or an immunoglobulin or portion thereof such as the Fc portion of an immunoglobulin preferably IgG. Other selectable marker genes include the ARG4 (argininosuccinate lyase) genes from P. pastoris and S. cerevisiae, the HIS4 (histidinol dehydrogenase) genes from P. pastoris and S. cerevisiae, the uracil utilization gene (URA), genes providing the capacity for leucine or adenine synthesis, and the like. Transcription of the selectable marker gene is monitored by changes in the concentration of the selectable marker protein such as beta-galactosidase, chloramphenicol acetyltransferase, or firefly luciferase. If the selectable marker gene encodes a protein conferring drug resistance, such as neomycin resistance, then transformant cells can be selected with G418. Cells that have incorporated the selectable marker gene will survive, while the other cells die. This makes it possible to visualize and assay for expression of recombinant expression vectors of the invention and in particular to determine the effect of a mutation on expression and phenotype. It will be appreciated that selectable markers can be introduced on a separate vector from the nucleic acid of interest.
The recombinant expression vectors may also contain genes which encode a fusion moiety which provides increased expression of the recombinant protein; increased solubility of the recombinant protein; and aid in the purification of the target recombinant protein by acting as a ligand in affinity purification. For example, a proteolytic cleavage site may be added to the target recombinant protein to allow separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Typical fusion expression vectors include pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the recombinant protein.
Recombinant expression vectors can be introduced into host cells to produce a transformant host cell. The term “transformant host cell” is intended to include prokaryotic and eukaryotic cells which have been transformed or transfected with a recombinant expression vector of the invention. The terms “transformed with”, “transfected with”, “transformation” and “transfection” are intended to encompass introduction of nucleic acid (e.g. a vector) into a cell by one of many possible techniques known in the art. Prokaryotic cells can be transformed with nucleic acid by, for example, electroporation or calcium-chloride mediated transformation. Nucleic acid can be introduced into mammalian cells via conventional techniques such as calcium phosphate or calcium chloride co-precipitation, DEAE-dextran mediated transfection, lipofectin, electroporation or microinjection. Suitable methods for transforming and transfecting host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks.
Suitable host cells include a wide variety of prokaryotic and eukaryotic host cells. For example, the proteins of the invention may be expressed in bacterial cells such as E. coli, insect cells (using baculovirus), yeast cells or mammalian cells. Other suitable host cells can be found in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1991).
More particularly, bacterial host cells suitable for carrying out the present invention include E. coli, B. subtilis, Salmonella typhimurium, and various species within the genus' Pseudomonas, Streptomyces, and Staphylococcus, as well as many other bacterial species well known to one of ordinary skill in the art. Suitable bacterial expression vectors preferably comprise a promoter which functions in the host cell, one or more selectable phenotypic markers, and a bacterial origin of replication. Representative promoters include the beta-lactamase (penicillinase) and lactose promoter system (see Chang et al., Nature 275:615 (1978)), the trp promoter (Nichols and Yanofsky, Meth in Enzymology 101:155, (1983) and the tac promoter (Russell et al., Gene 20: 231, (1982)). Representative selectable markers include various antibiotic resistance markers such as the kanamycin or ampicillin resistance genes. Suitable expression vectors include but are not limited to bacteriophages such as lambda derivatives or plasmids such as pBR322 (Bolivar et al., Gene 2:9 S, (1977)), the pUC plasmids pUC18, pUC19, pUC 118, pUC 119 (see Messing, Meth in Enzymology 101:20-77, 1983 and Vieira and Messing, Gene 19:259-268 (1982)), and pNH8A, pNH16a, pNH18a, and Bluescript M13 (Stratagene, La Jolla, Calif.). Typical fusion expression vectors which may be used are discussed above, e.g. pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.). Examples of inducible non-fusion expression vectors include pTrc (Amann et al., Gene 69:301-315 (1988)) and pET 11d (Studier et al., Gene Expression Technology Methods in Enzymology 185, Academic Press, San Diego, Calif., 60-89 (1990)).
Yeast and fungi host cells suitable for carrying out the present invention include, but are not limited to Saccharomyces cerevisae, the genera Pichia, Kluyveromyces, Hanensula, Candida and Torulopsis and various species of the genus Aspergillus. Examples of vectors for expression in yeast S. cerivisae include pYepSec1 (Baldari. et al., Embo J. 6:229-234 (1987)), pMFa (Kurjan and Herskowitz, Cell 30:933-943 (1982)), pJRY88 (Schultz et al., Gene 54:113-123 (1987)), and pYES2 (Invitrogen Corporation, San Diego, Calif.). Examples of vectors for expression in yeast P. pastoris include pPICZ.alpha.A. Protocols for the transformation of yeast and fungi are well known to those of ordinary skill in the art. (see Hinnen et al., Proc. Natl. Acad. Sci. USA 75:1929 (1978); Itoh et al., J. Bacteriology 153:163 (1983), and Cullen et al. (Bio/Technology 5:369 (1987)).
Pharmaceutical Compositions and Therapeutic Uses
Protein toxins of the invention and pharmaceutical compositions comprising such the modified bacterial protein toxins can be administered directly to the patient, e.g., for inhibition of virally infected cell growth in vivo, or for inhibition of cancer, tumor, or precancer cell growth in vivo.
Administration is by any of the routes normally used for introducing a compound into ultimate contact with the tissue to be treated. The compounds are administered in any suitable manner, preferably with pharmaceutically acceptable carriers. Suitable methods of administering such compounds are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route.
Pharmaceutically acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions of the present invention (see, e.g., Remington's Pharmaceutical Sciences, 17th ed. 1985)).
Formulations suitable for parenteral administration, such as, for example, by intravenous, intramuscular, intradermal, and subcutaneous routes, include aqueous and non aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. In the practice of this invention, compositions can be administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically or intrathecally. The formulations of compounds can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials. Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described.
The dose administered to a patient (“a therapeutically effective amount”), in the context of the present invention should be sufficient to effect a beneficial therapeutic response in the patient over time. The dose will be determined by the efficacy of the particular compound employed and the condition of the patient, as well as the body weight or surface area of the patient to be treated. The size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular compound in a particular patient
In determining the effective amount of the compound(s) to be administered in the treatment of a disease such as a viral infection or cancer, the physician evaluates circulating plasma levels of the respective compound(s), progression of the disease, and the production of anti-compound antibodies. In general, the dose equivalent of a compound is from about 1 ng/kg to 10 mg/kg for a typical patient.
Proteins of the present invention can be administered at a rate determined by the LD50 of the particular compound, and its side-effects at various concentrations, as applied to the mass and overall health of the patient. Administration can be accomplished via single or divided doses.
The following examples are presented in order to more fully illustrate certain embodiments of the invention. They should in no way, however, be construed as limiting the broad scope of the invention. One skilled in the art can readily devise many variations and modifications of the principles disclosed herein without departing from the scope of the invention.
The Examples disclosed herein describe the construction and analysis of rationally designed viral-protease activated chimeric toxins, also denoted herein as “zymoxins” for “zymogenized toxins”.
The following Materials and Methods were used in the Examples disclosed herein.
The following Escherichia coli strains were used: XL-1 Blue (Stratagene, USA) for plasmid propagation and Rosetta (DE-3) (Novagen, USA) for expression of the T7 promoter-driven recombinant toxins.
Recombinant DNA techniques were carried out according to standard protocols or as recommended by suppliers. Nucleotide sequences were determined using the PRISM 3100 Genetic Analyzer (Applied Biosystems, USA) according to the supplier's recommendations. The bacterial T7 promoter-based expression vector pET28a, used for expression of recombinant toxins in Escherichia coli, was from Novagen (USA). The eukaryotic tetracycline-inducible CMV promoter-based expression vector pcDNA 4/TO, used for expression of EGFP-scNS3 and EGFP-full NS3-4A in T-REx 293 Cell Line was from Invitrogen (USA). All plasmid and DNA fragment purifications were carried out with HiYield Plasmid Mini Kit and HiYield Gel/PCR DNA Extraction Kit (RBC bioscience, Taiwan). T4 DNA ligase and restriction enzymes were purchased from New England Biolabs (USA). DNA ligations were carried out at 16° C. overnight.
Genomic DNA extraction from Ricinus communis was performed as described in (Edwards et al., 1991)
The previously described NS4A-NS3 (single-chain NS3; scNS3) (Dimasi et al., 1998; Taremi et al., 1998; Berdichevsky et al., 2003; Gal-Tanamy et al., 2005) coding sequence was amplified by PCR using the plasmid pMGT14 (Gal-Tanamy et al., 2005) DNA as template, and the following primers:
The PCR product was digested with HindIII and ApaI (restriction sites are underlined in the primer sequences) and was cloned between the corresponding sites in pEGFP-C2 (Clontech, USA), generating plasmid pEGFP-C2-scNS3″. Next, a fragment containing the coding sequence of the EGFP-scNS3 fusion was excised from the above plasmid by digestion with Eco47III and ApaI and was cloned between the corresponding sites in the Tetracycline inducible vector pcDNA4/TO, generating plasmid pcDNA4/TO EGFP-scNS3.
The coding sequence of the full length NS3 (including the helicase domain) followed by NS4A from 1a HCV genotype was excised from the plasmid NS3/4A-pVAX1 (Frelin et al., 2003), by digestion with NarI and ApaI. The DNA fragment was then cloned between the corresponding sites in pcDNA4/TO EGFP-scNS3 (replacing the scNS3 sequence), generating plasmid “pcDNA 4/TO EGFP-Full NS3-4A”.
(iii) Plasmid PE-DTA-Cleavage Site-Defensin (Shown Schematically in
The coding sequence of amino acids 1-605 of Pseudomonas exotoxin A (PE), including the signal peptide, was amplified by PCR from a plasmid encoding a PE derivative (PE-QQΔ) kindly provided by Dr. Ira Pastan, NCI, NIH, Bethesda, Md., USA, in which lysines 590 and 606 are substituted with glutamine residues and lysine 613 was deleted (Debinski and Pastan, 1994).
In the same amplification process, a DNA sequence encoding the 10 amino acid minimal NS3 cleavage sequence EDVVCCSMSY (SEQ ID NO:1), also referred to as P6-P4′, from HCV NS5A/B site derived from HCV genotype 1b/1a (Steinkuhler et al., 1996) followed by MfeI site, PstI site, 6 histidine residues (6×HIS) and the KDEL ER retrieval signal was introduced to the 3′ end of the toxin coding sequence, using the primers:
The final PCR product was digested with XbaI and EcoRI and was cloned between the corresponding sites in the bacterial expression plasmid pET28a, generating the plasmid “pET28a PE QQ delta NS5AB-HIS-KDEL”. Next, the human alpha-defensin 1 (HNP 1) coding sequence, preceded by a flexible GS-rich linker of 15 amino acids (GGGGSGGGSGSGGSG) and followed by a linker of 4 amino acids (GSGS), was inserted between the NS5AB and the 6×HIS of the above plasmid. This insert was created by PCR using DNA of the plasmid “pET28a PE QQ delta NS5AB-HIS-KDEL” DNA as template, the reverse primer:
and the forward primers: (in this order, when PCR product of the reverse and the first forward primer used as a template for the reverse and the second forward primer, and so on):
The PCR product was digested with PstI and EcoRI and was cloned between the corresponding sites in the plasmid “pET28a PE QQ delta NS5AB-HIS-KDEL”, generating the plasmid “pET28a PE QQ delta NS5AB-15aa linker-HPNI-HIS-KDEL”. In the next step, a DNA fragment encoding diphtheria toxin A (kindly provided by Prof. Nadir Arber, Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Israel) was used as a template for PCR amplification of the region encoding amino acids 1-187 of the mature toxic A domain (without the signal peptide). In the same amplification process, a DNA sequence encoding the 1b derived P6-P4′ NS5A/B junction was introduced to the 3′ end of the toxin coding sequence.
The primers that have been used:
The PCR product was digested with restriction enzymes AatII and MfeI and was cloned between the corresponding sites in the plasmid “pET28a PE QQ delta NS5AB-15aa linker-HPNI-HIS-KDEL”, generating the plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III)-NS5AB-15aa linker-HNP-HIS-KDEL” in which the catalytic domain of PE (domain III) was replaced by amino acids 1-187 of DTA, followed by the NS3 cleavable NS5A/B junction sequence, a flexible linker of 15 amino acids rich in glycine and serine, the human alpha-defensin 1 (HNP 1) coding sequence (encoding ACYCRIPACIAGERRYGTCIYQGRLWAFCC), a short 4 amino acid linker, 6×HIS and the KDEL retrieval signal.
The minimal NS3 cleavage sequence (P6-P4′) derived from NS5A/B junction of HCV 1b/1a genotype in the plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III)-NS5AB-15aa linker-HNP-HIS-KDEL” was mutated by substituting P1 cysteine to arginine and P4′ tyrosine to alanine using the DNA of plasmid “pET28a PE QQDTA(1-187)(instead domain III) 15aa linker-HNP-NS5AB-HIS-KDEL” as template with the following primers:
The PCR product was digested with AatII and PstI and was cloned between the corresponding sites in the plasmid “pET28a PE QQ-DTa(1-187)(instead domain III) 15aa linker-HNP-NS5AB-HIS-KDEL” generating the plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III)-mutated NS5AB-15aa linker-HNP-HIS-KDEL”.
(v) Plasmid “pET28a PE QQ delta-DTA(1-187)(Instead Domain III) 15aa Linker-HNP-HIS-KDEL (Uncleavable)”.
For construction of the vector encoding the control DTA based uncleavable toxin, in which the whole NS3 cleavage site was deleted, a PCR was performed using DNA of the plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III) 15aa linker-HNP-NS5AB-HIS-KDEL” as template, the forward primer:
and the reverse primer:
The PCR product was digested with PstI and AatII and was cloned between the corresponding sites in the same plasmid that has been used as a template, generating the plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III) 15aa linker-HNP-HIS-KDEL (uncleavable)”
For construction of the vector encoding “PE-DTA-cleavage site-defensin” in which the P6-P4′ NS3 cleavage sequence derived from 1b genotype NS5A/B junction was replaced by the P10-P10′ cleavage sequence derived from 2a genotype NS5A/B junction, a PCR was performed using the DNA of plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III) 15aa linker-HNP-NS5AB-HIS-KDEL” as template, using the reverse primer:
and the forward primers (in this order, when PCR product of the reverse and the first forward primer used as a template for the reverse and the second forward primer, and so on):
The PCR product was digested with StuI and XhoI and was cloned between the corresponding sites in a plasmid similar to the one used as a template, in which the StuI site was introduced silently (without changing the protein sequence) upstream to the 1b derived NS5A/B sequence, generating plasmid “pET28a PE QQ delta-DTA(1-187)(instead domain III)-full 2a NS5AB-15aa linker-HNP-HIS-KDEL”.
(vii) Plasmid “PE-RTA-Cleavage Site-Stalk Peptide” (Shown Schematically in
For construction of the vector encoding the RTA based cleavable zymoxin “PE-RTA-cleavage site-stalk peptide”, the coding sequence of the catalytic domain, ricin toxin A chain (amino acids 1-267) was amplified from a Ricinus communis genomic DNA preparation by PCR using the forward primer:
and the reverse primer:
The PCR product was digested with SacII and MfeI and was cloned between the corresponding sites of plasmid “pET28a PE QQ delta NS5AB-HIS-KDEL”, generating the plasmid “pET28a PE QQ (I-II-Ib-RTA)-HIS-KDEL”, which served as a template for another PCR using the forward primer:
and the reverse primers (in this order, when PCR product of the forward and the first reverse primer used as a template for the forward and the second reverse primer, and so on):
The PCR product was digested with SacII and PstI, and was cloned between the corresponding sites in the same plasmid that has been used as a template, generating plasmid “pET28a PE QQ delta RTA-short linker-stalk peptide-HIS-KDEL” in which two repeats of the acidic 16 residue peptide corresponding to the conserved C terminus of the ribosomal stalk proteins (EESEESDDDMGFGLFD) have been fused to the C-terminus of RTA, preceded by the P6-P4′ NS3 cleavable NS5A/B junction sequence derived from 1b/1a genotype, a short linker of Gly-Gly-Gly-Gly-Ser and followed by 6×HIS and the KDEL ER retrieval signal.
(viii) Plasmid “PE-RTA-Mutated Cleavage Site-Stalk Peptide” (Shown Schematically in
For construction of the vector encoding the uncleavable control zymoxin “PE-RTA-mutated cleavage site-stalk peptide”, the minimal NS3 cleavage sequence (P6-P4′) derived from NS5A/B junction of HCV 1b/1a genotype in the plasmid “pET28a PE QQ delta RTA-short linker-stalk peptide-HIS-KDEL” was mutated by substituting P1 cysteine to arginine and P4′ tyrosine to alanine using the following primers with the DNA of plasmid “pET28a PE QQ delta RTA-short linker-stalk peptide-HIS-KDEL” as template:
The PCR product was digested with BamHI and EcoRI, and was cloned between the corresponding sites in the same plasmid that has been used as a template, generating the plasmid “pET28a PE QQ delta RTA-mutated NS5AB-short linker-stalk peptide-HIS-KDEL”.
For construction of the vector encoding “PE-RTA-cleavage site-stalk peptide” zymoxin in which the P6-P4′ NS3 cleavage sequence derived from 1b genotype NS5A/B junction was replaced by the P10-P10′ cleavage sequence derived from 2a genotype NS5A/B junction, a PCR was performed using the DNA of plasmid “pET28a PE QQ delta RTA-short linker-stalk peptide-HIS-KDEL” as template, the reverse primer:
and the forward primers (in this order, when PCR product of the reverse and the first forward primer used as a template for the reverse and the second forward primer, and so on):
The PCR product was digested with BamHI and XhoI and was cloned between the corresponding sites in the same plasmid that has been used as a template, generating the plasmid “pET28a PE QQ delta RTA-full 2a NS5AB-short linker-stalk peptide-HIS-KDEL”.
For construction of the vector encoding the NS3 cleavable substrate “MBP-EGFP-NS5AB-CBD” bearing the P6-P4′ NS3 cleavage sequence derived from 1b/1a genotype NS5A/B junction (shown schematically in
For construction of the vector encoding the NS3 cleavable substrate “MBP-EGFP-full 1b NS5AB-CBD” bearing the P10-P8′ NS3 cleavage sequence derived from 1b genotype NS5A/B junction, a PCR was performed using the DNA of plasmid “pCMV/MBP-EGFP-NS5AB-CBD” as template, the reverse primer: 5′-TAGAAGGCACAGTCGAGG-3′(SEQ ID NO:114) and the forward primers (in this order, when PCR product of the reverse and the first forward primer used as a template for the reverse and the second forward primer, and so on):
The PCR product was digested with NheI and HindIII and was cloned between the corresponding sites in the same plasmid that has been used as a template, generating plasmid “pCMV/MBP-EGFP-full 1b NS5AB-CBD”.
(xii) Plasmid “MBP-EGFP-Full 2a NS5AB-CBD”.
For construction of the vector encoding the NS3 cleavable substrate “MBP-EGFP-full 2a NS5AB-CBD” bearing the P10-P10′ NS3 cleavage sequence derived from 2a genotype NS5A/B junction, a PCR was performed using the DNA of plasmid “pCMV/MBP-EGFP-NS5AB-CBD” as template, the reverse primer: 5′-TAGAAGGCACAGTCGAGG-3′ and the forward primers (in this order, when PCR product of the reverse and the first forward primer used as a template for the reverse and the second forward primer, and so on):
The PCR product was digested with NheI and HindIII and cloned between the corresponding sites in the same plasmid that has been used as a template, generating plasmid “pCMV/MBP-EGFP-full 2a NS5AB-CBD”.
E. coli BL21 Rosetta (DE3) cells were transformed with pET28a based expression plasmids and grown in 1 liter of LB medium supplemented with 50 μg/ml Kanamycin, at 37° C. 250 rpm shaking to O.D. 600 nm of 0.8. The cells were chilled down to 30° C. and induced with 1 mM IPTG for 3-4 hours at 30° C., 250 rpm. The cells were collected by centrifugation at 5000 g, 4° C. 10 minutes. For preparation of periplasmic fractions, the cell pellet was gently re-suspended in 200 ml of ice-cold 20% sucrose, 30 mM Tris(HCl) (pH 7.4), 1 mM EDTA, using glass beads. The cell suspension was incubated on ice for 15 minutes and centrifuged at 6000 g, 4° C. 15 minutes. The cell pellet was gently re-suspended in 200 ml of ice cold sterile double distilled water (DDW), incubated on ice for 15 minutes and centrifuged at 8000 g, 4° C. 20 minutes. The supernatant periplasmic fraction was adjusted to 20 mM Tris-HCl (pH 8.0), 300 mM NaCl and 5 mM Imidazole. The periplasmic fraction was incubated over-night, in continues rotation with 700 μl of Ni-NTA resin (Favorgen, Taiwan) that was previously equilibrated with Binding buffer (20 mM Tris-HCl pH 8.0, 300 mM NaCl). Ni-NTA resin was then separated from the periplasmic supernatant by 5 minutes centrifugation at 70 g, 4° C., loaded on Poly Prep column (Bio-Rad, USA) and washed with 20 ml of binding buffer+5 mM imidazole. Bound His-tagged protein was subsequently eluted with 700 μl PBS containing 500 mM imidazole, and dialyzed twice against 1 liter of PBS.
Human embryonic kidney cells HEK293, stably expressing the tetracycline repressor protein (T-REx 293 Cell Line, Invitrogen, USA), and human hepatoma cells Huh7.5 (Blight et al., 2002) were used throughout this study. Cell lines were maintained in DMEM supplemented with 10% fetal calf serum (FCS), 2 mM 1-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin and 12.5 U/ml nystatin (Biological Industries, Israel) in a humidified 5% CO2 incubator at 37° C. The calcium-phosphate transfection method was applied for introducing 2 μg of the plasmids “pcDNA 4/TO EGFP-scNS3”, “pcDNA 4-TO EGFP-Full NS3-4A” or “pCMV/MBP-EGFP-NS5AB-CBD” into T-Rex 293 cells, seeded 1.5×106 cells per 6 cm plate 24 hours before transfection. Stable transfectants, inducibly expressing EGFP-scNS3 or EGFP-Full NS3-4A were selected in a medium containing zeocin (200 μg/ml) (CAYLA, France).
2 μg of the plasmids “pCMV MBP-EGFP-full 1b NS5AB-CBD” or “pCMV MBP-EGFP-full 2a NS5AB-CBD” were introduced into uninfected or HCV infected Huh7.5 Cells (seeded 3×105 cells per well in 6-well plate 24 hours before transfection) using FuGENE 6 reagent (Roche, Germany), according to the manufacturer instructions.
For protein extraction, 48 hours post-transfection the cells were washed with PBS, scraped and lysed in a buffer containing 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 10 mM Tris(HCl) pH 7.5, and protease inhibitors cocktail (Sigma, Israel). Following 30 minutes of incubation on ice, lysates were cleared by centrifugation at 20,000 g for 10 minutes, at 4° C. For immunoblotting, protein samples were electrophoresed on 12% SDS/polyacrylamide gel, transferred to nitrocellulose and detected using rabbit polyclonal anti-GFP antibody (Santa-Cruz, USA) or polyclonal mouse serum anti-MBP followed by HRP-conjugated goat anti-rabbit or anti-mouse mouse antibodies (Jackson ImmunoResearch Laboratories, USA) and ECL detection. immunoblotting of purified recombinant toxins was similarly performed, using rabbit polyclonal anti-PE antibody, kindly provided by Dr. Ira Pastan, NCl, NIH, Bethesda, Md., USA.
Virus assays were carried out with an inter-genotypic chimeric virus produced by replacing the core-NS2 segment of the JFH-1 virus genome with the comparable segment of the genotype 1a H77 virus. This chimeric virus, HJ3-5, contains two compensatory mutations that promote its growth in cell culture as described previously (Yi et al., 2007; McGivern et al., 2009). HCV RNAs were transcribed in vitro and electroporated into cells essentially as described previously (Yi and Lemon, 2004; Yi et al., 2006). In brief, 10 μg of in vitro-synthesized HCV RNA was mixed with 5×106 Huh7.5 cells in a 2-mm cuvette and pulsed twice at 1.4 kV and 25 μF. Cells were seeded into 12-well plates or 25-cm2 flasks, and passaged at 3- to 4-day intervals posttransfection by trypsinization and reseeding with a 1:3 to 1:4 split into fresh culture vessels. When infectivity reached >95%, as was monitored by immunofluorescent staining with anti HCV core protein, Cells were taken for cytotoxicity or substrate cleavage assays.
1×105 T-REx 293 cells inducibly expressing EGFP-scNS3 or EGFP-full NS3-4A were seeded on poly-L-lysine coated cover-slips in a 24 well-plate. After 12 hours, the cells were treated with 1 mg/ml of tetracycline for 24 hours (or remained untreated), washed with PBS, fixed with 4% paraformaldehyde in PBS at room temperature for 20 minutes, permeabilized with Triton X-100 (0.1% in PBS) for 5 minutes, and blocked with 90% fetal calf serum/10% PBS at room temperature for 25 minutes. Slides were incubated with 1:200 diluted rabbit-polyclonal anti-calnexin antibody (Sigma, USA) as primary antibody for 1 hour, and followed by 1:500 diluted Cy3-conjugated anti-rabbit IgG (Jackson ImmunoResearch Laboratories, USA) secondary antibody and Hoechst 33258 (5 μg/ml) (Sigma, USA) for 1 hour at room temperature. Slides were washed with PBS, mounted in ImmuGlo Mounting Medium (IMMCO Diagnostics, USA), and examined with a Zeiss LSM 510 META laser scanning confocal microscope.
HUH7.5 cells infected with HCV HJ3-5 chimeric virus were seeded into 8-well chamber slides (Nalge Nunc, USA). After 24 hours, cells were fixed and permeabilized as described above and stained with 1:300 diluted mouse monoclonal antibody C7-50 (Affinity BioReagents, USA) specific for the HCV core protein followed by staining with 1:100 diluted Cy2-conjugated goat anti-mouse IgG (Jackson ImmunoResearch Laboratories, USA). Slides were mounted and examined using a fluorescence microscope.
600 ng of DTA based toxins or 3000 ng of RTA based toxins were incubated with or without 500 ng or 1000 ng, respectively, of recombinant MBP-scNS3 fusion (Gal-Tanamy et al., 2005) in a reaction buffer (50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 0.05% tween 20, 20% glycerol and 1.7 mM of DTT) in a total volume of 600 for 1 hour at 37° C. NS3 mediated cleavage was verified by western blotting of 50 ng (DTA based toxins) or 250 ng (RTA based toxins) toxin samples using rabbit polyclonal anti-PE antibody.
ADP-ribosylation activity of DTA based toxins was determined by measuring transfer of ADP-ribose from [14C]NAD to EF-2 essentially as described at (Mansfield et al., 1996). Shortly, 30 ng of each toxin were diluted to 210 μL in 50 mM Tris-HCl (pH 8.0), 1 mM EDTA, and 0.1% BSA. Mixture was incubated with wheat germ extract in the presence of 2.4 μM [14C] NAD (6×105 cpm) (Amersham Biosciences, UK) for 40 minutes at RT. Reactions were terminated by addition of TCA to the reaction mixture which resulted in total protein precipitation. Level of ADP-ribosylated EF2 was assessed by measuring the radioactivity of the precipitated protein by a scintillation counter.
The catalytic activity of ricin A based toxins was determined by a modification of the in-vitro assay described at (May et al., 1989; Munishkin and Wool, 1995). A serial dilutions of the cleavable or uncleavable RTA based toxins (treated or untreated with NS3) were incubated with 10 μl of micrococcal nuclease-treated rabbit reticulocyte lysate (Promega, USA) for 30 minutes at 30° C., after which total RNA from each mixture was extracted with phenol and chloroform, precipitated in ethanol and suspended in 22 μl of water. Half of the RNA (11 μl) was then treated with 50 μl of acidic aniline (1M aniline in 2.8 M acetic acid) for 10 minutes at 40° C. and the other half remained untreated. Next, RNA was recovered by precipitation with ammonium acetate and ethanol, and analyzed by 3% TBE agarose gel electrophoresis.
Cell-killing activities of recombinant toxins of were measured by a MTT assay. For cytotoxicity assay on T-REx 293 cells inducibly expressing NS3 protease, 4×104 cells were seeded per well in 96-well plates. After 9 hours, cells were treated with 1 μg/ml of tetracycline or left untreated. 2 hours later, cells were incubated with serial dilutions of the toxins (presence of tetracycline was kept in the growth media of induced cells). After 72 hours, the media was replaced by fresh media (100 μl per well) containing 1 mg/ml MTT (Thiazolyl Blue Tetrazoliam Bromide (Sigma, USA) dissolved in PBS) reagent and the cells were incubated for another 30 minutes. MTT-formazan crystals were dissolved by the addition of extraction solution (20% SDS, 50% DMF, pH 4.7) (100 μl per well) and incubation for 16 hours at 37° C. Absorbance at 570 nm was recorded on an automated microtiter plate reader. The results were expressed as percentage of living cells relatively to the untreated controls. The IC50 value is the concentration of the toxin which inhibited cell growth by 50%.
For cytotoxicity assay on HCV infected or uninfected HUH7.5 cells, 1×104 Huh7.5 cells uninfected or infected with HJ3-5 chimeric virus were seeded per well in 96-well plates. After 24 hours, cells were incubated with serial dilutions of the toxins. 96 hours later, the media was replaced by fresh media (100 μA per well) containing 1 mg/ml MTT and the cells were incubated for another 60 minutes. Further steps were identical to theses described above.
For the purpose of establishing a model cell line expressing the HCV NS3 protease, we constructed a fusion protein between the previously described single chain construct NS4A-NS3 (single-chain NS3; scNS3) (Gal-Tanamy et al., 2005) in which a short synthetic peptide encompassing residues 21-34 of NS4A (of the 1b HCV genotype) was linked to the N terminus of the NS3 protease domain (Dimasi et al., 1998; Taremi et al., 1998; Berdichevsky et al., 2003), and enhanced green fluorescence protein (EGFP). In addition, another construct was made, comprising a fusion of EGFP and the full length NS3 (protease/RNA helicase) followed by full length NS4A (of the 1a HCV genotype) (Frelin et al., 2003). As opposed to EGFP-scNS3, which is predicted to be a soluble cytoplasmic or nucleocytoplasmic protein; the EGFP-full length NS3 (which strongly interacts with the full length NS4A following auto-cleavage) is expected to be associated with membranes when expressed in mammalian cells, more precisely mimicking the intracellular localization of this complex in HCV infected cells. The is based on the reasoning that the hydrophobic amino terminal domain of the full NS4A directs the NS3-NS4A complex to the ER membrane or an ER-like modified compartment (Wolk et al., 2000; Moradpour et al., 2003; Zemel et al., 2004; Moradpour et al., 2007).
A TET-ON inducible system was established to avoid toxic effects observed upon prolonged over-expression of EGFP-scNS3 and EGFP-full NS3-4A in HEK293 cells. In the TET-ON system, based on T-REx™ 293 cell line (Invitrogen), expression of EGFP-scNS3 or EGFP full NS3-4A (also referred to herein as “scNS3” and “full NS3-4A”, respectively) is induced by addition of tetracycline (Tet) to the growth medium.
In order to monitor specific NS3 proteolytic activity in Tet induced cells, we constructed another plasmid coding for a modification of our previously described polypeptide which serves as a substrate for proteolysis by the NS3 protease (Berdichevsky et al., 2003). This plasmid, denoted pCMV/MBP-EGFP-NS5AB-CBD, encodes a fusion protein of maltose binding protein (MBP), enhanced green fluorescence protein (EGFP), the 10 amino acid minimal NS3 cleavage sequence (P6-P4′) from HCV NS5A/B site derived from HCV genotype 1b/1a (for both 1b and 1a genotypes this sequence is identical) (Steinkuhler et al., 1996) and cellulose binding domain (CBD). As shown in
The toxin-substrate interaction model predicts that an intimate interaction between DTA and its intracellular target elongation factor 2 resides in the C terminal portion of the toxin (Jorgensen et al., 2005). The present inventors have now fused human alpha-defensin 1 (HNP 1) to the C-terminus of DTA, preceded by the 10 amino acid minimal NS3 cleavage sequence (P6-P4′) from HCV (genotype 1b/1a) NS5A/B site (referred as “cleavage site”) and a flexible linker of 15 amino acid rich in serine and glycine residues. This construct was then fused in its N-terminus to the binding and translocation domains of Pseudomonas exotoxin A (PE) in order to enable internalization and trafficking to the cytosol of mammalian cells, as the natural binding and translocation domains of the diphtheria toxin, which are positioned to the C-terminus of the wild type toxin, were substituted by the HNP1 polypeptide. In addition, a 6×His tag followed by a KDEL ER retrieval signal were placed at the most C terminal portion of the construct (“PE-DTA-cleavage site-defensin”), for facilitating the toxin purification and as the KDEL retrieval system is exploited by PE in order to reach the ER lumen (Jackson et al., 1999), respectively. This 6×His-KDEL extension was positioned at the C-terminus of all the chimeric constructs disclosed herein, which have been expressed in E. coli BL21 cells and purified from the periplasmic fraction as described in Materials and Methods. As a control, an uncleavable chimeric toxin was constructed, in which the NS3 cleavage site was mutated by substituting P1 cysteine to arginine and P4′ tyrosine to alanine (“PE-DTA-mutated cleavage site-defensin”), represented in
In order to evaluate the susceptibility of the constructs described in Example 2 to cleavage by the NS3 protease and to evaluate the influence of such cleavage on their ADP-ribosylation activity, an in vitro cleavage reaction was carried out by incubating the chimeric toxins with recombinant MBP-scNS3 fusion produced in E. coli (Gal-Tanamy et al., 2005), followed by an ADP-ribosylation activity assay using wheat germ extract as a source of elongation factor 2 (Collier and Kandel, 1971; Hwang et al., 1987). A schematic representation of the PE-DTA chimeric toxins, the in vitro cleavage products and the ADP-ribosylation assay results are shown in
In contrast, the toxin with the mutated cleavage site was resistant to cleavage by NS3 (
In order to evaluate the toxin activation by HCV protease in vivo, our model cell lines, induced or uninduced for NS3 expression, were treated with “PE-DTA-cleavage site-defensin” or “PE-DTA-mutated cleavage site-defensin”. As shown in
In order to provide chimeric toxins in which the toxicity of a ricin catalytic domain is “disarmed” prior to enzymatic cleavage of the chimeric protein, the present inventors have engineered a chimeric toxin comprising a fragment derived from the ribosomal stalk protein P1 (or P2) and RTA.
More specifically, we have cloned the coding sequence of the catalytic A chain of ricin (RTA) from a genomic DNA preparation of Ricinus communis into a bacterial expression plasmid. Subsequently, we constructed a chimeric toxin in which two repeats of the acidic 16 residue peptide (EESEESDDDMGFGLFD) corresponding to the conserved C-terminus of the ribosomal stalk proteins were fused to the C-terminus of RTA. Similar to the approach taken for construction of the diphtheria chimeric toxins described herein, the cleavable toxin “PE-RTA-cleavage site-stalk peptide” was prepared, in which the NS3 protease minimal cleavage sequence (P6-P4′) from genotype 1b/1a NS5A/B junction was inserted between RTA and the ribosome stalk peptide. In the uncleavable toxin “PE-RTA-mutated cleavage site-stalk peptide”, a mutated cleavage site was positioned at the corresponding location. These constructs were then fused in their N-termini to the binding and translocation domain of PE. By fusing RTA to the bacterially derived binding and translocation domains of PE, chimeric PE-RTA toxins that are capable of penetrate into the mammalian cell cytoplasm may be produced in E. coli by standard methods.
In order to assess the susceptibility of the constructs described in Example 5 to cleavage by NS3 and evaluate the influence of such cleavage on their ribosome depurination activity, an in vitro cleavage reaction was carried out (as previously described for the diphtheria toxin-based chimera), following by ribosome depurination assay using the acidic aniline method based on reticulocyte lysate derived ribosomes (May et al., 1989; Munishkin and Wool, 1995). In this method, the phosphodiester bond at the 3′ site of the depurinated adenine in the ricin treated rRNA is cleaved by treatment with aniline under acidic conditions, and a small fragment of about 460 nucleotides (“R fragment”) is released and can be detected by agarose or acrylamide gel electrophoresis and staining with ethidium bromide. A schematic representation of the PE-RTA chimeric toxins, the in vitro cleavage and the ribosome depurination assay results are represented in
As shown, incubation of the toxin “PE-RTA-cleavage site-stalk peptide” with the recombinant NS3 protease resulted in complete cleavage of the chimeric toxin that appeared as a lower weight product (
Moreover, cleavage of “PE-RTA-cleavage site-stalk peptide” led to an increase in ribosome depurination activity of the toxin, as indicated by the appearance of the “R fragment” (
In order to verify toxin activation by HCV protease in vivo, our model cell lines, induced or uninduced for NS3 expression, were treated with the chimeric toxins “PE-RTA-cleavage site-stalk peptide” or “PE-RTA-mutated cleavage site-stalk peptide”. As shown in
Current models for study of hepatitis C virus enable production of recombinant infectious HCV particles (for example, genotype 2a strain JFH1 and other chimeric viruses generated in the JFH1 background) in Huh7 hepatoma-derived cell lines that are permissive for HCV replication, rendering all steps of the viral life cycle, including entry and release of viral particles, amenable to systematic analysis. (Lohmann et al., 1999; Blight et al., 2002; Lindenbach et al., 2005; Wakita et al., 2005; Zhong et al., 2005; Brass et al., 2006; Pietschmann et al., 2006; Rychlowska and Bienkowska-Szewczyk, 2007; Gottwein et al., 2009).
In order to evaluate the potential of the chimeric toxins disclosed herein to be cleaved and active in vivo, Huh7.5 cells uninfected or infected with the 1a/2a chimeric virus HJ3-5 (encoding the structural proteins of genotype 1a strain H77S within the background of JFH1; see (Yi et al., 2007; McGivern et al., 2009) were transfected with vectors encoding cleavage substrates. The vectors designated “pCMV/MBP-EGFP-full 1b NS5AB-CBD” and “pCMV/MBP-EGFP-full 2a NS5AB-CBD”, encode the previously described NS3 cleavable substrate, modified in that the 10 amino acid minimal NS3 cleavage sequence from genotype 1b/1a NS5A/B junction was replaced by longer cleavage sequences of either 18 amino acids (P10-P8′), or 20 amino-acids (P10-P10′), from the 1b or 2a genotype NS5A/B junction sites, respectively.
Western blot analysis of lysate samples from uninfected and HJ3-5 infected cells indicated that the substrate incorporating the 2a NS5A/B site was cleaved in infected cells also expressing the NS3 protease (
Based on the results disclosed herein, it is apparent that the chimeric toxins according to the invention may be used in the development of anti-viral agents for a large variety of disease causing viruses which encode a viral protease. Such viral targets include, but are not limited to flaviviruses such as hepatitis C virus (HCV), West Nile virus (WNV), dengue fever virus (DFV) and yellow fever virus (YFV); retroviruses such as HIV-1; picornaviruses such as coxsackievirus, poliovirus and hepatitis A virus, nidoviruses such as coronaviruses (CoV), including the severe acute respiratory syndrome (SARS) causative SARS-CoV; and herpesviruses such as varicella-zoster virus (VZV) and Epstein-Bar virus (EBV).
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/IL11/00680 | 8/22/2011 | WO | 00 | 3/15/2013 |
| Number | Date | Country | |
|---|---|---|---|
| 61384342 | Sep 2010 | US |
