Patent Application
20230174599
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 15, 2021, is named 081906-1245167-238310PC_SL.txt and is 22,858 bytes in size.
The decoy vs. antibody approach[1,2,3] is a fundamental shift in viral diagnostic strategy. Zoonotic endemic pandemic threats require a universal solution which protects against the steady pace of evolutionary mutational variants from an original wild type crossover virus. The current focus is on SARS-CoV-2, first seen in Wuhan. This decoy approach vs. antibody approach represents a standard which can be employed against future zoonotic events in antigen assay diagnostics.
Our invention creates high affinity human receptor decoys for diagnostics. It replicates the point of infection (ACE2 receptor) and detects the virus by directly capturing virions from solution with efficacy that will not degrade as the virus mutates from wildtype. Multivalency leads to a binding affinity which can be up to 1,000,000 times stronger than ACE2 alone, and which can lead to dramatic improvements in diagnostic sensitivity, lowering of detection thresholds, and expansion of time windows for detection. These proteins are environmentally stable and inexpensively produced in standard microbial expression systems, offering further advantages over antibodies in antigen based diagnostic assays.
In some embodiments, an amyloid fibril comprising a plurality of modified β solenoid protein (mBSP) monomers is provided, wherein the monomers are linked to a pathogen-binding protein. In some embodiments, the mBSP monomers are derived from an antifreeze protein[4].
In some embodiments, the antifreeze protein is a spruce budworm antifreeze protein. In some embodiments, the mBSP has the sequence shown in SEQ ID NO: 1 or a sequence at least 90%, 95%, or 98% identical to SEQ ID NO: 1.
In some embodiments, the antifreeze protein is a rye grass antifreeze protein. In some embodiments, the mBSP has the sequence shown in SEQ ID NO: 2 or a sequence at least 90%, 95%, or 98% identical to SEQ ID NO: 2.
In some embodiments, the antifreeze protein is a rhagium inquisitor antifreeze protein. In some embodiments, the mBSP has the sequence shown in SEQ ID NO: 3 or a sequence at least 90%, 95%, or 98% identical to SEQ ID NO: 3.
In some embodiments, mBSP is modified to remove an end cap that prevents amyloid aggregation.
In some embodiments, the amyloid fibril is modified to include at least one amino acid residue that promotes attachment of the fibril to a solid support, a nanoparticle, a biological molecule, or a second amyloid fibril.
In some embodiments, the amyloid fibril is attached to a solid support, a nanoparticle, a biological molecule, or a second amyloid fibril.
In some embodiments, the pathogen is a virus. In some embodiments, the virus is SARS-COV-2 or HBV or HCV.
In some embodiments, the amyloid fibril is linked to a solid support. In some embodiments, the solid support is absorbent. In some embodiments, the solid support is paper.
In some embodiments, the pathogen-binding protein comprises the N-terminal ACE2 helix-turn-helix (HTH) domain (e.g., SEQ ID NO: 4 or a sequence at least 90%, 95%, or 98% identical to SEQ ID NO: 4).
In some embodiments, the pathogen binding protein is linked to a detectable label In some embodiments, the detectable label changes signal depending on whether the pathogen-binding protein is binding the pathogen.
Also provided is a method of detecting the presence or absence of a pathogen in a biological sample. In some embodiments, the method comprises contacting a biological sample with the amyloid fibril as described above or elsewhere herein under conditions that allow the pathogen to bind to the pathogen binding protein if the pathogen is present; and detecting the presence or absence of binding of the pathogen to the amyloid fibril. In some embodiments, the amyloid fibril is linked to a detectable label that changes signal depending on whether the pathogen-binding protein is binding the pathogen, and detection comprises detecting signal from the detectable label. In some embodiments, the detecting comprises washing unbound components of the sample from the amyloid fibril and contacting the amyloid fibril, and bound pathogen if present, with a secondary binding agent that specifically binds to the pathogen, if bound to the amyloid fibril.
In some embodiments, the secondary binding agent is a β solenoid protein linked to a pathogen binding protein. In some embodiments, the secondary binding agent is linked to a detectable label. In some embodiments, the β solenoid protein comprises a sequence that prevents polymerization.
Also provided is clothing or protective equipment coated with the amyloid fibril as described above or elsewhere herein.
The term “β-solenoid protein” (BSP) refers to proteins having backbones that turn helically in either a left- or right-handed sense around the long axis of the protein from the N-terminus to the C-terminus to form contiguous β-sheets, and have regular geometric structures (triangles, rectangles, etc.) with 1.5-2 nm sides. The wild type (WT) BSPs do not undergo end-to-end polymerization to give cross β-fibrils due to natural capping features and/or structural irregularities on one or both ends. Examples of non-amyloidogenic WT-BSPs that can form amyloid fibrils upon modification include, one-sided antifreeze proteins (Tenebrio molitor AFP- Protein Database (PDB) Accession No. 1EZG), two-sided antifreeze (Snow Flea AFP- PDB 2PNE and 3BOI), rye grass AFP (PDB- 3ULT), three-sided “type II” left handed β-helical solenoid antifreeze proteins, for example from the spruce budworm (PDB 1M8N), three-sided bacterial enzymes (PDB 1LXA, 1FWY, 1G95, 1HV9, 1J2Z, 1T3D, 1THJ, 1KGQ, 1MR7, 1SSM, 2WLC, 3R3R, 1KRV, 3EH0, 3Q1X, 3BXY, 3HJJ, 3OGZ, 4M98, 4IHH (acyltransferases, γ-class carbonic anhydrases and homologs), three-sided motor proteins subunits (e.g., PDB 3TV0), a three-sided “type I” left handed β-helical enzyme ydcK from Salmonellae cholera (2PIG), four-sided proteins (PDB 2BM6, 2W7Z, 2J8I), four-sided pentapeptide repeat proteins (2G0Y and 3DU1), and 1XAT. The full sequence of each of these proteins is available from the Protein Database.
The term “modified β solenoid protein (mBSP)” (also referred to as mBSP monomer) refers to genetically engineered β solenoid proteins that allow for amyloid self-assembly. A mBSP monomer can be engineered to be any desired length and can be tailored to the particular application. In a typical embodiment, the monomer will comprise at least two beta sheet rungs (about 30-36 residues) and more often at least three rungs (about 45-54 residues). The typical size of a beta strand face is about 3-6 residues, including bends the edge size will usually not exceed 5-8 residues, which is a range of about 2-3.2 nm. A number of modifications can be used to allow for self-assembly. For example, many BSPs include end caps that can be removed to allow for amyloid self-assembly. For example, in the spruce budworm antifreeze protein, the endcap inhibiting aggregation consists of a reverse in the helicity from left to right handed initiated at a bend at residue 102 and extending to the C-terminus at residue 121. This reversed helicity prevents precise epitaxy at the C-terminal to N-terminal interface of the wild type protein. The cap sequences in this case are:
For the wild type ryegrass antifreeze protein, the removed cap sequence is the C-terminal layer
For the wild type rhagium inquisitor antifreeze protein, the first N-terminal layer has right handed helicity
while the presented, removed, top layer has left handed helicity, inhibiting epitaxy
In addition, many BSPs include disulfides, bulges, and prolines that require removal to allow for amyloid self-assembly. The three dimensional structure of any given BSP can be used to design an mBSP of that desired shape. Means for modeling engineered proteins and characterizing their final properties are well known to those of skill. Exemplary techniques for these procedures are described in, e.g., U.S. Pat. No. 10,287,332[5]. Examples of mBSPs include SBAFP-m9 (SBAFP with endcap and disulfides removed), and RGAFP-ml (RGAFP with bulges and proline removed), both of which are described in more detail below. A detailed description for the RiAFP-m9 can be found in Ref. [11].
The mBSPs can be functionalized in designed ways to specifically carry designated functional units, for example pathogen binding proteins, which are fused to the amino- or carboxyl- or both termini of mBSPs. In some embodiments, the monomers can further include one or more amino acid residues at the end. In other embodiments, the functional units can be inserted at the corners of the mBSP structures, within the sequence of the mBSP. The residues can be selected to allow attachment of the mBSP or fibril to a solid support, a nanoparticle, a biological molecule (e.g., an enzyme), a bacterial or eukaryotic cell, or additional amyloid fibrils. For example, the mBSP monomers can be modified to include residues that enhance hydrophobic interactions and/or salt bridging. Peptide bond chemistry, threonine bonding, disulfide bridges, or metal mediated chelation of histidine side chains can also be used. By adjusting the side chain structures on different faces of mBSPs, programmable assembly of two and three dimensional structures can be achieved. Modifications of external side chains of the mBSPs can be used to enable binding to solid supports, or for specific lateral self-assembly.
The term “amyloid fibril” refers to fibrous proteins that polymerize end-to-end in one-dimensional protein arrays. Amyloid fibrils can form naturally or they can be produced out of intrinsically non-amyloidogenic proteins. As shown here, using a rational design concept, intrinsically non-amyloidogenic proteins (e.g., BSPs) with natural cross-β structure can be transformed into proteins that readily self-assemble into amyloid fibrils under benign conditions.
The term “mBSP scaffold” refers to a system of one or more amyloid fibrils comprising mBSP monomers, that can be a platform for biomaterial-based self-assembly.
The term “antifreeze protein or AFP” refers to a protein found in the body fluids of some poikilothermic organisms, such as, Choristoneura sp. C.fumiferana or C.occidentalis, the Tenebrio molitor mealworm and plants which have the commonly known property that they reduce non-colligatively the freezing point of water. As used herein, “antifreeze proteins” are chemically synthesized or recombinantly produced polypeptides having a protein sequence with substantial similarity to a naturally occurring antifreeze protein and retaining the properties of an antifreeze polypeptide. In some embodiments, the modified antifreeze proteins will have altered or improved antifreeze activity and can be used for that purpose, as well.
Many antifreeze proteins are BSPs. For example, those derived from Tenebrio, Snow Flea rye grass, and the spruce budworm. Other examples of antifreeze proteins useful in the present invention include those described in the following PDB Accessions: 3VN3_B, 3VN3_A, 4DT5_B, and 4DT5_A.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, (e.g., two mBSPs and polynucleotides that encode them) refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.
The phrase “substantially identical,” in the context of two nucleic acids or polypeptides of the invention, refers to two or more sequences or subsequences that have at least 60%, 65%, 70%, 75%, 80%, or 90-95% nucleotide or amino acid residue identity (e.g., to any of the sequences here, including but not limited to SEQ ID NO: 1, 2, and 3), when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. Preferably, the substantial identity exists over a region of the sequences that is at least about 50 residues in length, more preferably over a region of at least about 100 residues, and most preferably the sequences are substantially identical over at least about 150 residues. In a most preferred embodiment, the sequences are substantially identical over the entire length of the coding regions.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc.Nat’l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection (see generally, Current Protocols in Molecular Biology, F.M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).
Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschuel et al. (1977) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always < 0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word length (W) of 11, an expectation (E) of 10, M=5, N=-4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word length (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
“Biological sample” includes tissues and bodily fluids, e.g., blood, blood fractions, lymph, saliva, urine, feces, etc.
The terms “specific for,” “specifically binds,” and like terms refer to a molecule (e.g., antibody or antibody fragment) that binds to a target with at least 2-fold greater affinity than non-target compounds, e.g., at least any of 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 25-fold, 50-fold, or 100-fold greater affinity. Specificity can be determined using standard methods, e.g., solid-phase ELISA immunoassays (see, e.g., Harlow & Lane, Using Antibodies, A Laboratory Manual (1998) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity).
A “label” or a “detectable label” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins or other entities which can be made detectable, e.g., by incorporating a radiolabel into a peptide or antibody specifically reactive with a target peptide. Any method known for conjugating a protein to the label may be employed, e.g., using methods described in Hermanson, Bioconjugate Techniques 1996, Academic Press, Inc., San Diego.
The inventors have discovered that amyloid fibrils comprised of monomers linked to pathogen binding proteins can be used to effectively detect pathogens. Amyloid fibrils are of particular use because they are stable under many conditions and can present a high density of binding molecules allowing for high affinity binding to pathogens. Amyloid fibrils can be formed from a number of β solenoid proteins that can be modified to remove a naturally-occurring motif that blocks polymerization. By fusing a pathogen binding protein to one, some or all of the β solenoid protein monomers, and allowing the monomers to polymerize, one can form a polymer with numerous pathogen binding sites. The polymer can be optionally linked to a solid support and can be used to detect pathogens in samples.
Naturally occurring β-solenoid proteins (BSPs) can be modified to form amyloid fibrils. These proteins have backbones that turn helically in either a left- or right-handed sense from the N-terminus to form β-sheets, and have regular geometric structures (triangles, rectangles, etc.) with 1.5-2 nm sides. The naturally occurring proteins are inhibited from amyloid aggregation (end-to-end polymerization to give cross β-fibrils) by natural capping features and/or structural distortions on one or both ends. Modification for making linear polymers (amyloids) from these proteins, molecular simulations used to assess structural stability and geometric properties for comparison to measurements, and the protocol for expressing and folding of the engineered proteins are described in, e.g., U.S. Pat. No. 10,287,332, which is incorporated by reference[5]. The correct monomeric structures can be obtained after purification and folding, amyloid fibrils can be produced by incubation at elevated temperatures, and the kinetics of fibril formation are consistent with, though slightly faster than, other amyloid polymerization reactions.
The modified BSPs (mBSPs) offer excellent platforms for functionalization with pathogen binding proteins without interfering with the native β-sheet structure. This allows for presentation of a number of the same or different pathogen binding proteins while maintaining the beta-sheet.
In one embodiment, the BSP is modified to enable one-dimensional growth through cross-beta strand (amyloid) pairing mBSPs. The exteriors and interiors of the proteins can also be modified to enable more efficient production. In some embodiments, the protein units are allowed to self-assemble in one dimension after expressing proteins (for example but not limited to, in E.coli), followed by, for example, subsequent cell lysis, purification, denaturation, refolding, and polymerization of the proteins to create the one dimensional scaffolds.
In some embodiments, at least two different mBSP monomers are designed to self-assemble in a predetermined order. This can be achieved by modifying the ends of the monomers such that, for example, the N-terminus of a first monomer interfaces with the C-terminus of a second monomer, but not with the C-terminus of another copy of the first monomer. The resulting fibril comprises the two different monomers in predetermined order (e.g., A-B-A-B-A- B, or A-B-C-A-B-C). For example, A, B, and C can represent monomers fused to different pathogen binding proteins, where different pathogen binding proteins have different sequences but bind to the same pathogen (optionally to different locations of the same pathogen) or bind to different pathogens.
The correct molecular mass of the amyloid monomer can be verified through standard techniques, such as mass spectroscopy. The correct beta content can be determined through techniques such as circular dichroism. Amyloid aggregation can be confirmed by observing the growth of thioflavin T (ThT) fluorescence at 480 nm.
The length of the fibrils can be controlled, for example through a variety of approaches including varying of the temperature (e.g., between 5° C. to 45° C.), by following the incubation with sonication, by the addition of inhibitors of polymerization, or by modifying the buffer solution. For example, fibrils of several microns can be routinely produced. Alternatively, shorter fibrils (e.g., 100-200 nm) can be produced upon sonication.
Exemplary naturally-occurring BSPs include but are not limited to:
1. Chain A, Crystal Structure Of A Lumenal Pentapeptide Repeat Protein From Cyanothece Sp 51142 At 2.3 Angstrom Resolution. Tetragonal Crystal Form
PDB: 2G0Y A
2. Chain X, The 2.0 Angstrom Resolution Crystal Structure Of Hetl, A Pentapeptide Repeat Protein Involved In Heterocyst Differentiation Regulation From The Cyanobacterium Nostoc Sp. Strain Pcc 7120
PDB: 3DU1_X
3. Chain A, Crystal Structure Of Recombinant Human Alpha Lactalbumin
PDB: 3B0I_A
4. Chain B, Crystal Structure Of An Ice-Binding Protein From The Perennial Ryegrass, Lolium Perenne
PDB: 3ULT -B
5. Chain A, Crystal Structure Of An Ice-Binding Protein From The Perennial Ryegrass, Lolium Perenne
PDB: 3ULT_A
6. Chain B, Crystal Structure Of Ydck From Salmonella Cholerae At 2.38 A Resolution. Northeast Structural Genomics Target Scr6
PDB: 2PIG_B
7. Chain A, Crystal Structure Of Ydck From Salmonella Cholerae At 2.38 A Resolution. Northeast Structural Genomics Target Scr6
PDB: 2PIG_A
8. Chain A, Choristoneura Fumiferana (Spruce Budworm) Antifreeze Protein Isoform 501
PDB: 1M8N_A
9. Chain B, Choristoneura Fumiferana (Spruce Budworm) Antifreeze Protein Isoform 501
PDB: 1M8N_B
10. Chain C, Choristoneura Fumiferana (Spruce Budworm) Antifreeze Protein Isoform 501
PDB: 1M8N_C
11. Chain D, Choristoneura Fumiferana (Spruce Budworm) Antifreeze Protein Isoform 501
PDB: 1M8N_D
Exemplary mBSPs include but are not limited to:
SEQ ID NO:1 synthetic protein SBAFP-m9
SEQ ID NO:2 synthetic protein RGAEP-m1
SEQ ID NO: 3 synthetic protein RiAFP-m9
In some embodiments, binding of scaffolds to solid support (e.g., surface) can be achieved. For example, in some embodiments, binding can be achieved by: (a) sulfur chemistry of unoxidized cysteine to bind to thiols decorating a prepared surface; (b) peptide bond chemistry to link exposed lysine side chains to carboxyl groups decorating a prepared solid surface; and (c) the application of common types of bioconjugate chemistry, for example the biotin-avidin or biotin-streptavidin interacting pair.
In certain circumstances, the solid support can be mica, silicon, glass, or a transparent conducting oxide, for example, FTO or ITO. In some embodiments, the surface can be poly-L-lysine coated mica (0001) surfaces. In other embodiments, the solid support is absorbent. For example, the solid support can be paper. This will allow for collection of a liquid biological sample, for example, saliva, blood, urine, feces, waste water or other biological fluids.
As noted above, the BSP or mBSP is fused to a pathogen binding protein, which provides an affinity agent that is displayed in multiple copies in the amyloid fibril polymer. The fusion can be direct between the monomer and the pathogen binding protein or a linker can be used to link the two fusion partners. In some embodiments, the linker can be comprised of a majority or entirely of glycine, serine or alanine or combinations thereof. For example, an exemplary linker is GGG.
The pathogen binding protein can be any protein that can be formed in a translational fusion with a BSP or mBSP monomer. The pathogen binding protein will depend on the pathogen to be targeted. In some embodiments, the pathogen binding protein is a protein from a human or animal or plant cell to which the pathogen binds during infection, and thus has affinity for the pathogen. In the example of SARS-CoV-2, the virus enters cells by binding Angiotensin Converting Enzyme 2 (ACE2). Accordingly, a useful SARS-CoV-2 binding protein is the virus-binding portion of ACE2. In some embodiments, the SARS-CoV-2 binding protein comprises a 54 residue helix-turn-helix (HTH) motif from ACE2, for example
or an amino acid sequence substantially identical to SEQ ID NO:4. Alternatively, the pathogen binding protein can be a peptide (e.g., identified by phage panning or other techniques), a tetrameric, single domain or single chain antibody, or other protein that selectively binds to the pathogen. Aside from SARS-CoV-2, the pathogen can be any virus, bacterium, protozoan, or fungus.
In some embodiments the combined binding protein-BSP fusion construct may be comprised from the 233 residue RiAFP and helix-turn-helix sequence (RiAFP-HTH.1)
or an amino acid sequence substantially identical to SEQ. ID NO:5. In some embodiments the combined binding protein-BSP fusion construct may be comprised from the 266 residue RiAFP and helix-turn-helix sequence (RiAFP-HTH.2)
or an amino acid sequence substantially identical to SEQ ID NO:6. In this embodiment the helix-turn-helix on each side is flanked by spacing linkers so it sticks out further from the mBSP scaffold.
In some embodiments, the pathogen is a hepatitis virus, e.g., hepatitis A, hepatitis B (HBV) or hepatitis C (HCV). Exemplary HBV binding proteins include but are not limited to the heptapeptide
(interacting with the hydrophilic loop (residues 101-159 located on the surface of the virus) with the dissociation constant of 2.9 nM [Ho, K.L., et al., Selection of high affinity ligands to hepatitis B core antigen from a phage-displayed cyclic peptide library. J Med Virol, 2003. 69(1): p. 27-32]). Exemplary HCV binding proteins include but are not limited to
,_which binds to the Hepatitis C Virus Protein E2 [Hong, H.W., S.W. Lee, and H. Myung, Selection of peptides binding to HCV e2 and inhibiting viral infectivity. J Microbiol Biotechnol., 2010. 20(12): p. 1769-71] and
Lu, X., et al., Identification of peptides that bind hepatitis C virus envelope protein E2 and inhibit viral cellular entry from a phage-display peptide library, in Int J Mol Med. 2014, 2011 Elsevier Inc: Greece] and
[Chen, F., et al., Functional selection of hepatitis C virus envelope E2-binding Peptide ligands by using ribosome display. Antimicrob Agents Chemother., 2010. 54(8): p. 3355-64. doi: 10.1128/AAC.01357-09. Epub 2010 May 17].
In some embodiments, the amyloid fibril is composed of two or more mBSP monomer/pathogen binding protein fusions, wherein the two or more fusions differ by the pathogen binding protein. Thus, in some embodiments, the amyloid fibril comprises two or more different pathogen binding proteins that bind to the same pathogen, optionally at different targets on the pathogen. In some embodiments, the different pathogen binding proteins bind to different pathogens.
As noted above, the amyloid fibrils comprising pathogen binding proteins can be linked to a solid support, for example an absorbent solid support (e.g., paper or other cellulose or other polymer material), which can capture biological fluids. In some embodiments, the amyloid fibrils comprising pathogen binding proteins are linked to an absorbent solid support and used in detection of pathogen using lateral flow.
In other embodiments, the amyloid fibrils comprising pathogen binding proteins can be embedded in or coated on personal protective equipment (PPE). Exemplary PPE include but are not limited to clothing (e.g., lab gowns or jackets or hazmat suits), gloves, face masks, face screens or other physical barriers. In some embodiments, the amyloid fibrils comprising pathogen binding proteins can be formulated into a liquid, gel, or cream that can be applied to surfaces (e.g., countertops) or to the skin to bind and inactivate pathogen, if present, preventing the pathogens from being infectious.
In addition to binding pathogens to inactivate them, the amyloid fibrils comprising pathogen binding proteins can be used to capture and detect a pathogen. In some embodiments, the amyloid fibrils comprising pathogen binding proteins are linked to a solid support as described herein and contacted with a sample (e.g., a biological sample); pathogen specifically bound to the pathogen binding protein can be detected. In some embodiments, the bound pathogen is detected by a sandwich assay format, with a second binding agent binding the immobilized pathogen and subsequent detection of the bound second binding agent. The second binding agent can be labeled or can be contacted by a tertiary binder that comprises a detectable label. In some embodiments, the second binding agent is a mBSP comprising a cap sequence that prevents polymerization fused to a pathogen binding protein. In some embodiments, the second binding agent can be a peptide (e.g., 10-50 amino acids) or an antibody that specifically binds the pathogen. Alternatively, the amyloid fibrils comprising pathogen binding proteins can be linked to a detectable label that changes the signal depending on whether the pathogen is bound to the pathogen binding protein, thereby avoiding the need for a second binding agent.
We propose development of direct virion capture assays based upon patented mBSP technology[5, see also 6-11] using genetically engineered, highly functionalizable beta solenoid proteins (
Our approach to rapidly developing inexpensive SARS-CoV-2 POC direct viral capture tests will be two-fold. First, we provide a 54 residue helix-turn-helix (HTH) motif (SEQ ID NO:4 or a substantially similar sequence) from the cell-surface bound angiotensin converting enzyme 2 (ACE2) to which the SARS-CoV-2 viral spike protein binds. Second, phage display or other established biopanning technologies including ribosome display or yeast display can be used to find novel peptides that bind tightly and specifically to the SARS-CoV-2 spike protein.
This represents a significant innovation. The cell-surface ACE2 protein [12] is the cellular entry point for SARS-CoV-2. ACE2 binds tightly to the SARS-CoV-2 spike protein, with dissociation constants in the low nanomolar range[13]. However, the single N-terminal helix of the ACE2 by itself binds weakly to the spike protein, with dissociation constants of 1.3 micromolar. [14], and a computationally designed substitute which includes a portion of the first helix only modestly improves on this with a dissociation constant of 646 nanomolar [15] We have made stable constructs of a VEGF-binding HTH fusion with RiAFP, discussed extensively in Example 2 below. Here we employ the ACE2 N-terminal HTH as a SARS-CoV-2 capture sequence (see below). This is illustrated in
With a mBSP SARS-CoV-2 binding fusion construct in hand, a dense mBSP polymeric array is formed (
There are several built-in advantages to this mBSP based virion capture assay. First, it would likely be less expensive to employ than immunoassays and can potentially be quickly mass produced. Second, it requires no special technology and so can be implemented in field environments like drive-through test facilities. Third, it would likely detect the presence of either live or dead virus. Fourth, it is expected to be highly stable in extreme environments of heat or humidity. Our previous studies on mBSP polymers show stability in conditions of extreme alkalinity or acidity, high protein denaturant concentration, and extreme temperature (some survive autoclaving)[7]. They are however partially protease-sensitive, so do not present the same kind of potential health problems as say mammalian prions[16]. Fifth, it can be used for environmental sampling of viruses on surfaces. Sixth, a non-obvious consequence that will benefit the sensitivity and specificity of any assay based upon the polymeric capture proteins and a divalent conjugate labeling protein is at least divalent avidity compared to the monovalent binding of antibodies.
We have proven the ability of our mBSP-HTH constructs to bind VEGF by fusing a known VEGF binding HTH motif with mBSPs. We found tight binding in a simple assay based on ultrafiltration (
Development of secondary mBSPs bound to silica coated rare earth upconversion quantum nanoparticles (REUQN) for binding to RBD domains of SARS-CoV-2 spike proteins. REUQN make use of sequential two photon transitions from the infrared part of the spectrum followed by energy transfer to induce single photon luminescence in the visible spectrum; for example, one can use nanorings made from NaYF4 doped with Er,Yb[18]. REUQN (i) can be excited by inexpensive infrared lasers[19], potentially enabling cell phone based imaging of binding, (ii) are stabilized with a silica coat to provide a shelf life of 4 years [18], (iii) can be functionalized for binding to amine or carboxyl functional groups, and (iv) are inexpensive to synthesize or purchase, and to coat. A previous antibody based FLISA assay for hepatitis B,C viruses made use of rare earth dots [20].
Construction and testing of betabodyBSP polymer comprising VEGF-binding protein: To prove that a BSP (beta solenoid based synthetic antibody [6] can be engineered to capture proteins with high affinity, we engineered a mBSP polymer derived from the modified Ragium Inquisitor antifreeze protein (RiAFP) [4] with a helix-tum-helix (HTH) motif known to bind to the Vascular Endothelial Growth Factor (VEGF) protein with high affinity [Fedorova, A., et al., The Development of Peptide-Based Tools for the Analysis of Angiogenesis.Chemistry & Biology, 2011. 18(7): p. 839-845]. We used a flow-through assay to verify that the mBSP polymer captured the VEGF with high affinity (Kd < 10 nM).
Experimental Design 1: Capture mBSPs We took a previously identified miniZ-peptide with the helix-turn-helix motif (HTH) that has approximately Kd = 40 nM affinity to VEGF. We designed and synthesized a construct with the miniZ-HTH inserted at the edge (
Protein expression occurred from synthetic genes in the pET28a vector in E.coli followed by purification using standard methods. Polymerization was effected by incubating the proteins at 37° C. for 48 hours.
Experimental Design 2. We tested the binding of VEGF to the RiAFP-miniZ-HTH construct with a flow-through assay. The schematic is shown in
The samples analyzed were as follows:
I) Control 1: VEGF. This is shown in lane 3. After centrifugation, no VEGF is found in the retentate chamber, only in the flow-through chamber, confirming that it passes through the filter.
II) Control 2: RiAFP-miniZ-HTH. This is shown in lane 2. There is no protein found in the flow-through chamber, only in the retentate. This confirms that the filter blocks the RiAFP-miniZ-HTH construct.
III) Test sample. Both RiAFP-miniZ-HTH polymer and VEGF are added to the upper chamber prior to centrifugation. Both the RiAFP-miniZ-HTH polymer and VEGF appear only in the retentate, confirming VEGF binding by the polymer.
Analysis. The binding assay with controls demonstrates qualitatively high-affinity binding of VEGF to the RiAFP-miniZ-HTH construct. The limit of protein detection on SDS-PAGE gels stained with Coomassie R250 is generally accepted as ~30 ng. The SDS-PAGE gels were loaded with 20 µL of sample per lane. Thus, the test sample flow-through solution has less than 0.0015 mg/mL (~30 nM) VEGF. The concentrations of the RiAFP-miniZ-HTH and VEGF were each ~1 mg/mL (~40 µM RiAFP-miniZ-HTH; ~25 µM VEGF) in the initial mixture. Using the general equation for ligand binding combined with the values above allows us to estimate a Kd value of <10 nM for VEGF binding to RiAFP-miniZ-HTH.
The above examples are provided to illustrate the invention but not to limit its scope. Other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, databases, internet sources, patents, patent applications, and accession numbers cited herein are hereby incorporated by reference in their entireties for all purposes.
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The present application is a U.S. National Phase Application Under 371 of International Application PCT/US2021/029964 filed Apr. 29, 2021, which claims benefit of priority to U.S. Provisional Pat. Application No. 63/018,285, filed Apr. 30, 2020, each of which is incorporated by reference for all purposes.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/029964 | 4/29/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63018285 | Apr 2020 | US |
