Patent Grant
11892449
The instant application contains a Sequence Listing, which has been submitted electronically in XML format and is hereby incorporated by reference in its entirely. The XML copy, created on Nov. 23, 2022, is named “058636_00564_ST26.xml” and is 216,672 bytes.
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has, since December 2019, caused over million deaths with over 180 million confirmed cases worldwide. Great strides have been made through innovations in rapid testing and neutralizing antibody treatments in an effort to control the spread and fatality of the disease. However, the lack of immediate widespread testing at the beginning of the pandemic has proven fatal. The need for widely available therapies is also clear. If an infected person reaches the stage at which hospitalization is necessary, the COVID-19 patient faces a 21% fatality rate, more than five times greater than that of influenza. Hospitalization has also been linked to higher viral titers in hospitalized patients. In terms of surveillance of the virus, testing of SARS-CoV-2 has relied on specialized instruments in addition to costly reagents and supplies for carrying out the reactions. Low and middle income countries (LMICs) are especially vulnerable since the healthcare infrastructure and resources may not allow for widespread testing. One such proposed solution, lateral flow assays (LFAs) and enzyme-linked immunosorbent assays (ELISA), represent a point-of-care (POC) test for a simple, inexpensive, and fast diagnosis that also predominantly relies on protein-protein interactions (PPIs).
During infection by SARS-CoV-2, the spike (S) protein on the virus surface recognizes the peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2) of the host. Structural studies reveal that the N-terminal alpha-helix (residues 1-23) of human ACE2 receptor is critical to binding the S1 receptor binding domain (RBD) of SARS-CoV-2 involved in infection. Recently engineered recombinant ACE2 has shown an increased avidity to SARS-CoV-2 compared to the wild-type. Recombinant ACE2 has also been clinically proven to block early infection and reduce recovery. However, recent studies have also shown that isolation of this alpha-helix as an antibody or protein domain mimic (PDM) provides weak protein-protein interaction with the SARS-CoV-2 RBD.
HIF1α has been the subject of recent research in PPIs because of the high percentage of alpha-helicity at the interface for multiple binding interfaces and when inhibited by helix mimetics, has shown to reduce tumor growth in animal models. Recently, key residues of the C-terminal transactivation (CTAD, aa 786-826) of HIF1α that interact with the cysteine-histidine rich 1 (CH1) domain of the coactivator protein p300 has been mimicked into an effective PDM using the oxopiperazine helix mimetics (OHM) strategy. OHMs employ chemical conjugation of the nitrogen atoms in neighboring backbone amides with an ethylene bridge to create a chiral scaffold to maintain a structure and thus function akin to proteins. This design uses just the twelve CTAD residues with a binding affinity of up to 530 nM—as compared to the full length CTAD of HIF1α with a binding affinity of 38 nM by tryptophan fluorescence assay. The OHM PDM reduces HIF activity and down-regulated the expression of hypoxia-inducible genes and in vivo experiments reduces tumor volume by approximately 50%.
The present disclosure provides a multivalent protein that targets the interaction of SARS-CoV-2 spike receptor binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2) receptor protein and a multivalent protein that targets the interaction of p300 with the hypoxia induced factor 1α (HIF1α). These proteins rely on multi-valency rather than the sensitivity of a monomeric ligand to provide avidity to its target (See
In an aspect, the present disclosure provides molecules (e.g., multivalent assembled proteins (MAPs)) that bind to COVID-19 virus or the p300 peptide, wherein the molecules comprise a plurality of proteins (e.g., 5 proteins). In an embodiment, each multivalent molecule may be a pentamer, wherein each of the monomers (e.g., a protein of the present disclosure) of the pentamer comprise a plurality of blocks. For example, each monomer (e.g., protein) may comprise of one or more X1 blocks, X2 blocks, and X3 blocks, where the X1 block is a coiled-coil domain, the X2 block is a linker, and the X3 block is a binding domain. The blocks may oriented from the N to the C-terminus as (X1)a-(X2)b-(X3)c where a, b, and c are a number of repeats for that block. a, b, and c, may all be the same, all be different, or two of a, b, and c are the same and remaining one is different. The blocks may also be oriented from C-terminus to N-terminus as (X3)c-(X2)b-(X1)a. Examples of each block are provided herein. A protein may comprise one or more additional blocks. The multivalent molecules are formed by the self-assembling ability of the coiled-coil domain (X1 block) to form oligomers (e.g., trimers, tetramers, and pentamers).
The present disclosure also provides a rapid, simple, and effective point of care (POC) test. Multiplex lateral flow test strips for simultaneous detection of the virus and viral antibodies, including discrimination of antibody subtypes are described. A method using the multiplex lateral flow test strips to detect the virus, the antibodies, or simultaneously the virus and the antibodies is also described. The virus is detected by use of ACE-TAP, while the viral antibodies are detected by using S-TAP. Specific, colorimetrically detectable binding molecules directed against COVID-19 virus and antibodies generated against COVID-19 are also described.
This disclosure describes a lateral flow assay (LFA) which can be used as a point of care (POC) test for SARS-CoV-2 and therapeutic agents against SARS-CoV-2.
Throughout this application, the use of the singular form encompasses the plural form and vice versa. For example, “a”, or “an” also includes a plurality of the referenced items, unless otherwise indicated.
Where a range of values is provided in this disclosure, it should be understood that each intervening value, to the tenth of the unit of the lower limit between the upper and lower limit of that range, and any other intervening value in that stated range is encompassed within the invention, unless clearly indicated otherwise. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges encompassed within the disclosure.
The term “treatment” as used herein refers to alleviation of one or more symptoms or features associated with the presence of the particular condition or suspected condition being treated. Treatment does not necessarily mean complete cure or remission, nor does it preclude recurrence or relapses. Treatment can be effected over a short term, over a medium term, or can be a long-term treatment, such as, within the context of a maintenance therapy. Treatment can be continuous or intermittent.
The term “effective amount” as used herein refers to an amount of an agent sufficient to achieve, in a single or multiple doses, the intended purpose of treatment or administration. The exact amount desired or required will vary depending on the particular compound or composition used, its mode of administration, patient specifics and the like. Appropriate effective amount can be determined by one of ordinary skill in the art informed by the instant disclosure using only routine experimentation.
The term “neutralizing” as used herein in reference to an antibody (e.g., antibody generated as part of a host immune response) refers to antibody or the antigen binding fragment that inhibits SARS-CoV-2 virus from infecting a target cell for replication, regardless of the mechanism by which neutralization may be achieved. For example, the virus may be neutralized by inhibiting the entry of SARS-CoV-2 into host mammalian cells or inhibiting entry of pseudotype viruses displaying the Spike protein of SARS-CoV-2 into host mammalian cells. The term “pseudovirus” refers to recombinant viral particles containing a reporter gene that also expresses the Spike protein of SARS-CoV-2 on its surface.
As used in this disclosure, the singular forms include the plural forms and vice versa unless the context clearly indicates otherwise.
All nucleotide sequences described herein, their RNA and DNA equivalents, and complimentary sequences are included in this disclosure. Disclosure of protein sequences also includes corresponding RNA and DNA sequences encoding for such proteins. While specific sequences are listed in this disclosure, it will be appreciated that amino acid changes/substitutions may be made in the sequences without affecting the function/activity. Such, sequences which are 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% identical to the sequences disclosed herein or to the nucleotide sequences encoding the amino acid sequences disclosed herein are considered to be part of the disclosure.
In an aspect, the present disclosure provides molecules (e.g., multivalent assembled proteins (MAPs)) that bind to COVID-19 virus, wherein the molecules comprise a plurality of proteins (e.g., 5 proteins). In an embodiment, each multivalent molecule may be a pentamer, wherein each of the monomers (e.g., a protein of the present disclosure) of the pentamer comprise a plurality of blocks. For example, each monomer (e.g., protein) may comprise of one or more X1 blocks, X2 blocks, and X3 blocks, where the X1 block is a coiled-coil domain, the X2 block is a linker, and the X3 block is a binding domain. The blocks may oriented from the N to the C-terminus as (X1)a-(X2)b-(X3)c where a, b, and c are a number of repeats for that block. a, b, and c, may all be the same, all be different, or two of a, b, and c are the same and remaining one is different. The blocks may also be oriented from C-terminus to N-terminus as (X3)c-(X2)b-(X1)a. As an example for repeating blocks, each block may repeat any number of times and/or they may be ordered with multiple successive blocks such as X1-X1-X1-X2-X2-X3 where in this case a=3, b=2, and c=1. Examples of each block are provided herein. In various embodiments, a, b, and c are independently 1 to 50, including all values and ranges therebetween. A protein may comprise one or more additional blocks. The multivalent molecules are formed by the self-assembling ability of the coiled-coil domain (X1 block) to form oligomers (e.g., trimers, tetramers, and pentamers). The MAPs may be referred to as “ACE-MAPs” or “H-MAPs.”
The X1 block is a coiled-coil-based domain. Additionally, the X1 block may comprise a “kink” or “kinked region.” Non-limiting examples of X1 include CC-Type2-LL-L17Q octomer (PDB: 6G6F), CC-Type2-deLI hexamer (PDB: 6G6E), GCN4-pAA heptamer (PDB: 2HY6), CC-Type2-IL-Sg-L17E heptamer (PDB: 6G69), CC-Type2-LL-L-L17Q hexamer (PDB: 6G6B), CC-Type2-IL-Sg hexamer (PDB: 6G68), CC-Type2-deLI hexamer (PDB:6G6E), CC-Type2-IV hexamer (PDB: 6G66), COMPcc pentamer (PBD: 3v2p) and GCN4 trimer (PBD: 2O7H) or tetramer (PBD: 2IPZ), the sequences of which are incorporated herein by reference from PDB (www.resb.org) as of the date of filing. Examples of sequences for the X1 block include, but are not limited to:
Other examples, may comprise portions of any of the foregoing sequences. The sequences may be used without the His tag or beginning linker domain, or with or without a nuclear localization sequence (NLS) tag such as PKKKRKV (SEQ ID NO:7). For example, the sequence of X1 may comprise, consist essentially of, or consist of:
or (with full sequences below including His tag to show inclusion of NLS tag prior):
Other sequences provided herein as C sequences or ccCOMP sequences or variants thereof may also be used as X1 block. The “kink” (included in some of the sequences above) may have the following sequence: LLEIWK (SEQ ID NO:36). The “kink” may connect the X1 block to the X2 block. The X1 block may comprise, consist essentially of, or consist of any portion of any of the foregoing sequences.
X2 block is a linking group, which may be referred to as a linker. Examples of linking groups include, but are not limited to: (G4S)n (SEQ ID NO:22), [EAAAK]n, (SEQ ID NO:176), (EAAK)n (SEQ ID NO:23), (PAPAP)n (SEQ ID NO:24), A(EAAAK)4ALEA(EAAAK)4A (SEQ ID NO:25), AEAAAKEAAAKA (SEQ ID NO:26), (Ala-Pro)n, VSQTSKLTRAETVFPDV (SEQ ID NO:27), PLGLWA (SEQ ID NO:28), RVLAEA (SEQ ID NO:29), EDVVCCSMSY (SEQ ID NO:30), GGIEGRGS (SEQ ID NO:31), TRHRQPRGWE (SEQ ID NO:32), AGNRVRRSVG (SEQ ID NO:33), RRRRRRRRR (SEQ ID NO:34), GFLG (SEQ ID NO:35), AAAKEAAAKEAAAK (SEQ ID NO:189), LE, (G)n, or a disulfide bridge, where n is 1-50, including all integer values and ranges therebetween. Other examples of linkers include those provided in Table 1. In various examples, n is 1, 2, 3, 4, or 5. The X2 block may comprise, consist essentially of, or consist of any portion of any of the foregoing sequences.
X3 block is the binding domain. The binding domain binds to a target protein. The target protein is a protein to which binding is desired or intended, for example, in situations where reduction in the severity of infection caused by a microorganism exhibiting the target protein is desired. For example, the binding domain binds to coronaviruses having a spike protein. Non-limiting examples of binding domains include ACEBinder 1: (IEEQAKTFLDKFNHEAEDLFYQS) (SEQ ID NO:37), ACEBinder 2 (LEEQYKTFLDKFMHELEDLLYQL) (SEQ ID NO:38), and HIF1α-binder 1 (IEEQAKTFLDKFNGEELLRALDQVN) (SEQ ID NO:39). In various embodiments, HiF1αBINDER has the following sequence: LEEQAKTFLDKFNGEELLRALQDQVN (SEQ ID NO:190) A non-limiting list of binding domains that display one or more alpha helical structures in the binding interface, including HIF1α-binder 1, can be found at the HippDB database at www.nvu.edu/projects/arora/hippdb, the sequences described therein are incorporated herein by reference as of the date of filing. Additional examples may include: HUMAN GLUTATHIONE S-TRANSFERASE P1-1, COMPLEX WITH TER117, chains A or B (pdb: 10GS) or ANTAGONIST HIV-1 GAG PEPTIDES WITH HLA B8-HIV-1 GAG PEPTIDE—HUMAN IMMUNODEFICIENCY VIRUS 1 chains A, B, or C (pdb: 1AGB), the sequences of which are incorporated herein by reference from PDB (www.resb.org) as of the date of filing. The X3 block may comprise, consist essentially of, or consist of any portion of any of the foregoing sequences.
Provided are various MAPs. The MAPs may include the sequences the sequence GSACELAATATATATATATAACG (SEQ ID NO:102) or GSASELAATATATATATATAASG (SEQ ID NO:103). Non-limiting examples of MAPs comprise, consist essentially of, or consist of the following:
The proteins may be expressed in a different vector that does not necessarily bear the N-terminal histidine tag or its linker to the X1 block. Depending upon whether the sequence bears a N-terminal histidine tag and which vector is used for cloning, the N-terminal sequence of the polymer carrier can vary. Thus, in various examples, the MRGSHHHHHH (SEQ ID NO:119) or MRGSHHHHHHGSASELAATATATATATATAASG (SEQ ID NO:120) or MRGSHHHHHHGSASELAATATATATATATAACG (SEQ ID NO:121) or any portion of SEQ ID NOs:119-121 is optional in any of the aforementioned sequences. Further, any residual amino acids from expression and sequencing may also be deleted.
In various examples, a protein of the present disclosure has 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% homology with any of the sequences described herein (including sequences with and without a His tag and/or sequence portions from a cloning vector) or may comprise, consist essentially of, or consist of any portion of any one of the sequences of the present disclosure. Proteins of the present disclosure may be longer than the sequences described herein and comprise the sequences described herein. The proteins may further comprise additional amino acids, which may naturally occurring amino acids, or may be a mixture of naturally occurring and non-naturally occurring amino acids.
The molecular weight of the proteins of the present disclosure can vary depending upon the number of blocks and the number of amino acids in the blocks. For example, the molecular weight can be from about 10,000 Da to about 150,000 Da as a self-assembled protein or 6,000 to 20,000 Da as a monomeric unit. For example, the molecular weight of the self-assembled protein can be about 62 kDa.
For expression of the proteins, the nucleic acid sequences encoding the carrier protein may be inserted into a recombinant vector, which may be plasmids, viruses or any other vehicle known in the art that has been manipulated by the insertion or incorporation of the nucleic acid sequences encoding the chimeric peptides of the invention. The recombinant vector typically contains an origin of replication, a promoter, as well as specific genes that allow phenotypic selection of the transformed cells. Vectors suitable for use in the present disclosure include, but are not limited to, the T7-based expression vector for expression in bacteria or viral vectors for expression in mammalian cells, baculovirus-derived vectors for expression in insect cells, and cauliflower mosaic virus (CaMV), tobacco mosaic virus (TMV), and other vectors.
The proteins of the present disclosure may be prepared via solid phase peptide synthesis (SPPS) using fluorenylmethoxycarbonyl-based (Fmoc-based) chemistries or tert-butyloxycarbonyl (Boc) chemistries. The proteins may be prepared by a combination of SPPS and ligation techniques (e.g., native chemical ligation, Staudinger ligation, and the like).
The proteins of the present disclosure may be prepared via purification using a Co2+ charged affinity chromatography column under denaturing conditions (i.e. 6 M urea in purification buffer) followed by a stepwise dialysis consisting first of a 3 M urea (or other denaturing agent) 5 L buffer bucket, followed by a 1.5 M urea, and 0.75 M Urea (in buffer). The dialysis may then be continued for six buckets in buffer. Following the protein may then be separated from remaining impurities using a size exclusion chromatography column in the monomeric or other oligomerization states.
Depending on the vector utilized, any of a number of suitable transcription and translation elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etcetera, may be used in the expression vector. Such construction of expression vectors and the expression of genes in transfected cells can involve the use of molecular cloning techniques (for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo recombination/genetic recombination), bacterial systems for the expression of vectors, yeast systems with constitutive or inducible promoters, insect systems, prokaryotic and eukaryotic systems using transfection or co-transfections of DNA vectors, transgenic animals using for example viral infection, and embryonic stem cells. Methods and procedures for using and applying such vectors are widespread in publications and are known or easily obtainable by persons of ordinary skill in the art.
In one aspect, the present disclosure provides compositions suitable for delivering MAPs (e.g., ACE-MAPs and/or H-MAPs) to individuals. The compositions comprise the MAPs (e.g., ACE-MAPs and/or H-MAPs) disclosed herein in suitable carriers. Suitable carriers for use in such compositions are known in the art. Examples of suitable carriers for administration include water, saline solution, buffer solutions such as phosphate buffers, glycine solutions. Suitable carriers for in vitro use include all of the above and standard culturing media (e.g., DMEM and the like), with or without serum, such as fetal bovine serum or serum-free define media.
In one embodiment, suitable carriers include a diluent, adjuvant, excipient, or other vehicle with which the present complexes may be administered to an individual. The formulations may be in an injectable form (for administration via any of the standard injectable routes) to an individual. The individual may be a human being or a non-human animal. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, including sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; phosphate buffer solutions; and other non-toxic compatible substances employed in pharmaceutical formulations. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. Some examples of compositions suitable for mixing with the agent can be found in: Remington: The Science and Practice of Pharmacy (2012) 22nd Edition, Philadelphia, PA Lippincott Williams & Wilkins. In one embodiment, the agent is substantially purified (e.g., substantially free from substances that limit its effect or produce undesired side-effects).
In an embodiment, the compositions may be formulated for topical, transdermal, or mucosal use. Such formulations include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. The components may be mixed under sterile conditions with a pharmaceutically-acceptable carrier, and with any preservatives, buffers, or propellants which may be required. The ointments, pastes, creams and gels may contain additional excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof. Topical powders and sprays can also contain additional excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane. In one embodiment, a 3D collagen based matrix may be used. In one embodiment, transdermal patches may be used. These have the added advantage of providing controlled delivery to the body. Such dosage forms can be made by dissolving or dispersing the agent in the proper medium. Absorption enhancers can also be used to increase the flux of the active ingredient across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the active ingredient in a polymer matrix or gel. In one embodiment, the compositions are applied to dermal patches, bandages, gauges or other similar materials that can be directly applied to a desired area.
In one aspect, this disclosure provides a method of treating a SARS-CoV-2 infection or a severe (e.g., requiring hospitalization or virus-targeted medication) SARS-CoV-2 infection, also referred to herein as COVID-19 infection in a subject comprising administering to the subject an effective amount of a composition comprising one or more ACE-MAP proteins described herein. The composition may be administered once or multiple times, over a period of days, weeks or months. For example, the multiple doses of the composition may be administered with a suitable period in-between, such as days, weeks or months, and/or may be administered on an annual or any other periodic manner. The compositions may be delivered by any suitable route of administration, including oral, intraperitoneal, intramuscular and the like. Suitable dosages of the compositions may be administered to subjects who have contracted the SARS-COV-2 virus. The subjects may be symptomatic or asymptomatic. The therapeutic dosages may be combined with other therapies, including antibody therapy, steroids, anti-viral, anti-inflammatory and any other therapy.
In one aspect, this disclosure provides a method of preventing or reducing the severity of a SARS-CoV-2 infection in a subject comprising administering to the subject an effective amount of a composition comprising one or more ACE-MAP proteins described herein. The composition may be administered once or multiple times, typically over a period of days. The compositions may be delivered by any suitable route of administration, including oral, intraperitoneal, intramuscular and the like. Suitable dosages of the compositions may be administered to subjects who are considered to be at risk of contracting the SARS-COV-2 virus. Such subjects may include those who have come in contact with an infected individual (someone who has tested positive for COVID-19), or who are otherwise considered to be at a higher risk (e.g., immunocompromised individuals). For prophylactic use, the compositions may be administered to subjects who are symptomatic but testing as COVID negative, or who may be asymptomatic and COVID-testing negative. The prophylactic dosages may be combined with other prophylactic applications, such as vaccines and the like.
The present compositions can be effectively used for the prevention, treatment, reducing the severity of, or detection of different strains of SARS-COV-2. For example, the present proteins were found to be effective for the delta variant of the SARS-COV-2. In various examples, the present proteins and compositions may be used for prevention, treatment, reducing the severity of, or detection of alpha (e.g., B.1.1.7 and Q lineages), beta (e.g., B.1.351 and descendent lineages), delta (e.g., B.1.617.2 and AY lineages), gamma (e.g., P.1 and descendent lineages), epsilon (e.g., B.1.427 and B.1.429 lineages), eta (e.g., B.1.525), iota (e.g., B.1.526), kappa (e.g., B.1.617.1), 1.617.3, mu (e.g., B.1.621, B.1.621.1), and zeta (e.g., P.2).
The treatment dose of the composition may be in a range of 10−5 to 104 μmol/kg/day (μmol of drug per kg body weight per day) including all 1×10−6 μmol/kg/day values and ranges therebetween. For example, the dose comprises 1×10−6 μmol/kg/day to 104 μmol/kg/day of protein. In embodiments, the dose may comprise 1×10−6 to 100×10−6 μmol/kg/day (e.g., 1×10−6 to 100−6) or 10−6 to 50×10−6 μmol/kg/day (e.g., 10×10−6 to 50×10−6) or 5×10−6 to 10−6 μmol/kg/day (e.g., 5×10−6 to 10×10−6) or 1×10−6 to 10×10−6 μmol/kg/day or about 5×10−6 μmol/kg/day of protein.
In an aspect, the present disclosure provides a method for treating a subject in need of treatment that has or is suspected of having cancer, comprising administering to the subject an effective amount of a composition comprising one or more H-MAP proteins described herein. The composition may be administered once or multiple times, typically over a period of days. The compositions may be delivered by any suitable route of administration, including, but not limited to, parenteral, mucosal, topical, catheter-based, oral, intravenous, or transdermal means of delivery, or the like. Parenteral delivery can include, for example, subcutaneous, intravenous, intramuscular, intraperitoneal, intercranial, intra-arterial delivery, which may be injection into the tissue of an organ.
In various embodiments, the cancers are cancers associated with and/or affected by HIF1α, p53·mdm2, Bcl-xL/Bak, and the like.
Various cancers may be treated via a method of the present disclosure. Non-limiting examples of cancers include leukemia, lung cancer (e.g., non-small cell lung cancer), dermatological cancers, premalignant lesions of the upper digestive tract, malignancies of the prostate, malignancies of the brain, malignancies of the breast, colon cancer, solid tumors, melanomas, and the like, and combinations thereof.
A subject in need of treatment may be a human or non-human mammal. Non-limiting examples of non-human mammals include cows, pigs, mice, rats, rabbits, cats, dogs, other agricultural animal, pet, service animals, and the like.
The treatment dose of the composition may be in a range of 10−5 to 104 μmol/kg/day (μmol of drug per kg body weight per day) including all 1×10−6 μmol/kg/day values and ranges therebetween. For example, the dose comprises 1×10−6 μmol/kg/day to 104 μmol/kg/day of protein. In embodiments, the dose may comprise 1×10−6 to 100×10−6 μmol/kg/day (e.g., 1×10−6 to 100−6) or 10−6 to 50×10−6 μmol/kg/day (e.g., 10×10−6 to 50×10−6) or 5×10−6 to 10−6 μmol/kg/day (e.g., 5×10−6 to 10×10−6) or 1×10−6 to 10×10−6 μmol/kg/day or about 5×10−6 μmol/kg/day of protein.
In an aspect, the present disclosure provides a method for treating a subject in need of treatment that has or is suspected of having a disease or viral infection, comprising administering to the subject an effective amount of a composition comprising one or more MAP proteins described herein. The composition may be administered once or multiple times, typically over a period of days. The compositions may be delivered by any suitable route of administration, including, but not limited to, parenteral, mucosal, topical, catheter-based, oral, intravenous, or transdermal means of delivery, or the like. Parenteral delivery can include, for example, subcutaneous, intravenous, intramuscular, intraperitoneal, intercranial, intra-arterial delivery, which may be injection into the tissue of an organ.
Various diseases or viral infections may be affected by a method of the present disclosure. For example, any disease or viral infection that involves a protein-protein interaction that involves an alpha-helical epitope may be affected. An example of such a disease is Parkinson's Disease. Examples of viruses include, but are not limited to, HIV.
A subject in need of treatment may be a human or non-human mammal. Non-limiting examples of non-human mammals include cows, pigs, mice, rats, rabbits, cats, dogs, other agricultural animal, pet, service animals, and the like.
The treatment dose of the composition may be in a range of 10−5 to 104 μmol/kg/day (μmol of drug per kg body weight per day) including all 1×10−6 μmol/kg/day values and ranges therebetween. For example, the dose comprises 1×10−6 μmol/kg/day to 104 μmol/kg/day of protein. In embodiments, the dose may comprise 1×10−6 to 100×10−6 μmol/kg/day (e.g., 1×10−6 to 100−6) or 10−6 to 50×10−6 μmol/kg/day (e.g., 10×10−6 to 50×10−6) or 5×10−6 to 10−6 μmol/kg/day (e.g., 5×10−6 to 10×10−6) or 1×10−6 to 10×10−6 μmol/kg/day or about 5×10−6 μmol/kg/day of protein.
In an aspect, the present disclosure provides uses of ACE-TAP (MAP) in diagnostics.
During infection by SARS-CoV-2, the spike (S) protein on the virus surface recognizes the peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE 2) of the host (Yan et al., Science 2020, 367 (6485), 1444-1448). Specifically, the trimeric S protein undergoes a structural rearrangement that facilitates the fusion of the viral membrane to the host cell membrane, enabling the virus to inject its RNA (Wrapp et al., Science 2020, 367 (6483), 1260-1263). The S1 subunit receptor binding domain (RBD) can present itself in the up or down conformation via a hinge-like motion. In the up state, the receptor is accessible and able to interact with ACE 2. Structural studies reveal that the N-terminal alpha helix of ACE 2 receptor is critical to binding S1 RBD (Wrapp et al., Science 2020, 367 (6483), 1260-1263). The SARS-CoV-2 RBD·ACE 2 interface possesses 17 hydrogen bonds and 1 salt bridge (
Rather than relying on a PCR-based test that requires specialized equipment for identifying SARS-CoV-2 or detecting antibodies from individuals who have recovered, the present disclosure provides a lateral-flow approach that relies on protein-protein interactions between the SARS-CoV-2 S protein and ACE protein on human cells. The probes used for the present LFAs can be antibodies that recognize various protein markers/antigens or other antibodies. Because they employ capillary force on a polymeric strip with detection zones, they are: (i) easy-to-use; (ii) eliminate the need for specialized equipment; and (iii) carried out as a single step, reducing the amount of sample handling. For detection, the present disclosure uses multivalent molecules to tag Covid-19/shedding virus or to antibodies produced in response to recovery of infection. Furthermore, the present rapid tests can be used as at-home tests that do not require skilled laboratory personnel to perform which reduces the costs of the test and makes it widely accessible for low income communities.
Generally, LFA test strips contains a test pad as the function zone, and absorbance pad as the support. Test pads can be comprised of or predominantly comprised of nitrocellulose due to its excellent capillary properties and ease of immobilization. The absorbance pad can vary and in an embodiment, can comprise polyvinyl chloride and, optionally, filter paper. The immobilization of protein molecules is based on physical absorption. Dipping, drying and spraying can be used to functionalize the testing pad. For insoluble molecules or hydrophobic substrate, binder-assisted immobilization can be effective for radioactive or enzyme labels. Gold colloid test strips can also be used in LFAs, whereby antibodies can be directly linked to gold nanoparticles, which can be loaded onto the nitrocellulose substrate.
The present design relies on the self-assembly of a coiled-coil domain of the cartilage oligomeric matrix protein (C). In an embodiment, the disclosure provides a nanomaterials in which we fuse a part or the entirety of the ACE2 region that recognizes the spike proteins to produce ACE-tagged assembled protein (ACE-TAP). In an embodiment, the disclosure provides a nanomaterial in which we fuse a part or entirety of the receptor binding domain (RBD) of the COVID-19 S-protein to yield S-tagged assembled protein (S-TAP) as multivalent detectors for corona virus and human antibody respectively. (
A multiplex lateral flow test strip (MLFTS) can be used as the detection format for the present LFA design. MLFTS can reduce production costs and improve detection efficiency by providing multiple test types on a single strip, each line containing immobilized antibodies or other binding partners that targets specific species. In an embodiment, the present MLFTS comprises, consists essentially of or consists of (i) sample pad where the sample blood or sputum or other biological sample is deposited; (ii) conjugation pad infused with ACE-TAP and S-TAP. The ACE-TAP or S-TAP are not immobilized to the conjugation pad. Rather, they are present to allow for binding to the virus or antibody and then move through the strip. The ACE-TAP and S-TAP may be physically adsorbed to the conjugation pad; (iii) a test pad with multiple lines to serve as virus, IgM, IgG antibodies and control tests; (iv) an adsorption pad; and (v) a back support or substrate (
The present MFLTS design can comprise cellulose-based materials. As the most abundant recyclable and commercially available biopolymer material for POC diagnostic tests, they have the advantage of low-cost, high thermal stability, porosity, sorption capabilities and biocompatibility. MLFTS produced with nitrocellulose membranes (NC), the key material for the test pads, and cellulose pads have been employed for numerous POC testing, including ZIKA and Covid-19 (Tsai et al., Sci Rep 2019, 9 (1), 15679). Pore size, porosity, surface groups' interaction between biomolecules and nanometals, and surface area of membrane pads can be modified to improve adsorption of ACE-TAP and S-TAP on test lines of immobilized biomolecules on substrate surface (analyte to pore ratio). For depositing the materials, inkjet printing (Taylor et al., Journal of Power Sources 2007, 171 (1), 101-106) and spraying assembly (Weng et al., Advanced Functional Materials 2018, 28 (44), 1803360) may be used. In an embodiment, inkjet printing can be applied to produce narrow test lines while spraying can be employed for the large area conjugation pads.
In an embodiment, the coiled-coil domain of cartilage oligomeric matrix protein (ccCOMP, COMPcc, or C) fused to a variety of proteins can be used. C is an α-helical homopentamer, which forms a hydrophobic pore (7.3 nm×0.2-0.6 nm) capable of interacting with variety of small molecules (
Some variants are:
Additional examples are provided in Table 1 below.
C can be engineered to exert specificity for target compounds. Using C, fusion molecules, termed herein as “tagged assembled protein” (TAP) can be generated in which the ACE or S proteins are engineered C-terminal to C yielding ACE-TAP and S-TAP, respectively. C harbors the ability to encapsulate small molecules and in an embodiment, a colorimetric marker can be entrapped/encapsulated for detection purposes. Colorimetric markers are known in the art. Examples include curcumin, Nile red, 4,4′-Dianilino-1,1′-Binaphthyl-5,5′-Disulfonic Acid, Dipotassium Salt, (Bis-ANS), 1-anilinonaphthalene-8-sulphonic acid (1,8-ANS), 8-anilino-1-naphthalene sulfonic acid (ANS), 5-dimethylaminonaphthalene-1-(N-2-aminoethyl)sulphonamide (DANSen), 1,6-Diphenyl-1,3,5-hexatriene, or 6-propionyl-2-(N,N-dimethylamino)naphthalene (PRODAN). For example, curcumin can be used as a colorimetric marker for detection. At the N-terminus, a hexahistidine can be integrated for purification and tagging with gold nanoparticles (AuNPs) for an added method of detection (
MLFTS bearing ACE-TAP and S-TAP as the probes for detecting both Covid-19 virus and shed virus particles as well as antibodies in a single test. In an embodiment, the test will bear a sample pad, followed by a conjugation pad that contains the ACE-TAP and S-TAP bearing AuNPs. Downstream of the conjugation pad (in terms of the lateral flow), four detection strips bearing immobilized: ACE-TAP without AuNP for virus capture; anti-IgM for detection of the first antibody produced against Covid-19; anti-IgG for detection of the optimized antibody produced against Covid-19; and anti-His tag antibody for capturing free ACE-TAP and S-TAP bearing AuNPs (
The TAP and MLFTS designs and integration are used in the present disclosure to produce an all-in-one cellulose-based test. Advantages for TAP include that the multi-functional protein-based nanomaterials can: 1) strongly bind to SARS-CoV-2 via the multivalent display of the ACE 2 sequence; 2) recognize and strongly bind to human serum antibodies via the multivalent display of the S sequence; 3) serve as a colorimetric tag via curcumin probe and AuNP binding; and 4) provide insight into sensitivity and selectivity of TAP surface display of proteins. Advantages for MLFTS design include that the inkjet/spray printing technology can be a universal method for fast protein loading where it can reach the detection limit of 25 mIU/mL.
Exemplary sequences for C (COMPcc) domain/variants, linkers (such as between S or ACE proteins and the C-terminal of COMPcc, interacting regions of S and ACE proteins for binding, are provided in Table 1 below.
The present technology will aid in decreasing community spread of infection and will help mitigate the negative economic impacts of the COVID-19 pandemic. This will provide robust health information to individuals and the world alike so as to hone in contact tracing and prevent a second proliferation of the virus. Reducing spread will also decrease the acuity of COVID-19 cases and lessen the burden of a high influx of patients on the healthcare system and level the supply of high-demand life-saving equipment like respirators. This will be especially impactful in low resource communities where current testing technologies are unaffordable.
While the present disclosure provides specific reference to COVID-19 virus and antibodies, the present MLFTS can be used for detection of any virus and its antibodies in a single test.
The following Statements provide various embodiments of the present disclosure:
or a sequence having at least 85% homology with any of the aforementioned sequences.
or a sequence having at least 85% homology with any of the aforementioned sequences.
The following examples are provided as illustrative examples and are not intended to be restrictive in any way.
Described are the results of an ACE2 fused, multivalent assembled protein (ACE-MAP) where the N-terminal alpha helix (ACEBINDER) is joined with a computationally designed kinked linker to C leading to high binding affinity of SARS-CoV-2 RBD for future applications as a biosensor or therapeutic. ACE-MAP joins only one other reported thermostable antibody-mimics with picomolar binding affinity to the SARS-CoV-2 RBD as a potential therapeutic for COVID-19.
Chemically competent AFIQ E. coli cells were gifted from David Tirrell at California Institute of Technology. ACE-MAP/pQE30 plasmid was cloned and purchased from Eurofins. Bacto-tryptone, sodium chloride, yeast extract, tryptic soy agar, ampicillin, chloramphenicol, sodium phosphate dibasic anhydrous (Na2HPO4), sodium hydroxide (NaOH), dextrose monohydrate (D-glucose), magnesium sulfate, calcium chloride (CaCl2)), manganese chloride tetrahydrate (MnCl2·4H2O), cobaltous chloride hexahydrate (CoCl2·6H2O), isopropyl β-D-1-thiogalactopyranoside (IPTG), Pierce bicinchoninic acid (BCA) assay kit, Pierce snakeskin dialysis tubing 3.5 K MWCO, sodium dodecyl sulfate, Pierce C18 tips with 10 μL bed, bissulfosuccinimidyl suberrate (BS3), ascorbic acid, Immulon 4 HBX ninety-six well plates, Nunc ninety-six well plates, Dulbecco's Modified Eagle medium (DMEM), Nunc EasYFlask Cell Culture Flasks, Quant-iT PicoGreen dsDNA Assay Kit, IL-6 Mouse ELISA Kit, Pierce High Capacity Endotoxin Removal Spin Columns, and ELISA wash buffer (30×) were acquired from Thermo Fisher Scientific. The twenty naturally occurring amino acids, thiamine hydrochloride (vitamin B), dimethylsulfoxide (DMSO), and 3,3′,5,5′-tetramethylbenzidine (TMB) were purchased from Sigma Aldrich. Hydrochloric acid (HCl), Coomassie® Brilliant Blue G-250, and milk powder (non-fat, skimmed) were purchased from VWR. HiTrap Q HP 5 mL columns for protein purification were purchased from GE Healthcare Life Sciences. Macrosep and Microsep Advance Centrifugal Devices 3K molecular weight cutoff (MWCO) and 0.2 μm syringe filters were purchased from PALL. Acrylamide/bis solution (30%) 29:1, Mini Trans-Blot filer paper, Trans-Blot Transfer Medium (nitrocellulose membrane), and natural polypeptide sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) standard were purchased from Bio-Rad, and Dulbecco's phosphate buffered saline were purchased from ATCC.
ACE-MAP protein was expressed in phenylalanine auxotrophic AFIQ E. coli cells. pQE30/ACE-MAP plasmid was transformed via heat shock in chemically competent AFIQ cells. Transformed cells were grown for 14-16 hours at 37° C. on tryptic soy agar plates containing 200 μg/mL ampicillin and 35 μg/mL chloramphenicol. A single colony was inoculated in 16 mL supplemented M9 minimal medium (0.5 M Na2HPO4, 0.22 M KH2PO4, 0.08 M NaCl, and 0.18 M NH4Cl) containing all 20 natural amino acids (100 μg/mL), ampicillin (200 μg/mL), chloramphenicol (35 μg/mL), vitamin B (35 μg/mL), D-glucose (100 μg/mL), magnesium sulfate (1 mM), calcium chloride (0.1 mM), and trace metals (0.02% v/v) and incubated at 37° C. and 350 rpm for 16 hours. Following, 8 mL of the starter culture was added to 200 mL of supplemented M9 medium and incubated at 37° C. and 350 rpm until the optical density at 600 nm (OD600) reached 0.7. Protein expression was induced with 200 μg/mL IPTG and incubated at 37° C. and 350 rpm for 3 hours. After the expression, cells were harvested by centrifugation at 5000×g at 4° C. for 20 minutes in an Avanti J-25 centrifuge (Beckman Coulter) and stored at −20° C. until purification. Expression of ACE-MAP was confirmed via 12% SDS-PAGE (
Cell pellets were thawed and resuspended in Buffer A (50 mM Tris HCl, 250 mM NaCl, 6M urea, pH 8.0). Cells were lysed via Q500 probe sonicator (QSonica) at 65% amplitude, pulse on for 5 seconds and off for 30 seconds for a total of 2 minutes. The lysed cells were centrifuged at 11,000×g for 45 min at 4° C. to remove cell debris (Beckman Coulter). The supernatant was removed and purified using a syringe-pump driven IMAC Q Sepharose high performance 5 mL column (HiTrap Q HP 5, GE Health Sciences) charged with CoCl2. Protein was eluted from the column using a gradient (0-100%) of Buffer B (50 mM Tris HCl, 250 mM NaCl, 6 M urea, 500 mM imidazole, pH 8.0) (
The plasmid used for protein expression and purification of SARS-CoV-2 RBD was constructed by insertion of a secretion signal, the coding sequence of a 5A tag, RBD, and a 6×His tag into an expression vector pVRC8400 (kindly provided by the Vaccine Research Center, National institute of Health). The gene construct was codon optimized for mammalian cell expression and synthesized by GenScript. The plasmid was transiently transfected into HEK293S cells for 5 days. Cell supernatants were filtered through 0.22-μm filters, loaded onto Ni-nitrilotriacetic acid (NTA) beads, and proteins were eluted with 600 mM imidazole. The elution was then dialyzed in PBS, flash frozen and stored at −80° C.
Secondary structure of ACE-MAP was measured using the Jasco J-815 CD spectrometer with a PTC-423S single position Peltier temperature control system. Wavelength scans of ACE-MAP (10 μM) were performed from 195 to 250 nm at 1 nm step sizes. Temperature scans were performed from 25° C. to 85° C. at 1° C. step sizes. The mean residue ellipticity (MRE) and melting temperature (Tm) were calculated as described in previous studies. The secondary structure content (α-helicity, β-content, and unordered structure) was predicted with CONTIN/LL software.
Addition of 3 mM bis(sulfosuccinimidyl) suberate (BS3) to a 10 μM concentration of ACE-MAP in PBS pH 7.4 was performed for chemical crosslinking to assess oligomerization. The reaction was allowed to incubate at room temperature and 300 rpm for 3 hours in the dark on an Eppendorf Thermomixer C. The reaction was then quenched using 25 mM Tris HCl at pH 7.5 and sampled into a 12% SDS-PAGE and oligomerization was confirmed using Western Blot analysis. To detect and analyze the oligomer bands, Amersham Imager 680 and corresponding analysis software (Cytiva Life Sciences) were used to detect and analyze relative intensities of oligomer bands.
The ELISA protocol was adapted from previously established protocols. A ninety-six well plate was coated overnight at 4° C. with 50 μL per well of a 2 μg/mL solution of SARS-CoV-2 RBD. The next morning, the coating solution was removed and 100 μL per well of 3% non-fat milk prepared in PBS with 0.1% Tween 20 (TPBS) was added to the plate at room temperature (RT) for 2 hours as blocking solution. The blocking solution was removed and 100 μL of serial dilutions of ACE-MAP, C, and ACE2 proteins were added to the plates for 2 hours at RT. The plates were washed three times at 200 μL volumes using 0.1% TPBS. Approximately 100 μL of a 1:3000 anti-Histag horseradish peroxidase (HRP) conjugated secondary antibody (Sino Biological) was prepared in 0.1% TPBS and added to each well for 1 hour. Plates were then washed three times with 200 μL of 1×ELISA wash buffer (Thermo Scientific) and then air dried in a hood. While drying, TMB solution was prepared as described by Sigma Aldrich protocol. 1 mg/mL TMB was prepared in DMSO and then added to 0.05 mM citrate-phosphate buffer with 0.01% hydrogen peroxide (0.01%). Once completely dry, 100 μL of 3,3′,5,5′-tetramethylbenzidine (TMB) solution was added to the plates for 10 minutes. To quench the reaction, 50 μL of 3M HCl was added to the plates. Absorbance at OD450 was immediately read using a microplate reader (BioTek Synergy H1).
RAW 264.7 Mouse Macrophage cell line were incubated in DMEM media (Thermofisher). The adherent cells were grown to 70-80% confluence in a flask incubated at 37° C. ACE-MAP was simultaneously subjected to Endotoxin Removal using Pierce High Capacity Endotoxin Removal Spin Columns (Thermofisher). 10,000 cells were then diluted in serial dilutions of ACE-MAP (starting at 500 ng/uL) in 200 μL of DMEM and plated on three 96-well plates. For three days, cells were harvested from each plate at 24, 48, and 72 hour time points and counted using Quant-iT PicoGreen dsDNA Assay Kit (Thermofisher). Mouse IL-6 was detected using Invitrogen IL-6 Mouse ELISA Kit (Thermofisher). Mouse IL-6 concentration was calculated from a Mouse IL-6 standard curve (Thermofisher) and normalized to the control-relative cell count.
Initial structure of C protein was taken from PDBID 3V2P and the 23-residue “binder protein” was taken from residues 21-44 of chain B in PDB 6M17, which was shown to have micromolar affinity to SARS-CoV-2 RBD. In order to fuse the C and binder protein, a series of linker proteins consisting of [EAAAK]n (SEQ ID NO:176), (n=3, 4, 5) motif were designed computationally using Rosetta (data not shown). Initial monomeric structure of ACE-MAP was made in PyMOL (Schrodinger). Using the symmetry information taken from PDBID 3V2P and Rosetta's symmetric modeling protocol a pentameric structure was produced and relaxed with FastRelax and REF2015 score function. The first five residues in the linker region were manually designed to provide a kink at the junction of C domain and linker, which provided an opening for binding to multiple S-RBDs (
Structural studies of ACE-MAP were performed via circular dichroism spectroscopy. Wavelength scans performed at 25° C. revealed a double-minima of −17,000±700 deg·cm2·dmol−1 208 nm and −16,000±600 deg·cm2·dmol−1 at 222 nm indicative of helical conformation (
To assess the extent of n-oligomerization due to the coiled-coil domain, BS3 crosslinking of ACE-MAP was employed. After running the sample on a 12% SDS-PAGE, the gel was subjected to western blot analysis and imaged (
The binding affinity of ACE-MAP was tested against SARS-CoV-2 RBD as described previously (
The elicited immune response of ACE-MAP to RAW 264.7 cells were tested for IL-6 concentration each day for three days (
Typically, overnight to 48-hour incubation of cells after stimulation of the test protein is used to assay early phase cytokine response for immunogenicity and IL-6 has been shown to be a viable analog biomarker for presence of an immune response. ACE-MAP appears to trigger an acute immune response (<20 pg IL-6/pg dsDNA) after one day stimulation of RAW 264.7 cells (
A coiled-coil self-assembled fusion protein capable of binding to SARS-CoV-2 RBD at picomolar affinity is described herein. Its characterization has revealed insights into the utility of multivalent alpha-helical binders for this and future coronavirus variants. Several proteins and antibodies have been recently generated to bind to SARS-CoV-2 RBD. These proteins tend to use either mammalian expression systems and/or be >140 kDa. The protein binders that have been computationally designed to increase the avidity to SARS-CoV-2 based on ACE2 possess Kd values ranging from 970 nM to 100 pM. E. coli expression systems have the unparalleled advantage of low cost, rapid growth, and good productivity; however, it is a host that is out of reach for many recombinant proteins >60 kDa, and especially antibodies, that require post-translational modifications. While ACE-MAP exhibits picomolar binding affinity to SARS-CoV-2 RBD like antibodies, it can be expressed in E. coli and is significantly smaller in size-12 kDa as a monomer (62 kDa as a pentamer). The present approach described herein fundamentally differs from such prior work as the tethering or multivalency is part of the design from the onset.
The present protein ACE-MAP can be used as a non-immunogenic therapeutic. ACE-MAP demonstrates insignificant immune response until Day 3 of incubation at the recommended FDA sensitivity of 100 ng/mL, the lowest concentration at which a therapeutic may be associated with clinical events, with p-values of 0.44, 0.06, and 0.001 for Day 1, Day 2, and Day 3, respectively using an unpaired t-test with the control. This reveals the benefit of using ACE-MAP as a protein therapeutic platform.
Notably, the fusion of ACEBINDER by a kinked linker has resulted in a similarly thermostable protein relative to its C counterpart. In comparison, C with all cysteine residues (C48 and C54) mutated to serines (denoted as CSS) reduces the melting temperature of CSS to 45° C. Thus, despite the reduced helical secondary structure, likely due to the kinked region of ACE-MAP reducing the fraction of coiled-coil structure contribution, ACE-MAP maintains a Tm higher than CSS and a Tm more characteristic to wild-type C. Interchain disulfide-bond formation is a property only characteristic of a parallel n=5 oligomer revealing that similarly ACE-MAP is likely to exist in the pentameric coiled-coil conformation. In addition to the pentamerization after BS3 crosslinking, we deduce that the multivalency created by ACE-MAP through oligomerization of the C domain is responsible for the increased binding affinity in comparison to ACEBINDER and ACE2. Also of importance, is that that the strong alpha-helical structure of C may lend itself as a scaffold that stabilizes the ACEBINDER region to become functional against the SARS-CoV-2 RBD. The structural data shown here elucidates this picture well with previous helical content prediction of the ACEBINDER domain noted to be just 6% and optimization of the domain's helicity only creates a modest improvement in binding affinity. The picomolar binding affinity and stability at high temperatures bodes well for future studies into its applications as a stable biosensor or therapeutic.
Using a modified helical binder in ACE-MAP-2 results in improved performance over predecessor ACE-MAP-1 in binding affinity against SARS-CoV-2 RBD. Most significantly the modifications resulted in no change to the biosynthesis process and boasts the interchangeability of the ACEBINDER region to scaffold other binders for SARS-CoV-2 or even other targets such as HIF1α-MAP. Where the ACE-MAP-2 binding domain (ACEBINDER) alone shows a 15-fold improvement over ACE2, ACE-MAP-2 results in a 50-fold improvement over ACE2 also signifying the effect of its multivalency in amplifying the ability to bind SARS-CoV-2 RBD.
ACE-MAP was biosynthesized, a small binder protein against SARS-CoV-2 RBD. ACE-MAP may be used as a neutralizing therapeutic or diagnostic protein for immunoassay testing. Fusion of ACEBINDER to C was shown via a computationally designed kinked linker has created a protein with increased thermostability compared to C and increased binding affinity through multivalency compared to just the ACEBINDER region as previously reported. ACE-MAP furthermore shows the utility of generating a PDM utilizing multivalency as the source of high affinity without further design techniques. The increased efficacy of the protein, low immunogenicity, and thermostability at room temperature indicates the utility of simple multivalent fusions. The high avidity of ACE-MAP to SARS-CoV-2 RBD by utilizing its target receptor, ACE2, reveals that ACE-MAP may be useful in a variety of rapid testing applications especially among the growing concern for SARS-CoV-2 mutant escape.
The following example provides description of using the proteins of the present disclosure.
As an example, blood (via finger prick) and/or sputum or spit or tear sample can be directly applied or collected and applied to the sample pad. The capillary force driving the fluids will determine how long it will incubate with the components. In general, it may take 15 minutes to process and detect results. No washing is needed since the flow occurs via capillary force.
The following example provides description of using the proteins of the present disclosure.
The PDM requires oxopiperazine functionalization and the binding affinity of the HIF1α OHM provides a 14-fold decrease in its ability to bind to p300. The reduced sensitivity of the PDM to its target is expected for a mimetic. For these reasons, the HIF1α CTAD represents a desirable candidate for incorporation into the MAP design to create HIF1α-MAP. Instead of imbuing structure through a post-expression chemical bond, the MAP is hypothesized to imbue the critical residues with the necessary alpha-helical secondary structure and thus provide it functionality to bind to p300. It was not expected that this strategy would provide an increased binding affinity or capability of reducing tumor volume should it have just been a function of an alpha-helical scaffold in comparison to the OHM PDM strategy. However, in addition to the MAP scaffold being of a multivalent self-assembly, it is hypothesized it would result in an improvement to the binding affinity.
Described is a scaffold that is inherently multivalent through the self-assembly of helical coiled-coils, which stabilize the helical structure of an immediately fused PPI recognition sequence as a rational approach to PDM stabilization. The multivalency of the protein provides a jump start in the race to increased affinity before undergoing its own evolutionary process, affinity maturation, to become a highly sensitive protein binder to a specific target. In this approach, a coiled-coil domain is used to not only induce α-helicity and structure to present the proper epitope for PPI, but also, it self-assembles into a multivalent pentamer that improves affinity rivaling that of the native protein of which the design is based—a deficit of current PDM strategies. Employing a scaffold based on the coiled-coil domain of cartilage oligomeric matrix protein (C), to the present disclosure provides new fusions or “multivalent assembled protein” (MAP) in which the helix bearing the crucial recognition residues is engineered C-terminal to C (
Innovation: PDMs have increasingly shown to be desirable candidates for the development of therapeutics that target PPIs. While they can show efficacy in binding their targets, the domains are both designed for a specific target and do not heavily improve on the binding affinity of the native complex. These deficiencies are buoyed by the current approaches to PDM design that include phenotypic or target-based screenings, and structure-based designs such as fragment-based design. These design approaches are inherently restrictive and are tailored for a specific PPI. To emphasize the advantage of facile research and development for PDMs, an emphasis must be made on creating more recyclable design strategies. Thus, the present disclosure provides has several innovations:
Described herein is a new strategy for the design of multivalent assemblies that can stabilize the helical epitope bearing the PPI recognition sequence with affinities that rival or exceed those of the natural protein on which the design was based. While several strategies have been explored as PDMs, all of them focus on the design of a monomeric scaffold that can be later tethered as a dimer or multimer to improve affinities. Although each of these strategies produced molecules that bind proteins, they still are unable to bind with affinities as strong as the natural parent protein.
Multivalent Approach for targeting PPIs. The present disclosure differs from other methods. Rather than focusing on designing a monomeric scaffold to target the PPI, multivalency is integrated at the onset of the design where a multimeric coiled-coil is employed to stabilize the helical epitope (
HIF1α has been the subject of recent research in PPIs because of the high percentage of α-helicity at the interface for multiple binding interfaces and when inhibited by helix mimetics, has shown to reduce tumor growth in animal models. Recently, key residues of the C-terminal transactivation (CTAD, aa 786-826) of HIF1α that interact with the cysteine-histidine rich 1 (CH1) domain of the coactivator protein p300 has been mimicked into an effective PDM using the oxopiperazine helix mimetics (OHM) strategy. OHMs employ chemical conjugation of the nitrogen atoms in neighboring backbone amides with an ethylene bridge to create a chiral scaffold to maintain a structure and thus function akin to proteins. This simple design uses just the twelve CTAD residues with a binding affinity of up to 530 nM—as compared to the full length CTAD of HIF1α with a binding affinity of 38 nM by tryptophan fluorescence assay. The OHM PDM significantly reduces HIF activity and down-regulated the expression of hypoxia-inducible genes and in vivo experiments reduces tumor volume by approximately 50%. The use of a PDM is well validated for the HIF1α·p300 complex, however, the PDM requires oxopiperazine functionalization and the binding affinity of the HIF1α OHM provides a 14-fold decrease in its ability to bind to p300. The reduced sensitivity of the PDM to its target is expected for a mimetic, which is inherently reductive from its native inspiration. For these reasons, the HIF1α CTAD represents a desirable candidate for incorporation into the MAP design to create HIF1α-MAP. Instead of imbuing structure through a post-expression chemical bond, the MAP would be expected to inherently imbue the critical residues with the necessary α-helical secondary structure and thus provide it functionality to bind to p300. It was not expected that this strategy would provide an increased binding affinity or capability of reducing tumor volume should it have just been a function of an α-helical scaffold in comparison to the OHM PDM strategy. However, in addition to the MAP scaffold being of a multivalent self-assembly, it is hypothesized an improvement to the binding affinity would occur.
Based on the preliminary data suggesting C and its kinked linker as a conduit for improved binding via multivalency and α-helical scaffolding, a 13-mer α-helical binding domain derived from HIF1α was be grafted to the solvent-exposed residues ACE-MAP to create HIF1α-MAP. Analogs of short α-helices of HIF1α have been shown to bind p300 and inhibit its binding to HIF1α, making the complex not only important for the research of in vivo modulation of hypoxia-inducible signaling but for validation of the MAP assemblies for binding domain flexibility.
To develop a first iteration of HIF1α-MAP, the ACE-MAP1/SARS-CoV-2 RBD scaffold was used as a rational starting pose in PyMOL (
HIF1α-MAP genetic sequence was constructed and cloned into PQE30. The resulting PQE-HIF1α-MAP1 was expressed in AFIQ E. coli cells. As described in the prior aim, cell pellets were thawed and resuspended in Buffer A and lysed via Q500 probe sonicator. The lysed cells were centrifuged and supernatant purified using a syringe-pump driven IMAC Q Sepharose high performance 5 mL charged with CoCl2. Protein was eluted using the same gradient (0-100%) of Buffer B. Elutions bearing pure protein were removed and dialyzed as before. The elutions will be then purified via SEC column on FPLC and HIF1α-MAP concentration was determined (
Surprisingly, HIF1α-MAP-1 (H-MAP-1) revealed a high affinity with a Kd of 8.08 pM to p300 in comparison to native HIF1α (Kd=380 pM) protein with a 47-fold improvement (
While the present invention has been described through illustrative embodiments, routine modification will be apparent to those skilled in the art and such modifications are intended to be within the scope of this disclosure.
This application claims priority to U.S. Provisional Application No. 63/282,487, filed on Nov. 23, 2021, the disclosure of which is incorporated herein by reference.
This invention was made with government support under grant numbers 1644681 and 2031364 awarded by the National Science Foundation and W911NF-19-1-0150 awarded by the Army Research Office. The government has certain rights in the invention.
| Number | Name | Date | Kind |
|---|---|---|---|
| 20130331465 | Montclare | Dec 2013 | A1 |
| Number | Date | Country | |
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| 20230280343 A1 | Sep 2023 | US |
| Number | Date | Country | |
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| 63282487 | Nov 2021 | US |
