WO2022260877A1 - Shark vnars for treating covid-19 - Google Patents

Shark vnars for treating covid-19 Download PDF

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Publication number
WO2022260877A1
WO2022260877A1 PCT/US2022/031359 US2022031359W WO2022260877A1 WO 2022260877 A1 WO2022260877 A1 WO 2022260877A1 US 2022031359 W US2022031359 W US 2022031359W WO 2022260877 A1 WO2022260877 A1 WO 2022260877A1
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vnar
amino acid
acid sequence
seq
peptide
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PCT/US2022/031359
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French (fr)
Inventor
Aziz Gauhar
Cyril V. Privezentzev
Pawel STOCKI
Julia Lynn Rutkowski
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Ossianix, Inc.
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Priority claimed from US17/343,444 external-priority patent/US11345742B1/en
Application filed by Ossianix, Inc. filed Critical Ossianix, Inc.
Publication of WO2022260877A1 publication Critical patent/WO2022260877A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • the present disclosure relates to the identification of single domain VNARs derived by bio-panning against the spike protein from the SARS-CoV-2 Wuhan variant.
  • the screen identified ten VNAR Fc fusion proteins (VNAR antibodies) that were shown in biochemical and cells-based assays to be highly effective in blocking the interaction of recombinant spike protein with ACE2 receptor and eight were confirmed to neutralize live Wuhan variant virus using in vitro assays.
  • VNAR antibodies retained high affinity binding and blocking activity against the Sl-RBD N501 Y mutant, and three had activity against the Sl- RBD E484K mutant.
  • the VNAR antibody panel directed against the SARS CoV-2 spike protein expands the molecular toolbox of novel antibody therapeutic approaches directed against COVID-19.
  • passive immunization via direct administration of purified antibodies may provide a solution to both prevent and treat infections (Yang, Liu et al. 2020).
  • the receptor binding domain (Sl-RBD) of the spike protein is the main target for various vaccine and antibody neutralization approaches. However, it is highly protected by being tightly folded within the structure and covered by a glycan shield (Watanabe, Allen et al. 2020). Furthermore, neutralizing antibodies to only a single dominant epitope can result in selective pressure for viral mutants that escape inhibition. Neutralizing antibodies to the Sl- RBD domain have been isolated by cloning human B cells from infected patients and by immunizing humanized mice (Baum, Ajithdoss et al. 2020; Cao, Su et al. 2020; Liu, Wang et al. 2020) but these approaches are not without issues.
  • RNA viruses spontaneously evolve as they spread across populations and mutations are already accumulating in the SARS-CoV-2 spike protein both within and outside the Sl-RBD domain (Korber, Fischer et al. 2020), which makes targeting a single immunodominant epitope highly prone to escape upon mutation.
  • a potent antibody-evasion strategy employed by viruses is the so-called “glycan shield” present on many viral glycoproteins, which masks neutralizing antibody to antigenically conserved sites (Watanabe, Bowden et al. 2019).
  • Shark VNAR single domain antibodies also known as IgNARs
  • IgNARs which have evolved to compliment conventional antibodies, offer an important alternative with significant advantages for combating viral defenses.
  • Surface-exposed epitopes available to conventional IgGs are generally more tolerant of mutations which allow viral escape (Thyagarajan and Bloom 2014; Doud, Hensley et al. 2017; Doud, Lee et al. 2018).
  • VNAR single domain antibodies are ideally designed to access buried epitopes beneath the glycan shield (Stanfield, Dooley et al. 2004; Konning, Zielonka et al. 2017).
  • VNARs have been developed which target the spike protein within Sl-RBD and N-terminal domain (Sl-NTD).
  • Sl-NTD N-terminal domain
  • the VNAR domains directed against the SARS-CoV-2 spike protein expands the molecular toolbox of antibody therapeutic approaches directed against COVID-19 disease.
  • the present disclosure provides coronavirus SI -fragment specific binding moieties comprising Type II VNAR domains, VNAR antibodies, methods of using those moieties and antibodies to treat COVID-19, and improved Type II VNAR libraries for screening, selecting and/or identifying VNARs that bind specifically to a target molecule of interest.
  • a VNAR antibody originally selected from a phage display library as a VNAR clone using SI fragments from the SARS-CoV-2 Wuhan strain, are also effective at specifically binding to and/or neutralizing SARS-CoV-2 and certain SARS-CoV-2 mutants.
  • the SI fragment-binding moieties comprise a Type II VNAR domain represented by the formula, from N to C terminus,
  • CDR1 comprises or consists essentially of a peptide having an amino acid sequence of one of DSICALSS, DSNCALPS, DSVCALSS, or DSNCALSS (SEQ ID NOS.
  • CDR3 comprises or consists essentially of a peptide having an amino acid sequence of one of VHMEDMNVRD YGGFWGED V, VNLRSVLPCGWPDV, VENLPGSGSCLRYYLSDV, VREWACEDDGRVWGWEDV, V ART S GCE V YT YT GD V, VKNPSGCGVWYSQEDL, SEFKSGCGVFYELTDV, MVFKSVCEDNPYQYGL, or IWAHSGCEVITHAMDL (SEQ ID NOS. 154-162, respectively), and wherein said moiety is capable of specifically binding to an SI fragment comprising amino acids 16-685 of a SARS- CoV-2 spike protein.
  • HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively).
  • HV4 is SGSKS or RGSKS (SEQ ID NOS. 167-168, respectively).
  • the VNAR domain comprises one of the CDRls and CDR3s together with any one of the HV2s, with any one of the HV4s, or with both of any one of the HV2s and an HV4s.
  • the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRD YGGFWGED V (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 156) (from VNAR 61; the CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and the CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWE
  • the CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and the CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL (SEQ ID NO:
  • the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV (SEQ ID NO:
  • the CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and the CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL (SEQ ID NO:
  • the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL (SEQ ID NO:
  • the moiety comprises any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135).
  • any of the moieties of the disclosure further comprise at least one heterologous agent operably linked thereto to thereby form a conjugate.
  • heterologous agents include but are not limited to, one or more of a small molecule diagnostic or therapeutic; a DNA, RNA, or hybrid DNA-RNA; a traceable marker; a radioactive agent; an antibody; a single chain variable domain; or an immunoglobulin fragment.
  • the heterologous agent is an immunoglobulin fragment and is operably linked to the VNAR domain to form a fusion protein.
  • the immunoglobulin fragment is a Fc domain, and preferably a human Fc domain.
  • the human Fc domain can be from any immunoglobulin isotype.
  • the isotype is an IgG.
  • a further aspect relates to pharmaceutical compositions comprising at least one moiety, conjugate or fusion protein of the disclosure. In embodiments, such compositions can also have, independently, two, three, four, five or more of such moieties, conjugates or fusion proteins.
  • the disclosure provides a method of passive immunization against SARS-CoV-2, and variants thereof, which comprises administering a pharmaceutical composition of the disclosure to a subject in need thereof.
  • the disclosure provides a method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19.
  • the subject or mammal has tested positive for SARS-CoV-2.
  • the subject or mammal has suspected exposure to SARS-CoV-2 and/or tested negative for SARS-CoV-2.
  • the composition is administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
  • this disclosure provides VNAR antibodies which comprise a moiety of the disclosure fused to a human Fc domain, which upon expression form a bispecific VNAR antibody.
  • the moiety has a VNAR domain wherein the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 15
  • the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV (SEQ ID NO:
  • the CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and the CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL (SEQ ID NO:
  • the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL (SEQ ID NO:
  • VNAR domain is any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135).
  • a VNAR antibody is capable of neutralizing infection of SARS-CoV-2
  • a further aspect relates to pharmaceutical compositions comprising at least one VNAR antibody of the disclosure.
  • such compositions can also have, independently, two, three, four, five or more VNAR antibodies.
  • the disclosure provides a method of passive immunization against SARS-CoV-2, and variants thereof, which comprises administering a pharmaceutical composition comprising one or more VNAR antibodies of the disclosure to a subject in need thereof.
  • the disclosure provides a method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition comprising one or more VNAR antibodies of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19.
  • the subject or mammal has tested positive for SARS-CoV-2. In some embodiments of these methods, the subject or mammal has suspected exposure to SARS-CoV-2 and/or tested negative for SARS-CoV-2. In some embodiments of these methods, the composition is administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
  • the disclosure provides a coronavirus SI fragment binding moiety comprising a Type II VNAR domain capable of specifically binding to an SI fragment comprising amino acids 16-685 of SARS-CoV-2 spike protein, wherein the said VNAR domain comprises an amino acid sequence of any one of VNAR clones 1-149 in Table 3 or Table 4 (SEQ ID NOS.1-149).
  • these moieties further comprise at least one heterologous agent operably linked to the moiety to thereby form a conjugate.
  • embodiments include nucleic acids encoding a moiety, conjugate, fusion protein or VNAR antibody of the disclosure.
  • a nucleic acid of the disclosure is in a vector having the nucleic acid operably linked to a promoter to enable expression of the binding moiety, conjugate or VNAR antibody in a host cell.
  • Another aspect provides host cells comprising a nucleic acid or vector of the disclosure.
  • the disclosure provides a synthetic nucleic acid-containing library whose members each encode a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
  • FW Type II VNAR framework
  • HV hypervariable
  • CDR complementary determining region
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine;
  • X b is Y, L, D, S or G;
  • X c is D, V, W, Y or G;
  • X d is W, E, Y, D, or G;
  • X e is Y, L, D, V or L;
  • X f is D or G; and
  • X g is V or L;
  • the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
  • the disclosure provides a synthetic nucleic acid-containing library whose members each comprise a nucleic acid encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
  • FW Type II VNAR polypeptide with Type II VNAR framework
  • HV hypervariable
  • CDR complementary determining region
  • FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide, none of the residues are cysteine except as provided in (a) to (i) and, wherein, (a) FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
  • CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
  • FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
  • HV2 is 9 amino acids in length
  • FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
  • HV4 is 5 amino acids in length
  • FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine, X b is Y, L, D, S or G; Xc is D, V, W, Y or G; X d is W, E, Y, D, or G; X e is Y, L, D, V or L; X f is D or G; and X g is V or L; and
  • FW4 is 10 amino acids in length and has an amino acid sequence comprising
  • the residue at each position of said VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
  • any of the nucleic acid libraries of the disclosure are phage display libraries. Such libraries may comprise approximately 10 9 theoretically distinct nucleic acid sequences.
  • nucleic acid libraries hereof are used in various methods for identifying polypeptides that bind selectively to target molecules of interest.
  • An embodiment provides a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises: (a) exposing a target molecule of interest to polypeptides produced by expression of a nucleic acid library of the disclosure; and (b) separating polypeptides that selectively bind from those that do not selectively bind the target molecule.
  • the target molecule of interest is expressed on the surface of a phage, bacterium or cell, or is attached to, tethered to or otherwise associated with a solid support.
  • Another embodiment provides a method of screening a library for a polypeptide that selectively binds with high affinity to a target molecule of interest, the library comprising a plurality of polypeptides produced by expression of a nucleic acid library of the disclosure and comprises: (a) incubating a sample of the library with a concentration of a target molecule under conditions suitable for specific binding of the polypeptides to the molecule; (b) incubating a second sample of the library under the same conditions but without target molecule; (c) contacting each of the first and second samples with immobilized target molecule under conditions suitable for binding of the polypeptide to the immobilized target antigen; (d) detecting the polypeptide bound to immobilized target molecule for each sample; (e) determining the affinity of the polypeptide for the target molecule by calculating the ratio of the amounts of bound polypeptide from the first sample over the amount bound polypeptide from the second sample.
  • Yet another embodiment provides a method of identifying one or more VNARs that selectively bind to a target molecule of interest which comprises: (a) contacting said target molecule with a phage display library of Claim 40 or 41; (b) separating phage that selectively bind the target molecule from those that do not selectively bind the target molecule to produce an enriched phage library; (c) repeating steps (a) and (b) with the enriched phage library to produce a further enriched phage library; (d) repeating step (c) until the further enriched phage library is enriched from at least about 10- to about 10 6 -fold or more relative to the original phage library; and (e) plating the further enriched phage library and isolating and characterizing individual clones therefrom to thereby identify one or more VNAR polypeptides that selectively bind to the target molecule of interest.
  • either the target molecule or phage display library can be bound to
  • the target molecule is a SARS- CoV-2 spike protein, a domain of the spike protein or a mutant thereof.
  • a still further aspect relates to a polypeptide library composition
  • a polypeptide library composition comprising a plurality of synthetic or recombinant polypeptides, each of which encodes a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C- terminus, FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 — CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide,
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine;
  • X b is Y, L, D, S or G;
  • X c is D, V, W, Y or G;
  • X d is W, E, Y, D, or G;
  • X e is Y, L, D, V or L;
  • X f is D or G; and
  • X g is V or L;
  • the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
  • the disclosure provides a polypeptide library composition whose members each comprise a polypeptide encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
  • FW Type II VNAR framework
  • HV hypervariable
  • CDR complementary determining region
  • FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
  • CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
  • FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
  • HV2 is 9 amino acids in length
  • FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
  • HV4 is 5 amino acids in length
  • FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine, X b is Y, L, D, S or G; Xc is D, V, W, Y or G; X d is W, E, Y, D, or G; X e is Y, L, D, V or L; X f is D or G; and X g is V or L; and
  • FW4 is 10 amino acids in length and has an amino acid sequence comprising
  • the residue at each position of the VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
  • Yet a further aspect relates to a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises (a) exposing a target molecule of interest to a polypeptide library composition of the disclosure; and (b) separating polypeptides that selectively bind to said target molecule from those that do not selectively bind the target molecule.
  • FIG. 1 Schematic representation of VNAR domain variable regions. Variable regions include CDR1 (26-33), HV2 (44-52), HV4 (61-65) and CDR3 (85-100).
  • the OSX6 phage library was generated by random assembly of 1068 synthesized N-terminal fragments designed as provided in Table 1 with approximately lxlO 6 C-termini fragments designed as provided in Table 2.
  • the encoded amino acid sequences of the 1068 synthesized N-terminal fragments of Scaffold l to Scaffold_1068 are provided in the Sequence Listing as SEQ ID NOS. 177-1244, respectively.
  • FIG. 1 Schematic representation of SARS-CoV-2 spike protein and its domains. The SI and S2 fragments are indicated. Protein domains illustrated are: N-terminal domain (NTD), receptor-binding domain (RBD), fusion peptide (FP), heptad repeat 1 (HR1), central helix (CH), connector domain (CD), and transmembrane domain (TM).
  • NTD N-terminal domain
  • RBD receptor-binding domain
  • FP fusion peptide
  • HR1 heptad repeat 1
  • CH central helix
  • CD connector domain
  • TM transmembrane domain
  • FIG. 1 VNAR Binding to Spike Protein Domains.
  • the bar graph depicts antigen binding of VNAR clones isolated from the OSX3 phage library by selection against recombinant Sl-RBD protein and reformatted as VNAR-hFc fusions (VNAR antibodies).
  • VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 ( ⁇ 3 fold over blank) are presented on the graph.
  • FIG. 1 VNAR Binding to Spike Protein Domains.
  • the bar graph depicts antigen binding of VNAR clones isolated from the OSX3 phage library by selection against recombinant SI protein and reformatted as VNAR-hFc fusions (VNAR antibodies).
  • VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 ( ⁇ 3 fold over blank) are presented on the graph.
  • FIG. 1 VNAR Binding to Spike Protein Domains.
  • the bar graph depicts antigen binding of VNAR clones isolated from the OSX6 phage library by selection against recombinant Sl-RBD protein and reformatted as VNAR-hFc fusions (VNAR antibodies).
  • VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 ( ⁇ 3 fold over blank) are presented on the graph.
  • FIG. 1 VNAR Binding to Spike Protein Domains.
  • the bar graph depicts antigen binding of VNAR clones isolated from the OSX6 phage library by selection against recombinant SI protein and reformatted as VNAR-hFc fusions (VNAR antibodies).
  • VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 ( ⁇ 3 fold over blank) are presented on the graph.
  • FIG. 7 ECso binding curves of VNAR antibodies to Sl-RBD for VNARs selected against Sl-RBD. Binding was assessed by ELISA with serial dilutions of diluted VNAR antibody and immobilized recombinant Sl-RBD protein. For the simplicity, the binding curves for eleven VNAR antibodies are shown (VNAR antibodies 7, 19, 20, 22, 25, 26, 103, 104, 105, 106, and 108). Calculated ECso values for all tested VNAR antibodies are presented in Table 8.
  • FIG. 8 ECso binding curves of VNAR antibody 137 to recombinant Sl-RBD and SI. Binding was assessed by ELISA with serially-diluted VNAR antibody and immobilized recombinant Sl-RBD or SI proteins.
  • VNAR antibody 137 is an example of a specific binder to the NTD domain present in the SI construct which does not bind RBD domain. Its calculated ECso value is provided in Table 9.
  • Figure 9. ICso curves of three VNAR antibodies (25, 105 and 106) that block the interaction of Sl-RBD with ACE2 protein.
  • ACE2 at a fixed concentration was premixed with serially-diluted VNAR antibodies before incubation with Sl-RBD immobilized on ELISA plates, followed by washing. ACE2 binding was detected by anti- FLAGHRP conjugated antibody. Data presented as normalized OD at 450nm. The calculated IC50 values for the tested VNAR antibodies are presented in Table 10.
  • FIG. 10 ICso curves of three VNAR antibodies (25, 105 and 106) that block binding of SI to cells overexpressing ACE2.
  • Expi293 cells transiently expressing ACE2 were used for the assay.
  • SI was premixed with serially-diluted VNAR antibodies before incubation with the cells. Binding was measured by flow cytometry and the data presented as normalized median fluorescence intensity (MFI) of the transfected cell population. Calculated IC50 values for the tested VNAR antibodies are presented in Table 11.
  • MFI median fluorescence intensity
  • FIG. 11 ECso binding curves of SI mutants to ACE2.
  • the mutants included Sl-RBD recombinant protein with a single E484K or N501Y mutation as well as quadruple mutant of SI protein containing K417N, E484K, N501Y and D614G mutations. Binding to immobilized SI mutants with serial dilutions of recombinant ACE2 ectodomain receptor was assessed by ELISA. Calculated EC50 values are presented in Table 12.
  • FIG. 12 ECso binding curves of VNAR antibody 25 to spike Sl-RBD domain and mutants. Binding was assessed with serially-diluted VNAR antibody on immobilized recombinant spike proteins Sl-RBD (circles), Sl-RBD N501Y (squares), Sl-RBD E484K (upright triangles) and SI K417N, E484K, N501 Y and D614G (inverted triangles).
  • FIG. 13 ICso curves of VNAR antibody 25 that blocks Spike protein interactions with ACE2.
  • ACE2 at a fixed concentration was premixed with serially-diluted VNAR antibodies before incubation with recombinant Sl-RBD, Sl-RBD N501Y or Sl-RBD E484K immobilized on ELISA plates.
  • ACE2 binding was detected by anti-FLAG HRP conjugated antibody.
  • FIG. 14 Neutralization of SARS-CoV-2 virus by VNAR antibodies. Vero CCL81 cells were exposed to SARS-CoV-2 Wuhan strain preincubated with or without VNAR antibodies at 5 pg/mL (65 nM) for 48 hr using VNAR antibodies 25, 46, 61, 68, 105, 106, 115, 119, 132 and 135. Viral load was determined at the start of the experiment and after 48 hr using RT-qPCR. Infection was assessed relative to cells treated with the virus in the absence of VNAR antibodies. [0050] Figure 15. Neutralization of SARS-CoV-2 virus by VNAR antibody 137.
  • Vero CCL81 cells were exposed to SARS-CoV-2 Wuhan strain preincubated with or without VNAR antibody 137 at 5, 10, 50 pg/mL (65, 130, 650 nM) for 48 hr. Viral load was determined at start of the experiment and after 48 hr using RT-qPCR. Infection was assessed relative to cells treated with the virus in the absence of VNAR antibodies.
  • FIG. 16 Epitope binning of VNAR antibodies by cross competition ELISA.
  • VNAR antibodies (25, 46, 61, 68, 105, 106, 115, 119, 132 and 135) were used to coat ELISA microplate wells, followed by addition of Sl-RBD or premixed biotinylated Sl-RBD and a competitor VNAR antibody. Binding of biotinylated Sl-RBD to immobilized VNAR antibodies was detected by streptavidin-HRP. Black color indicate competition between two antibodies for the overlapping epitope bin. White color indicates no competition, thus a unique epitope bin.
  • phage display library contains a plurality of phage equal to its titer (which may be the same or different), and by extension encodes a corresponding plurality of polypeptides.
  • patient may be used interchangeably and refer to either a human or a non-human animal. These terms include mammals such as humans, primates, livestock animals (e.g ., cows, pigs), companion animals (e.g., dogs, cats) and rodents (e.g., mice and rats).
  • livestock animals e.g ., cows, pigs
  • companion animals e.g., dogs, cats
  • rodents e.g., mice and rats
  • non-human mammal means a mammal which is not a human and includes, but is not limited to, a mouse, rat, rabbit, pig, cow, sheep, goat, dog, non-human primate, or other non-human mammals, typically as used in research.
  • “mammals” includes the foregoing non-human mammals and humans.
  • treating or “treatment” and grammatical variants thereof refer to an approach for obtaining beneficial or desired clinical results.
  • the term may refer to slowing the onset or rate of development of a condition, disorder or disease, reducing or alleviating symptoms associated with it, generating a complete or partial regression of the condition, or some combination of any of the above.
  • beneficial or desired clinical results include, but are not limited to, reduction or alleviation of symptoms, diminishment of extent of disease, stabilization (i.e., not worsening) of state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable.
  • Treatment can also mean prolonging survival relative to expected survival time if not receiving treatment.
  • a subject e.g., a human
  • treatment includes inhibition or reduction of an increase in severity of a pathological state or symptoms relative to the absence of treatment and is not necessarily meant to imply complete cessation of the relevant disease, disorder or condition.
  • preventing and grammatical variants thereof refer to an approach for preventing the development of, or altering the pathology of, a condition, disease or disorder. Accordingly, “prevention” may refer to prophylactic or preventive measures.
  • beneficial or desired clinical results include, but are not limited to, prevention or slowing of symptoms, progression or development of a disease, whether detectable or undetectable.
  • a subject e.g., a human
  • prevention includes slowing the onset of disease relative to the absence of treatment and is not necessarily meant to imply permanent prevention of the relevant disease, disorder or condition.
  • preventing or “prevention” of a condition may in certain contexts refer to reducing the risk of developing the condition or preventing or delaying the development of symptoms associated with the condition.
  • an “effective amount,” “therapeutically-effective amount” or “effective dose” is an amount of a composition (e.g., a therapeutic composition or agent) that produces at least one desired therapeutic effect in a subject, such as preventing or treating a target condition or beneficially alleviating a symptom associated with the condition.
  • a physiologically-acceptable solution for use in an amount and for a time sufficient to effectively reduce a circulating concentration of the plurality of polypeptides is referred to herein as a perfusate.
  • the amount of perfusate and time of perfusion depends on the non human mammal and can be readily determined by those of skill in the art. For example, with a mouse, using a volume of perfusate approximately lOx the blood volume of the mouse is effective at reducing the circulating concentration of polypeptides.
  • any volume of perfusate that reduces the circulating concentration of the plurality of polypeptides by about 10%, 25%, 50% or more (relative to the theoretical concentration of the plurality of polypeptides) being delivered is considered effective at reducing the circulating concentration of that plurality.
  • VNAR domain As used herein, a “VNAR domain” or “VNAR” has the general structure, from N to C terminus, given by the formula FW1-CDR1-FW2-HV2-FW2 , -HV4-FW3-CDR3-FW4, wherein the FWs are framework regions, CDRs are complementarity determining regions and HVs are hypervariable regions that form the variable domain of a shark IgNAR.
  • the CDR3 region in naturally-occurring VNARs is of heterogeneous size, ranging from about 7 to about 32 amino acid residues in length.
  • the VNAR domains of the invention can optionally have a His-Tag (or other convenient tag for purification purposes). In some cases, such tags are removable.
  • Typical VNAR domains have amino acid residues (aa) 1-25 of the framework 1 (FW1) region; aa 26-33 of the complimentary determining region 1 (CDR1); aa 34-43 of FW2; aa 44-52 of the hypervariable 2 region (HV2); aa 53-84 of FW3; aa 61-65 of HV4; the CDR3 region (of variable length begins with aa 85) and FW4 (11 residues starting immediately after CDR3 at XGXG).
  • binding to the target of interest is called specific binding, while binding to other sites is called nonspecific binding.
  • a binding moiety, specific binding moiety, antibody or VNAR domain that “specifically binds” to its target does so selectively or preferentially.
  • moieties, antibodies and VNARS can exhibit specific binding to multiple targets such as occurs when one of these entities exhibits species cross reactivity.
  • Abbreviations used herein for conventional antibodies include: VL, variable region, light chain; VH, variable region, heavy chain; CL, constant region of light chain; HC, constant region of heavy chain.
  • the present invention relates to coronavirus SARS-CoV-2 SI -fragment-specific binding moieties comprising Type II VNAR domains obtained by in vitro selection against recombinant spike protein fragments, including the recombinant SI domain encoded by amino acids 16-685 of the spike protein and the Sl-RBD domain encoded by amino acids 319-541 of the spike protein, using VNAR OSX3 and OSX6 phage display libraries.
  • the disclosure provides a coronavirus SI -fragment binding moiety comprising a Type II VNAR domain capable of specifically binding to an SI fragment comprising amino acids 16-685 of SARS-CoV-2 spike protein, wherein the VNAR domain comprises an amino acid sequence of any one of VNAR clones 1-149 in Table 3 and Table 4 (SEQ ID NOS.1-149; see Example 2).
  • the CDR1, HV2, HV4 and CDR3 sequences for each of the foregoing VNAR domains identified from the OSX3 and OSX6 libraries are also listed in Tables 5 and 6 for convenience.
  • Each CDR1, HV2, HV4 and CDR3 sequence is a subsequence of its respective VNAR domain set forth in SEQ ID NOS. 1-149.
  • the CDR1 sequence is found at amino acids 26-33 of the corresponding SEQ ID NO: for that domain; the HV2 sequence at amino acids 44-52; the HV4 sequence at amino acids 61-65; and the CDR3 sequence beginning at amino acid 85 and continuing the length of the particular CDR3.
  • the foregoing moieties further comprise at least one heterologous agent operably linked to the moiety to thereby form a conjugate.
  • the disclosure provides further SI fragment-binding moieties which comprise a Type II VNAR domain represented by the formula, from N to C terminus, FW 1 -CDR1 -FW2-HV2-FW2’ -HV4-FW3 -CDR3 -FW4, wherein CDR1 comprises or consists essentially of a peptide having an amino acid sequence of one of DSICALSS, DSNCALPS, DSVCALSS, or DSNCALSS (SEQ ID NOS.
  • CDR3 comprises or consists essentially of a peptide having an amino acid sequence of one of VHMEDMNVRD YGGFWGED V, VNLRSVLPCGWPDV, VENLPGSGSCLRYYLSDV, VREWACEDDGRVWGWEDV, V ART S GCE V YT YT GD V, VKNPSGCGVWYSQEDL, SEFKSGCGVFYELTDV, MVFKSVCEDNPYQYGL, or IWAHSGCEVITHAMDL (SEQ ID NOS. 154-162, respectively), and wherein said moiety is capable of specifically binding to an SI fragment comprising amino acids 16-685 of a SARS- CoV-2 spike protein.
  • HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively).
  • HV4 is SGSKS or RGSKS (SEQ ID NOS. 167-168, respectively).
  • the VNAR domain comprises one of the CDRls and CDR3s together with any one of the HV2s, with any one of the HV4s, or with both of any one of the HV2s and an HV4s.
  • the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 156) (from VNAR 61; the CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and the CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWE
  • the FW1, FW2, FW2’, FW3 and FW4 regions of the Type II VNAR domains have naturally occurring VNAR sequences or altered VNAR sequences with amino acid substitutions, insertions or deletions (typically, but not limited to, no more than 1- 10 amino acids changes, insertions or deletions) provided that such alterations maintain the overall primary and tertiary structure of the Type II VNAR, and provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs.
  • the FW1, FW2, FW2’, FW3 and FW4 regions of the Type II VNAR domains have a sequence for those regions as set forth in Tables 3 and 4 (in any independent combination), and, again, provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs.
  • these further moieties comprise any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135).
  • the VNAR domains of any of the moieties of the disclosure can optionally have a His-Tag (or other convenient tag for purification purposes). In some cases, such tags are removable.
  • any of the moieties of the disclosure further comprise at least one heterologous agent operably linked thereto to thereby form a conjugate.
  • heterologous agents include but are not limited to, one or more of a small molecule diagnostic or therapeutic; a DNA, RNA, or hybrid DNA-RNA; a traceable marker; a radioactive agent; an antibody; a single chain variable domain; or an immunoglobulin fragment.
  • the heterologous agent is an immunoglobulin fragment and is operably linked to the VNAR domain to form a fusion protein.
  • the immunoglobulin fragment is a human Fc domain.
  • the human Fc domain can be from any immunoglobulin isotype.
  • the isotype is an IgG, and more preferably IgGl. Fusion proteins are generally monospecific but can be bispecific.
  • any of the VNAR domains described herein can form all or part of the variable domain of a single variable domain antibody, a bi- or tri functional VNAR, a conventional antibody, or any fragment or fusion protein of said antibody as well as variable domains with antibody-like backbones.
  • Such constructs can be made by methods known to those of skill in the art.
  • single variable domain antibodies include, but are not limited to, a shark or other cartilaginous fish antibodies, camelid antibodies and nanobodies.
  • conventional antibodies include, but are not limited to, immunoglobins having both heavy and light chains, such as IgM’s, IgA’s, IgG’s, IgE’s, single chain Fv’s,
  • Fab fragments or any fragment or fusion protein of such antibodies or fragments.
  • any of the VNAR domains disclosed herein can be fused to an Fc domain of a conventional antibody to form a VNAR-Fc conjugate. Such fusions can be made at the N terminus or the C terminus of the Fc domain.
  • the Fc domain is a mammalian Fc domain, including primate Fc domains. More particularly, the Fc domain is a human Fc domain (hFc), a cynomolgus macaque Fc domain (cFc) or a murine Fc domain. Most preferably the Fc domain is an hFc domain.
  • the Fc domain is from an IgG, and preferably from IgGl.
  • Such fusions are also referred to herein as VNAR antibodies. Methods of making fusion proteins are well known in the art.
  • antibody -like backbones that may be used according to the disclosure include monospecific and bispecific backbones, such as multimerizing scFv fragments (diabodies, triabodies, tetrabodies), disulfide stabilized antibody variable (Fv) fragments, disulfide stabilized antigen-binding (Fab) fragments consisting of the V L , V H , C L and C H 1 domains, bivalent F(ab’)2 fragments, Fd fragments consisting of the heavy chain and C H I domains, dimeric C H 2 domain fragments (C H 2D), FC antigen binding domains (Fcabs), single chain FV-C H 3 minibodies, bispecific minibodies, isolated complementary determining region 3 (CDR3) fragments, constrained FR3-CDR3- FR4 polypeptides, SMIP domains, and any genetically manipulated counterparts of the foregoing that SI binding function (see e.g., Weiner L,
  • this disclosure provides VNAR antibodies which comprise an SI -specific binding moiety of the disclosure in which its VNAR domain is fused to a human Fc domain (hFc).
  • hFc human Fc domain
  • two chains can associate to form a dimer and thus produce a bispecific molecule, herein referred to as a bispecific VNAR antibody.
  • the VNAR antibodies of the disclosure are suitable for use in humans, particularly for providing passive immunity against SARS-CoV-2, and variants thereof, and for treating and ameliorating COVID-19 disease and associated symptoms.
  • the VNAR antibodies are capable of blocking the interaction and/or binding of the SARS-CoV-2 spike protein with the ACE2 receptor. In some embodiments, the VNAR antibodies are capable of blocking the interaction and/or binding of mutant SARS-CoV-2 spike protein with the ACE2 receptor. In some embodiments the mutant spike protein has a single mutation, including the E484K or N501 Y mutation. In some embodiments, the mutant spike protein is a quadruple mutant of SI containing K417N, E484K, N501 Y and D614G mutations.
  • spike mutations are referenced relative to the amino acid sequence of the spike protein from the Wuhan strain, for example, the E484K mutant has the amino acid glutamic acid (E) found at position 484 of the spike protein replaced with the amino acid lysine (K). Similarly, for the N501 Y mutation, the amino acid aspartic acid (N) found at position 501 is replaced with tyrosine (Y), and so on for the quadruple mutant and other mutants.
  • the VNAR antibodies are capable of neutralizing viral infection, including but not limited to the Wuhan strain and mutants thereof, including the mutants single E484K or N501Y mutation as well as a quadruple mutant of SI protein containing K417N, E484K, N501 Y and D614G mutations.
  • the VNAR domain is operably linked via a linker peptide to the C-terminus and/or N-terminus of the Fc domain, and preferably at the N-terminus.
  • the Fc domain is from an IgG, and preferably from IgGl but other human Fc domain isotype are contemplated.
  • VNAR antibody include but are not limited to SI -specific binding moieties having a Type II VNAR domain represented by the formula, from N to C terminus, FW1-CDR1-FW2-HV2-FW2 , -HV4-FW3-CDR3-FW4, wherein the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VEN
  • HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively).
  • HV4 is SGSKS or RGSKS (SEQ ID NOS. 167- 168, respectively).
  • the VNAR domain comprises the CDR1 and CDR3 pair together with any one of the HV2s, with any one of the HV4s, or with both of any one of the HV2s and an HV4s.
  • the FW1, FW2, FW2’, FW3 and FW4 regions can have naturally occurring VNAR sequences or altered VNAR sequences with amino acid substitutions, insertions or deletions (typically, but not limited to, no more than 1-10 amino acids changes, insertions or deletions) provided that such alterations maintain the overall primary and tertiary structure of a Type II VNAR domain, and provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs.
  • the FW1, FW2, FW2’, FW3 and FW4 regions of the Type II VNAR domains have a sequence for those regions as set forth in Tables 3 and 4 (in any independent combination), and, again, provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs.
  • the VNAR domain is any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135).
  • a VNAR antibody is capable of neutralizing infection of SARS-CoV-2
  • VNAR domains VNAR polypeptides
  • VNAR antibodies disclosed herein may optionally be conjugated (e.g., using linkers such as chemical linkers and/or linker peptides which are not usually associated with the domains being associated) to one or more additional agents which may include therapeutic and/or diagnostic agents.
  • Such agents include but are not limited to chemotherapeutics such as cytostatic drugs, cytotoxins, radioisotopes, chelators, enzymes, nucleases, nucleic acids such as DNA, RNA or mixed nucleic acid oligonucleotides, including siRNAs, shRNAs, microRNAs, aptamers and the like; immunomodulators such as therapeutic antibodies, antibody and antibody-like fragments, inflammatory and anti-inflammatory cytokines, anti-inflammatory agents, radiotherapeutics, photoactive agents, diagnostic markers and the like.
  • the pharmaceutically active moieties comprise at least one scFv molecule that is operably linked via a linker peptide to the C-terminus and/or N-terminus of an Fc region.
  • the moieties, VNAR domains (VNAR polypeptides) and VNAR antibodies disclosed herein are multispecific, i.e., have at least one binding site that binds to a first molecule or epitope of a molecule (i.e., the SI fragment) and one or more other binding sites that bind to at least one heterologous molecule or to an epitope of either SI, another SARS-CoV-2 protein or another molecule.
  • Multispecific binding molecules of the disclosure may comprise at least two binding sites, three binding sites, four binding sites or more.
  • the invention provides an isolated nucleic acid which encodes an Sl- fragment-specific binding moiety, conjugate, or VNAR antibody disclosed herein, or a fragment or derivative thereof.
  • the invention also provides an isolated nucleic acid molecule comprising a sequence that hybridizes under stringent conditions to a nucleic acid sequence which encodes a moiety, conjugate, or VNAR antibody of the disclosure , or a fragment or derivative thereof, or the antisense or complement of any such sequence.
  • the invention provides an isolated nucleic acid molecule encoding a fusion protein comprising at least two segments, wherein one of the segments comprises a moiety or VNAR domain disclosed herein.
  • a second segment comprises a heterologous signal polypeptide, a heterologous binding moiety, an immunoglobulin fragment such as a Fc domain, or a detectable marker.
  • a further aspect includes isolated nucleic acid molecules that encode moieties, conjugates, or VNAR antibodies of the disclosure or biologically active portions thereof.
  • nucleic acid fragments sufficient for use as hybridization probes to identify SI -fragment binding moieties encoding nucleic acids and fragments for use as polymerase chain reaction (PCR) primers for the amplification or mutation of nucleic acid molecules encoding VNAR domains disclosed herein.
  • PCR polymerase chain reaction
  • nucleic acid molecule is intended to include DNA molecules, RNA molecules (e.g., mRNA, shRNA, siRNA, microRNA), analogs of the DNA or RNA generated using nucleotide analogs, and derivatives, fragments and homologs thereof.
  • RNA molecules e.g., mRNA, shRNA, siRNA, microRNA
  • analogs of the DNA or RNA generated using nucleotide analogs and derivatives, fragments and homologs thereof.
  • the nucleic acid molecules of the disclosure may be single-, double-, or triple- stranded.
  • a nucleic acid molecule of the present disclosure may be isolated using sequence information provided herein and well known molecular biological techniques (e.g., as described in Sambrook et ah, Eds., MOLECULAR CLONING: A LABORATORY MANUAL 2ND ED., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; and Ausubel, et ah, Eds., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1993).
  • a nucleic acid molecule of the disclosure may be amplified using any form of nucleic acid template and appropriate oligonucleotide primers according to standard PCR amplification techniques. Amplified nucleic acid may be cloned into an appropriate vector and characterized, e.g., by restriction analysis or DNA sequencing. Furthermore, oligonucleotides corresponding to nucleotide sequences that encode a moiety, conjugate, or VNAR antibody of the disclosure may be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • oligonucleotide refers to a series of covalently linked nucleotide (or nucleoside residues, including ribonucleoside or deoxyribonucleoside residues) wherein the oligonucleotide has a sufficient number of nucleotide bases to be used in a PCR reaction.
  • Oligonucleotides comprise portions of a nucleic acid sequence having at least about 10 nucleotides and as many as 50 nucleotides, preferably about 15 nucleotides to 30 nucleotides. Oligonucleotides may be chemically synthesized and may be used as probes. A short oligonucleotide sequence may be used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue.
  • nucleic acid molecules (or proteins) of the disclosure include, inter alia , nucleic acid (or polypeptide) molecules having regions that are substantially homologous to the nucleic acid molecules or proteins of the invention, e.g., by at least about 45%, 50%, 70%, 80%, 95%, 98%, or even 99% identity (with a preferred identity of 80-99%) over a nucleic acid or amino acid sequence of the same size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art.
  • a percent identity for any candidate nucleic acid or polypeptide relative to a reference nucleic acid or polypeptide may be determined by aligning a reference sequence to one or more test sequences using, for example, the computer program ClustalW (version 1.83, default parameters), which enable nucleic acid or polypeptide sequence alignments across their entire lengths (global alignment) or across a specified length. The number of identical matches in such a ClustalW alignment is divided by the length of the reference sequence and multiplied by 100.
  • ClustalW version 1.83, default parameters
  • nucleic acid molecules capable of hybridizing to the complement of a sequence encoding the proteins of the disclosure under stringent or moderately stringent conditions. See e g. Ausubel, et ah, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1993, and below.
  • An exemplary program is the GAP program (Wisconsin Sequence Analysis Package, Version 8 for UNIX, Genetics Computer Group, University Research Park, Madison, Wis.) using the default settings, which uses the algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482489).
  • Derivatives and analogs may be full length or other than full length, if the derivative or analog contains a modified nucleic acid or amino acid, as described below.
  • Stringent conditions are known to those skilled in the art and may be found in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. In certain embodiments, stringent conditions typically permit sequences at least about 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% homologous to each other to remain hybridized to each other.
  • a non-limiting example of stringent hybridization conditions is hybridization in a high salt buffer comprising 6> ⁇ SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 mg/ml denatured salmon sperm DNA at 65° C. This hybridization is followed by one or more washes in 0.2> ⁇ SSC, 0.01% BSA at 50° C.
  • stringent hybridization conditions refers to conditions under which a nucleic acid probe, primer or oligonucleotide will hybridize to its target sequence, but only negligibly or not at all to other nucleic acid sequences.
  • Stringent conditions are sequence- and length-dependent and depend on % (percent)-identity (or %- mismatch) over a certain length of nucleotide residues. Longer sequences hybridize specifically at higher temperatures than shorter sequences. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.
  • the moieties, conjugates, and VNAR antibodies of the disclosure may be manufactured by standard synthetic methods, by use of recombinant expression systems, or by any other suitable method.
  • these entities may be synthesized in a number of ways, including, e.g., methods comprising: (1) synthesizing a polypeptide or polypeptide component thereof using standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide compound product; (2) expressing a nucleic acid construct that encodes the polypeptide or polypeptide component thereof in a host cell and recovering the expression product from the host cell or host cell culture; or (3) cell-free in vitro expression of a nucleic acid construct encoding the polypeptide or polypeptide component thereof, and recovering the expression product; or by any combination of the methods of (1), (2) or (3) to obtain fragments of the peptide component, subsequently joining (e.g., ligating) the fragments to obtain the peptide component, and recovering the
  • peptides may be synthesized by, e.g., methods comprising synthesizing the peptide by standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide product.
  • the present disclosure also relates to methods for producing a moiety, conjugate, or VNAR antibody of the disclosure according to above recited methods; a nucleic acid molecule encoding part or all of such polypeptides, a vector comprising at least one nucleic acid of the disclosure, expression vectors comprising at least one nucleic acid of the disclosure capable of producing a moiety, conjugate, or VNAR antibody of the disclosure when introduced into a host cell, and a host cell comprising a nucleic acid molecule, vector or expression vector of the disclosure invention.
  • the moieties, conjugates, and VNAR antibodies of the disclosure may be prepared using recombinant techniques well known in the art.
  • methods for producing such polypeptides by culturing host cells transformed or transfected with a vector comprising the encoding nucleic acid and recovering the polypeptide from cell culture are described in, e.g., Sambrook et ah, Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989); Dieffenbach et ah, PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995).
  • a nucleic acid encoding a desired polypeptide may be inserted into a replication vector for further cloning (amplification) of the DNA or for expression of the nucleic acid into RNA and protein.
  • a multitude of cloning and expression vectors are publicly available and suitable for use.
  • Expression vectors capable of directing transient or stable expression of genes and having promoters operably linked to such genes are well known in the art.
  • the vector components generally include, but are not limited to, one or more of the following: a heterologous signal sequence or peptide, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence, each of which is well known in the art.
  • Optional regulatory control sequences, integration sequences, and useful markers that can be employed are known in the art.
  • Any suitable host cell may be used to produce moieties, conjugates, and VNAR antibodies of the disclosure.
  • Host cells may be cells stably or transiently transfected, transformed, transduced or infected with one or more expression vectors which drive expression of a polypeptide of the invention.
  • Suitable host cells for cloning or expressing nucleic acids of the invention include prokaryote, yeast, or higher eukaryote cells.
  • Eukaryotic microbes such as filamentous fungi yeast, Arabidopsis, and other plant and animal eukaryotic host cells that may be grown in liquid culture are suitable cloning or expression hosts for vectors. Suitable host cells for the expression of glycosylated polypeptides may also be derived from multicellular organisms.
  • Mammalian cells are preferred host cells for expression of polypeptides.
  • Particularly useful mammalian cells include, inter alia , HEK 293, NSO, DG-44, and CHO cells, but any other suitable host cell may be used according to the invention.
  • the moieties, conjugates, or VNAR antibodies of the disclosure are secreted into the medium in which the host cells are cultured, from which the moieties, conjugates, or VNAR antibodies of the disclosure may be recovered or purified.
  • a polypeptide When a polypeptide is produced in a recombinant cell other than one of human origin, it is typically free of polypeptides of human origin. In certain embodiments, it is advantageous to separate a polypeptide away from other recombinant cell components such as host cell polypeptides to obtain preparations that are of high purity or substantially homogeneous.
  • culture medium or cell lysates may be centrifuged to remove particulate cell debris and suitable protein purification procedures may be performed.
  • Such procedures include, inter alia , fractionation (e.g., size separation by gel filtration or charge separation by ion-exchange column); ethanol precipitation; Protein A Sepharose columns to remove contaminants such as IgG; hydrophobic interaction chromatography; reverse phase HPLC; chromatography on silica or on cation-exchange resins such as DEAE and the like; chromatofocusing; electrophoretic separations; ammonium sulfate precipitation; gel filtration using, for example, Sephadex beads such as G-75. Any number of biochemical purification techniques may be used to increase the purity of a SI -binding moiety, conjugate, or VNAR antibody of the disclosure.
  • the disclosure provides a method of passive immunization against SARS-CoV-2, and variants thereof, which comprises administering a pharmaceutical composition of the disclosure to a subject in need thereof.
  • the disclosure provides a method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19.
  • a pharmaceutical composition of the disclosure comprises administering a pharmaceutical composition of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19.
  • Such compositions are described in more detail below but include pharmaceutical compositions comprising at least one SI -specific binding moiety, conjugate or VNAR antibody of the disclosure.
  • such compositions can also have, independently, two, three, four, five or more moieties, conjugates or VNAR antibodies of the disclosure.
  • the moieties, conjugates, and VNAR antibodies of the disclosure can be used the preparation of a medicament to for passive immunization against SARS-CoV-2 and viral variants (mutants) thereof or to treat or prevent COVID-19 in a mammalian subject in need thereof.
  • the subject or mammal has tested positive for SARS-CoV-2. In embodiments of these methods, the subject or mammal has suspected exposure to SARS-CoV-2 and/or tested negative for SARS-CoV-2. In some embodiments of these methods, the composition is preferably administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
  • a further aspect relates to pharmaceutical compositions comprising at least one moiety, conjugate, or VNAR antibody of the disclosure.
  • such compositions can also have, independently, two, three, four, five or more of such moieties, conjugates or VNAR antibodies.
  • the moieties, conjugates and VNAR antibodies may be present as a pharmaceutically acceptable salt or solvate, together with a pharmaceutically acceptable carrier, excipient or vehicle. Certain embodiments of the pharmaceutical compositions of the invention are described in further detail below.
  • moieties, conjugates and VNAR antibodies of the present disclosure may be formulated as pharmaceutical compositions prepared for storage or administration, which typically comprise a therapeutically effective amount of a compound of the disclosure, or a salt thereof, in a pharmaceutically acceptable carrier.
  • the therapeutically effective amount of a moiety, conjugate or VNAR antibody of the present disclosure will depend on the route of administration, the type of mammal being treated, and the physical characteristics of the specific mammal under consideration. These factors and their relationship to determining this amount are well known to skilled practitioners in the medical arts. This amount and the method of administration can be tailored to achieve optimal efficacy, and may depend on such factors as weight, diet, concurrent medication and other factors, well known to those skilled in the medical arts. The dosage sizes and dosing regimen most appropriate for human use may be guided by the results obtained by the present invention and may be confirmed by clinical trials.
  • An effective dosage and treatment protocol may be determined by conventional means, starting with a low dose in laboratory animals and then increasing the dosage while monitoring the effects, and systematically varying the dosage regimen as well. Numerous factors may be taken into consideration by a clinician when determining an optimal dosage for a given subject. Such considerations are known to the skilled person.
  • pharmaceutically acceptable carrier includes any of the standard pharmaceutical carriers. Pharmaceutically acceptable carriers for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985). For example, sterile saline and phosphate- buffered saline at slightly acidic or physiological pH may be used.
  • pH buffering agents may be phosphate, citrate, acetate, tris/hydroxymethyl)aminom ethane (TRIS), N- Tris(hydroxymethyl)methyl-3-aminopropanesulphonic acid (TAPS), ammonium bicarbonate, diethanolamine, histidine, which is a preferred buffer, arginine, lysine, or acetate or mixtures thereof.
  • TIS tris/hydroxymethyl)aminom ethane
  • TAPS N- Tris(hydroxymethyl)methyl-3-aminopropanesulphonic acid
  • ammonium bicarbonate diethanolamine
  • histidine which is a preferred buffer
  • arginine arginine
  • lysine or acetate or mixtures thereof.
  • the term further encompasses any agents listed in the US Pharmacopeia for use in animals, including humans.
  • salt refers to the salt of the compounds.
  • a pharmaceutically-acceptable salt retains qualitatively a desired biological activity of the parent compound without imparting any undesired effects relative to the compound.
  • Salts include pharmaceutically acceptable salts such as acid addition salts and basic salts.
  • Acid addition salts include salts derived from nontoxic inorganic acids, such as hydrochloric, nitric, phosphorous, phosphoric, sulfuric, hydrobromic, hydroiodic and the like, or from nontoxic organic acids such as aliphatic mono- and di-carboxylic acids, phenyl- substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like.
  • nontoxic inorganic acids such as hydrochloric, nitric, phosphorous, phosphoric, sulfuric, hydrobromic, hydroiodic and the like
  • nontoxic organic acids such as aliphatic mono- and di-carboxylic acids, phenyl- substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like.
  • Examples of basic salts include salts where the cation is selected from alkali metals, such as sodium and potassium, alkaline earth metals such as calcium and magnesium, and ammonium ions + N(R 3 ) 3 (R 4 ), where R 3 and R 4 independently designate optionally substituted Ci- 6 -alkyl, optionally substituted C2-6-alkenyl, optionally substituted aryl, or optionally substituted heteroaryl, and more specifically, the organic amines, such as N, N'-dibenzylethylenediamine, N-methylglucamine, chloroprocaine, choline, diethanolamine, ethylenediamine, procaine and the like.
  • alkali metals such as sodium and potassium
  • alkaline earth metals such as calcium and magnesium
  • R 3 and R 4 independently designate optionally substituted Ci- 6 -alkyl, optionally substituted C2-6-alkenyl, optionally
  • Treatment is an approach for obtaining beneficial or desired clinical results.
  • beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable.
  • Treatment can also mean prolonging survival as compared to expected survival if not receiving treatment.
  • Treatment is an intervention performed with the intention of preventing the development or altering the pathology of a disorder.
  • treatment refers to both therapeutic treatment and prophylactic or preventative measures in certain embodiments.
  • Those in need of treatment include those already with the disorder as well as those in which the disorder is to be prevented.
  • treatment is meant inhibiting or reducing an increase in pathology or symptoms when compared to the absence of treatment and is not necessarily meant to imply complete cessation of the relevant condition.
  • the pharmaceutical compositions can be in unit dosage form.
  • the composition is divided into unit doses containing appropriate quantities of the active component.
  • the unit dosage form can be a packaged preparation, the package containing discrete quantities of the preparations, for example, packeted tablets, capsules, and powders in vials or ampoules.
  • the unit dosage form can also be a capsule, cachet, or tablet itself, or it can be the appropriate number of any of these packaged forms. It may be provided in single dose injectable form, for example in the form of a pen.
  • Compositions may be formulated for any suitable route and means of administration.
  • Pharmaceutically acceptable carriers or diluents include those used in formulations suitable for oral, rectal, nasal or parenteral (including subcutaneous, intramuscular, intravenous, intradermal, and transdermal) administration.
  • the formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. Subcutaneous or transdermal modes of administration may be particularly suitable for the compounds described herein.
  • An acceptable route of administration may refer to any administration pathway known in the art, including but not limited to aerosol, enteral, nasal, ophthalmic, oral, parenteral, rectal, vaginal, or transdermal (e.g., topical administration of a cream, gel or ointment, or by means of a transdermal patch).
  • parenteral administration is typically associated with injection at or in communication with the intended site of action, including infraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrastemal, intrathecal, intrauterine, intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal, or transtracheal administration.
  • a composition e.g., a pharmaceutical composition, comprising one moiety, conjugate or VNAR antibody of the present disclosure, or a combination of different such or a combination of different such moieties, conjugates or VNAR antibodies, and at least one pharmaceutically acceptable carrier.
  • compositions of the invention may be administered alone or in combination with one or more other therapeutic or diagnostic agents.
  • a combination therapy may include a moiety, conjugate or VNAR antibody of the present disclosure combined with at least one other therapeutic agent selected based on the particular patient, disease or condition to be treated.
  • agents include, inter alia, a cytotoxic, anti cancer or chemotherapeutic agent, an anti-inflammatory or anti-proliferative agent, an antimicrobial or antiviral agent, growth factors, cytokines, an analgesic, a therapeutically active small molecule or polypeptide, a single chain antibody, a classical antibody or fragment thereof, or a nucleic acid molecule which modulates one or more signaling pathways, and similar modulating therapeutics which may complement or otherwise be beneficial in a therapeutic or prophylactic treatment regimen.
  • a cytotoxic, anti cancer or chemotherapeutic agent an anti-inflammatory or anti-proliferative agent
  • an antimicrobial or antiviral agent growth factors
  • cytokines an analgesic
  • a therapeutically active small molecule or polypeptide a single chain antibody, a classical antibody or fragment thereof, or a nucleic acid molecule which modulates one or more signaling pathways, and similar modulating therapeutics which may complement or otherwise be beneficial in a therapeutic or prophylactic treatment regimen.
  • pharmaceutically acceptable carrier includes any and all physiologically acceptable, i.e., compatible, solvents, dispersion media, coatings, antimicrobial agents, isotonic and absorption delaying agents, and the like.
  • the carrier is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal or epidermal administration (e.g., by injection or infusion).
  • the conjugate of the invention may be coated in a material or materials intended to protect the compound from the action of acids and other natural inactivating conditions to which the active conjugate may encounter when administered to a subject by a particular route of administration.
  • a pharmaceutical composition of the invention also optionally includes a pharmaceutically acceptable antioxidant.
  • exemplary pharmaceutically acceptable antioxidants are water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propylgallate, alpha-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
  • water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite and the like
  • oil-soluble antioxidants such as ascorbyl palmitate, butylated hydroxy
  • aqueous and nonaqueous carriers examples include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyloleate.
  • polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
  • vegetable oils such as olive oil
  • injectable organic esters such as ethyloleate.
  • Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
  • compositions of the disclosure may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of presence of microorganisms may be ensured both by sterilization procedures, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. Isotonic agents, such as sugars, sodium chloride, and the like into the compositions, may also be desirable. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as, aluminum monostearate and gelatin.
  • adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of presence of microorganisms may be ensured both by sterilization procedures, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. Isotonic agents, such
  • Exemplary pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • Such media and reagents for pharmaceutically active substances are known in the art.
  • the pharmaceutical compositions of the invention may include any conventional media or agent unless any is incompatible with the active conjugate of the invention. Supplementary active compounds may further be incorporated into the compositions.
  • compositions are typically sterile and stable under the conditions of manufacture and storage.
  • the composition may be formulated as a solution, microemulsion, liposome, or other ordered structure suitable to high drug concentration.
  • the carrier may be a solvent or dispersion medium containing, for example, water, alcohol such as ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol), or any suitable mixtures.
  • the proper fluidity may be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by use of surfactants according to formulation chemistry well known in the art.
  • isotonic agents e.g., sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride may be desirable in the composition.
  • Prolonged absorption of injectable compositions may be brought about by including in the composition an agent that delays absorption for example, monostearate salts and gelatin.
  • Solutions or suspensions used for intradermal or subcutaneous application typically include one or more of: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates; and tonicity adjusting agents such as, e.g., sodium chloride or dextrose.
  • a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents
  • antibacterial agents such as benzyl alcohol or methyl parabens
  • antioxidants such as ascorbic acid or sodium bisulfite
  • chelating agents such as
  • the pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide, or buffers with citrate, phosphate, acetate and the like. Such preparations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • acids or bases such as hydrochloric acid or sodium hydroxide, or buffers with citrate, phosphate, acetate and the like.
  • Such preparations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • Sterile injectable solutions may be prepared by incorporating a conjugate of the invention in the required amount in an appropriate solvent with one or a combination of ingredients described above, as required, followed by sterilization microfiltration.
  • Dispersions may be prepared by incorporating the active compound into a sterile vehicle that contains dispersion medium and other ingredients, such as those described above.
  • a sterile vehicle that contains dispersion medium and other ingredients, such as those described above.
  • the methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient in addition to any additional desired ingredient from a sterile-filtered solution thereof.
  • the binding agent When a therapeutically effective amount of a moiety, conjugate or VNAR antibody of the present disclosure is administered by, e.g., intravenous, cutaneous or subcutaneous injection, the binding agent will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. Methods for preparing parenterally acceptable protein solutions, taking into consideration appropriate pH, isotonicity, stability, and the like, are within the skill in the art.
  • a preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection will contain, in addition to binding agents, an isotonic vehicle such as sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection, or other vehicle as known in the art.
  • a pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives well known to those of skill in the art.
  • the amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending on a variety of factors, including the subject being treated, and the particular mode of administration. In general, it will be an amount of the composition that produces an appropriate therapeutic effect under the particular circumstances. Generally, out of one hundred percent, this amount will range from about 0.01 per cent to about ninety-nine percent of active ingredient, from about 0.1 per cent to about 70 per cent, or from about 1 percent to about 30 percent of active ingredient in combination with a pharmaceutically acceptable carrier.
  • Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic response). For example, a single bolus may be administered, several divided doses may be administered over time, or the dose may be proportionally reduced or increased as indicated by the particular circumstances of the therapeutic situation, on a case by case basis. It is especially advantageous to formulate parenteral compositions in dosage unit forms for ease of administration and uniformity of dosage when administered to the subject or patient.
  • a dosage unit form refers to physically discrete units suitable as unitary dosages for the subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce a desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention depend on the specific characteristics of the active compound and the particular therapeutic effect(s) to be achieved, taking into consideration and the treatment and sensitivity of any individual patient.
  • the dosage range will generally be from about 0.0001 to 100 mg/kg, and more usually 0.01 to 5 mg/kg, of the host body weight.
  • Exemplary dosages may be 0.25 mg/kg body weight, 1 mg/kg body weight, 3 mg/kg body weight, 5 mg/kg body weight or 10 mg/kg body weight or within the range of 1-10 mg/kg.
  • An exemplary treatment regime is a once or twice daily administration, or a once or twice weekly administration, once every two weeks, once every three weeks, once every four weeks, once a month, once every two or three months or once every three to 6 months.
  • Dosages may be selected and readjusted by the skilled health care professional as required to maximize therapeutic benefit for a particular subject, e.g., patient.
  • the moieties, conjugates or VNAR antibodies of the present disclosure will typically be administered on multiple occasions. Intervals between single dosages can be, for example, 2-5 days, weekly, monthly, every two or three months, every six months, or yearly.
  • two or more moieties, conjugates or VNAR antibodies of the present disclosure with different binding properties may be administered simultaneously or sequentially, in which case the dosage of each administered compound may be adjusted to fall within the ranges described herein.
  • a moiety, conjugate or VNAR antibody of the present disclosure may be administered as a sustained release formulation, in which case less frequent administration is required. Dosage and frequency vary depending on the half-life of the conjugate in the subject or patient. The dosage and frequency of administration may vary depending on whether the treatment is therapeutic or prophylactic (e.g., preventative), and may be adjusted during the course of treatment. In certain prophylactic applications, a relatively low dosage is administered at relatively infrequent intervals over a relatively long period of time. Some subjects may continue to receive treatment over their lifetime. In certain therapeutic applications, a relatively high dosage at relatively short intervals is sometimes required until progression of the disease is reduced or until the patient shows partial or complete amelioration of symptoms of disease. Thereafter, the patient may be switched to a suitable prophylactic dosing regimen.
  • prophylactic e.g., preventative
  • a selected dosage level will depend upon a variety of factors, such as pharmacokinetic factors, including the activity of the particular conjugate or composition employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the subject or patient being treated, and similar factors well known in the medical arts.
  • factors such as pharmacokinetic factors, including the activity of the particular conjugate or composition employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the subject or patient being treated, and similar factors well known in the medical arts.
  • Therapeutic compounds or compositions of the invention may be administered with one or more of a variety of medical devices known in the art.
  • a therapeutic conjugate of the invention may be administered with a needleless hypodermic injection device.
  • implants and modules useful in the present invention are in the art, including e.g., implantable micro-infusion pumps for controlled rate delivery; devices for administering through the skin; infusion pumps for delivery at a precise infusion rate; variable flow implantable infusion devices for continuous drug delivery; and osmotic drug delivery systems. These and other such implants, delivery systems, and modules are known to those skilled in the art.
  • the VNAR domain has the basic structure of an Ig variable domain with two b sheets held together by two canonical cysteine residues that stabilize the framework. Unlike Ig variable domains, however, VNARs typically have one or two additional disulfide bonds and are classified into four isoforms based on the number and position of these non-canonical cysteines (Zielonka, Empting 2015). Semi -synthetic VNAR libraries based on the Type I and Type II VNAR isoforms are available (W02015/200883, published December 30, 2015) and on the Type IV VNAR isoforms (WO2019/246288).
  • the Type I VNAR contains non- canonical cysteines in CDR3 that form two disulfide bonds with cysteine in the framework and has only been reported in the nurse shark ( Ginglymostoma cirratum) to date.
  • the Type II VNAR which is the most predominant isoform among the various shark species, is distinguished by a disulfide bond between a cysteine in CDR3 and another cysteine in CDR1.
  • the additional disulfide bonds in both Type I and Type II VNARs serve to stabilize and orient the CDR3 such that it can protrude into binding pockets and grooves (Diaz 2002).
  • Type IV VNARs contain the framework cysteines that form the Ig fold but lack any additional cysteines.
  • VNAR domain libraries disclosed herein are Type II isoform libraries designed from analysis of the natural diversity found in the VNAR scaffold that occurs during the nurse shark immune response. Using nurse sharks immunized with a variety of immunogens, blood samples were collected pre- and post-immunization at different time points from 6 animals, in total producing 30 individual immune repertoire libraries that were subsequently analyzed by next-generation sequencing (NGS). The most common type II VNAR N-termini were identified and overlapping oligonucleotides encoding selected N-terminal fragments covering residues 1-84 with canonical cysteines in positions 22, 29 and 83 were synthesized containing residue substitutions depicted in Table 1.
  • the CDR1, HV2 and HV4 regions cover positions 26-33, 44-52 and 61-65, respectively.
  • the CDR3 region within the C-terminal fragment was designed based on NGS analysis of these immune repertoire libraries, which had the most common lengths for CDR3 as 15, 16 and 17 residues with a canonical cysteine located approximately in the middle of CDR3 (Table 2).
  • a library was generated by enzymatic ligation of 1068 different N- terminal fragments-encoding oligonucleotides (having the amino acid sequences of SEQ ID NOS.
  • Methods to make the libraries disclosed herein include but are not limited to, direct synthesis of nucleic acid libraries and site-directed mutagenesis, and for peptide libraries, direct chemical synthesis.
  • Direct synthesis methods are preferred, in part, because the N- terminal and the randomized C-terminal fragments can be designed to exclude potentially detrimental motifs such as: glycosylation (NxS NxT, where x is not P), asparagine deamidation (NG, NS, NT, NH), aspartate isomerization (DG, DS, DT, DD), lysine glycation (LE, LD, LL), integrin binding a ⁇ ; b3 (RGD, RYD, KGD, NGR), integrin binding a4b1 (LDV), integrin binding a2b1 (DGE), CD11 c/CD 18 binding (GRP), fragmentation (DP, DQ) and hydrophobicity (FF, FW, WW, WF).
  • VNAR domain structure is shown in Figure 1, with the N- and C-terminal fragments indicated below the domain.
  • the size of the library is sufficiently large enough and diverse enough to produce many suitable VNARs to bind to targets of interest during the screening process.
  • one aspect of the present invention relates to improved Type II VNAR libraries based on nurse shark immune repertoire library analysis across the entire VNAR domain. These libraries have optimized VNAR scaffolds (i.e., for the framework regions) and/or improved CDR3 loops in accordance with the disclosures herein.
  • libraries of the disclosure comprise synthetic polypeptide compositions and/or nucleic acid molecules encoding them and may be used in assays, e.g., in phage display libraries, to identify and select sequences within the synthetic library which bind selectively to one or more molecular mammalian target molecules of interest.
  • Libraries of the invention enable the generation of novel therapeutic products, in particular, specific binding moieties which bind selectively and with high affinity to a select cellular target, thereby producing a target antagonist compound or mimicking the activity of a native molecule.
  • binding moieties and molecular target antagonist compounds which may be identified and isolated using the libraries of the invention include, inter alia , high affinity polypeptide binding domains specific for wildtype and mutant proteins, such as those described herein against coronavirus SARS-CoV-2 spike protein SI domain and mutants thereof as well as for species cross reactive proteins, such as human and mouse CD98hc and other targets of interest such as human BAFF, human and mouse transferrin receptor hTrR-1, myostatin and other antigens.
  • the present disclosure is directed to a synthetic nucleic acid-containing library whose members each encode a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C- terminus,
  • FW Type II VNAR framework
  • HV hypervariable
  • CDR complementary determining region
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine;
  • X b is Y, L, D, S or G;
  • X c is D, V, W, Y or G;
  • X d is W, E, Y, D, or G;
  • X e is Y, L, D, V or L;
  • X f is D or G; and
  • X g is V or L;
  • the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
  • the disclosure provides a synthetic nucleic acid-containing library whose members each comprise a nucleic acid encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
  • FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
  • CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
  • FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
  • HV2 is 9 amino acids in length;
  • FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
  • HV4 is 5 amino acids in length
  • FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine, X b is Y, L, D, S or G; Xc is D, V, W, Y or G; X d is W, E, Y, D, or G; X e is Y, L, D, V or L; X f is D or G; and X g is V or L; and
  • FW4 is 10 amino acids in length and has an amino acid sequence comprising
  • the residue at each position of said VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
  • any of the nucleic acid libraries of the disclosure are phage display libraries. Such libraries may comprise approximately 10 9 theoretically distinct nucleic acid sequences.
  • the nucleic acid libraries hereof are used in various methods for identifying polypeptides that bind selectively to target molecules of interest.
  • An embodiment provides a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises: (a) exposing a target molecule of interest to polypeptides produced by expression of a nucleic acid library of the disclosure; and (b) separating polypeptides that selectively bind from those that do not selectively bind the target molecule.
  • the target molecule of interest is expressed on the surface of a phage, bacterium or cell, or is attached to, tethered to or otherwise associated with a solid support.
  • Another embodiment provides a method of screening a library for a polypeptide that selectively binds with high affinity to a target molecule of interest, the library comprising a plurality of polypeptides produced by expression of a nucleic acid library of the disclosure and comprises: (a) incubating a sample of the library with a concentration of a target molecule under conditions suitable for specific binding of the polypeptides to the molecule; (b) incubating a second sample of the library under the same conditions but without target molecule; (c) contacting each of the first and second samples with immobilized target molecule under conditions suitable for binding of the polypeptide to the immobilized target antigen; (d) detecting the polypeptide bound to immobilized target molecule for each sample; (e) determining the affinity of the polypeptide for the target molecule by calculating the ratio of the amounts of bound polypeptide from the first sample over the amount bound polypeptide from the second sample.
  • Yet another embodiment provides a method of identifying one or more VNARs that selectively bind to a target molecule of interest which comprises: (a) contacting said target molecule with a phage display library of Claim 40 or 41; (b) separating phage that selectively bind the target molecule from those that do not selectively bind the target molecule to produce an enriched phage library; (c) repeating steps (a) and (b) with the enriched phage library to produce a further enriched phage library; (d) repeating step (c) until the further enriched phage library is enriched from at least about 10- to about 10 6 -fold or more relative to the original phage library; and (e) plating the further enriched phage library and isolating and characterizing individual clones therefrom to thereby identify one or more VNAR polypeptides that selectively bind to the target molecule of interest.
  • the number of cycles needed to obtain a sufficiently further enriched phage library to readily isolate the desired, individual clones typically ranges from three to eight rounds of selection and more typically can be done with 3-4 rounds of selection.
  • either the target molecule or the phage display library can be bound to or attached to a solid support to facilitate selective binding (and simplify wash conditions, which stringency can be varied in successive rounds (see, the Examples). Any method known in the art for eluting and recovering bound phage can be used.
  • the target molecule is a SARS- CoV-2 spike protein, a domain of the spike protein or a mutant thereof.
  • a still further aspect relates to a polypeptide library composition
  • a polypeptide library composition comprising a plurality of synthetic or recombinant polypeptides, each of which encodes a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C- terminus,
  • FW Type II VNAR framework
  • HV hypervariable
  • CDR complementary determining region
  • X ai and X a 2 are independently any amino acid except cysteine;
  • X b is Y, L, D, S or G;
  • Xc is D, V, W, Y or G;
  • X d is W, E, Y, D, or G;
  • X e is Y, L, D, V or L;
  • X f is D or G; and
  • X g is V or L;
  • the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
  • the disclosure provides a polypeptide library composition whose members each comprise a polypeptide encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
  • FW Type II VNAR framework
  • HV hypervariable
  • CDR complementary determining region
  • FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
  • CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
  • FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
  • HV2 is 9 amino acids in length
  • FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
  • HV4 is 5 amino acids in length
  • FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
  • CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
  • X ai and X a 2 are independently any amino acid except cysteine, X b is Y, L, D, S or G; Xc is D, V, W, Y or G; X d is W, E, Y, D, or G; X e is Y, L, D, V or L; X f is D or G; and X g is V or L; and
  • FW4 is 10 amino acids in length and has an amino acid sequence comprising YG[D/G]GT[A/V]VTVN (SEQ ID NO: 1245).
  • the residue at each position of the VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
  • a plurality is 50 or more or as defined herein (see above).
  • the composition can have from 100 to 10 10 polypeptides as determined by the phage titer.
  • Yet a further aspect relates to a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises (a) exposing a target molecule of interest to a polypeptide library composition of the disclosure; and (b) separating polypeptides that selectively bind to said target molecule from those that do not selectively bind the target molecule.
  • VNAR libraries may be screened and clones comprising putative binding moiety sequences (polypeptide and/or nucleic acid) may be enriched, purified and tested in whatever in vitro and in vivo biological assays are known and available to the art for the particular molecular target molecule of interest. Once molecular target-binding clones are isolated, polypeptide and/or nucleic acid molecules encoding the synthetic VNAR binding moieties may be identified and optionally isolated.
  • One of skill in the art can use standard genetic and molecular engineering, e.g., affinity maturation and other well-known techniques to optimize the characteristics of the binding moiety for its intended purpose, e.g., to produce improved diagnostic agents or therapeutic versions by making sequence variants and derivatives expected to be more potent or otherwise more drug-like with respect to half-life, pK, solubility, bioavailability, cellular or tissue targeting, in vivo clearance and the like.
  • the OSX6 library was designed based on natural diversity found in the VNAR scaffold that occurs during the nurse shark immune response. Nurse sharks were immunized with a variety of immunogens and blood samples were collected pre- and post-immunization at different time points from 6 animals in total producing 30 individual immune repertoire libraries that were subsequently analyzed by next-generation sequencing (NGS). The most common type II VNAR N-termini were identified and overlapping oligonucleotides encoding selected N-terminal fragments covering residues 1-84 with canonical cysteines in positions 22, 29 and 83 were synthesized containing residue substitutions depicted in Table 1.
  • the CDR1, HV2 and HV4 regions cover positions 26-33, 44-52 and 61-65, respectively.
  • the library was generated by enzymatic ligation of 1068 different N-terminal fragments encoding oligonucleotides (having the amino acid sequences of SEQ ID NOS. 177-1244) with approximately lxlO 6 of C-terminal fragments-encoding oligonucleotides containing the CDR3 that were synthesized following residue representation instructions outlined in Table 2.
  • the CDR3 fragment covers residues 85-100 with a canonical cysteine in position 91.
  • the CDR3 region within C-terminal fragment was designed based on NGS analysis of the immune repertoire libraries, which had the most common lengths for CDR3 as 15, 16 and 17 residues with canonical cysteine located approximately in the middle of CDR3 (Table 2).
  • the amino acid representation in each position for positions 85-100 of the C-terminal fragments was as follows:
  • the randomized C-terminal fragments were designed to exclude potentially detrimental motifs such as: glycosylation (NxS NxT, where x is not P), asparagine deamidation (NG, NS, NT, NH), aspartate isomerization (DG, DS, DT, DD), lysine glycation (LE, LD, LL), integrin binding aUb3 (RGB, RYD, KGD, NGR), integrin binding a4b! (LDV), integrin binding a2b1 (DGE), GDI 1 c/CD 18 binding (GRP), fragmentation (DP, DQ) and hydrophobicity (FF, FW, WW, WF).
  • NxS NxT glycosylation
  • NG asparagine deamidation
  • DG aspartate isomerization
  • DG aspartate isomerization
  • LDV lysine glycation
  • LUV integrin binding a2b
  • the final OSX6 library size and diversity was approximately lxlO 9 .
  • the full OSX6 library was cloned into the expression vector phagemid pOsD2, a modified version of pSEX81 (Progen) in which a 6XHis tag, (SEQ ID NO: 169), a FLAG tag, and an amber stop codon were inserted between the VNAR domain (inserted into Sfil sites) and the full-length PHI protein of the M13 phage as described in U S Patent No 10,479,990.
  • the OSX6 phage library has a framework as well as a CDR3 loop closely resembling the natural repertoire of VNAR domains found in nurse sharks.
  • the framework diversity included modifications to the germline sequence that spread across the whole VNAR scaffold and were not limited to CDR1, HV2, HV4 and CDR3.
  • Such a design should increase stability, expression yields and developability, thus increasing the success rate for the discovery of functional antibodies despite reduced diversity in CDR3 loop.
  • the direct synthesis of the fragments used for generation of the OSX6 library rather than the use of the degenerate NNK codon method, assured a high level of accuracy and nearly exact match between theoretical and achieved design.
  • the direct synthesis also allowed the removal of know liability motifs including glycosylation, asparagine deamidation, aspartate isomerization, lysine glycation, integrin binding, CD 11 c/CD 18 binding, fragmentation and hydrophobicity patches that further improved developability characteristics of VNAR domains isolated from the OSX6 library.
  • the phage selection process was performed with two different Type II VNAR semi-synthetic libraries, the OSX3 library described in U.S. Pat. No. 10,479,990, and the OSX6 library prepared as described in Example 1.
  • the OSX3 library contains approximately 1.6 x 10 10 unique sequences with CDR3 lengths from 11 to 18 amino acids and a flexible position for the canonical cysteine in the CDR3 loop.
  • the OSX6 library contains a single length CDR3 of 14 amino acid residues with a centrally fixed canonical cysteine within approximately 10 3 framework variants identified from naive and immune repertoire libraries by NGS.
  • SARS-CoV-2 spike protein (Accession: YP 009724390.1) SI domain (amino acids 16-685) and Sl-RBD domain (amino acids 319-541) ( Figure 2) were synthesized and cloned into the pFUSE expression vector (InvivoGen). Both constructs contained AVI and 6xHis tags (SEQ ID NO: 169) at the C-terminal end separated by G 4 S linkers (SEQ ID NO: 170). ACE2 (UnitProt entry:
  • Q9BYF1 ectodomain (amino acids 18-740) was synthesized with FLAG and 6xHis tags (SEQ ID NO: 169) at the C-terminal end separated by G 4 S (SEQ ID NO: 170) linkers before cloning into the pFUSE vector.
  • SI, Sl-RBD and ACE2 recombinant proteins were expressed in Expi293 cells for 5 days following transient transfection using Expifectamine 293 Transfection Kit (Thermo Fisher Scientific). Cell cultures were centrifuged at 4500 for 40 min, supernatants were collected and filtered on 0.45 pm membranes before being loaded on a HisTrap Excel column (Cytiva).
  • PEG/NaCl precipitated phage libraries blocked in 5% BSA in PBS were deselected with streptavidin magnetic beads prior to bio-panning against biotinylated SI or Sl-RBD.
  • Phage bound to biotinylated target protein were captured by streptavidin coupled Dynabeads (Thermo Fisher Scientific), washed and eluted in 100 nM triethylamine.
  • Eluted phages were adjusted to neutral pH and propagated in TGI E. coli.
  • M13K07 helper phage was used to induce phage production for subsequent rounds of selection. The amount of antigen used in each subsequent selection round was 100, 50, and 25 nM for round 1, 2 and 3, respectively.
  • Phage ELISA Phage ELISA. Individual clones were picked from agar plates and grown at 37°C with shaking in a 96-well block in 2YT media supplemented with 2% glucose and 100 pg/ml ampicillin until visible growth occurred. The cultures were super-infected with M13K07 helper phage (New England Biolab) for 1 hr and the media was replaced with 2YT media supplemented with 100 pg/ml ampicillin and 50 pg/ml kanamycin. After 16 hr at 30°C, supernatants were collected by centrifugation and blocked in a final concentration of 2.5% milk in PBS with 0.1% Tween-20 (PBST) for 1 hr at room temperature (RT).
  • M13K07 helper phage New England Biolab
  • High binding, 96 well microplates (Greiner) were coated with 100 pi (5 pg/ml) of purified SI or Sl-RBD or commercial human serum albumin (HSA; Sigma-Aldrich) and incubated overnight at 4°C. Plates were blocked with 2.5% milk in PBST for 1 hr at RT. Blocked phage supernatants were transferred to blocked microplates and incubated for 1 hr followed by washing with PBST on a plate washer (BioTek). Anti-M13-HRP antibody (Sino Biological) was used for detection at 1:4000 dilution in blocking buffer.
  • the reaction was developed with 1-Step Ultra TMB-ELISA Substrate Solution (Thermo Fisher Scientific), stopped with 1% HC1 and absorbance was measured at 450 nm on VarioSkan plate reader (Thermo Fisher Scientific).
  • Three rounds of selection with the OSX3 and OSX6 libraries produced 149 unique VNAR clones as identified by DNA sequencing.
  • the OSX3 library produced 60 and 40 clones from selection with Sl-RBD and SI, respectively (Table 3).
  • the OSX6 library produced 34 and 15 clones from selection with Sl-RBD and SI, respectively (Table 4).
  • the SEQ ID NO: is also used as the name for the VNAR clone or VNAR domain having that sequence.
  • the CDR1, HV2, HV4 and CDR3 sequences of VNARs identified from the OSX3 and OSX6 libraries, respectively are also listed in Tables 5 and 6.
  • Sequences in Table 5 are residues of the SEQ ID NO in the left column as follows: CDR1 is residues 26-33, HV2 is residues 44-52, HV4 is residues 61-65, and CDR3 is the residues listed in the far-right column.
  • Sequences in Table 6 are residues of the SEQ ID NO in the left column as follows: CDR1 is residues 26-33, HV2 is residues 44-52, HV4 is residues 61-65, and CDR3 is the residues listed in the far-right column.
  • the amino acid sequence for CDR1 is found at amino acids 26-33 of the indicated SEQ ID NO: for that domain; for HV2 at amino acids 44- 52; for HV4 sequence at amino acids 61-65; and for CDR3 sequence, it begins at amino acid 85 and continues the length of the particular CDR3 (typically 11- 20 amino acids, as shown).
  • VNAR-Fc formatting The VNAR clones that showed specific binding to the antigen in phage ELISAs from Example 2 were identified by Sanger sequencing and cloned into the pFUSE expression vector containing the IgGl human Fc (hFc) domain to produce VNAR human Fc fusions (VNAR-hFc).
  • the final constructs are bivalent antibodies with the VNAR domain fused to the N-terminus of the hFc domain; these fusions are also referred to herein interchangeably as VNAR antibodies.
  • Expi293 cells were transiently transfected with a VNAR-hFc following the manufacturer protocol at small scale (0.5 ml).
  • Figure 3 shows antigen binding of VNAR antibodies selected against Sl-RBD isolated from the OSX3 phage library
  • Figure 4 shows antigen binding of VNAR antibodies selected against SI protein isolated from the OSX3 phage library
  • Figure 5 shows antigen binding of VNAR antibodies selected against Sl-RBD isolated from the OSX6 phage library
  • Figure 6 shows antigen binding of VNAR antibodies selected against SI protein isolated from the OSX6 phage library.
  • the larger OSX3 library produced 37 VNAR antibodies (with 17 from the Sl-RBD and 20 from the SI selection), whereas 20 antibodies came from OSX6 library (with 14 from the Sl-RBD and 6 from the SI selection).
  • VNAR antibodies that specifically bound to either SI or Sl-RBD were expressed at a larger scale (50ml) and purified to measure their binding potency by ELISA.
  • the transiently-transfected cell cultures were centrifuged at 2,000 rpm for 10 min, supernatants were filtered using 0.22 pm membrane filters and loaded onto HiTrap MabSelect SuRe columns (Cytiva) pre-equilibrated against PBS, pH 7.4. Protein A-bound antibodies were eluted with 0.1 M glycine, pH 3.5 and the buffer exchanged to PBS, pH 7.4 using HiPrep 26/10 desalting column (Cytiva). Purity of the purified protein samples was determined by analytical SEC and SDS-PAGE.
  • the plates were washed, and binding was detected with an anti-human IgG (Fc specific) (1:5000 dilution, Sigma-Aldrich, A0170) or anti-FLAG (1:1000 dilution, Sigma-Aldrich, A8592) HRP-conjugated antibodies for VNAR-hFc antibodies or ACE2, respectively.
  • the signal was developed with 1-StepTM Ultra TMB- ELISA substrate solution (Thermo Fisher Scientific) and the reaction was stopped with 1% HC1. Absorbance measured at 450 nm and EC50 values were calculated by 4-parametric non linear regression using GraphPad Prism 8.0.
  • the EC50 values were determined for thirty VNAR antibodies (16 from OSX3 and 14 from OSX6) and showed a binding potency for Sl-RBD in the low nM range (Table 8; Figure 7). None of the clones selected against Sl-RBD regardless of library origin showed a binding EC50 >3E-08 M (Table 8). In addition, eleven VNAR antibodies (9 from OSX3 and 2 from OSX6) selected against SI were assessed. Of those, six VNAR antibodies (4 from OSX3 and 2 from OSX6) bound to either SI or Sl-RBD with high potency (Table 9; Figure 8). One VNAR antibody (derived from clone 137) may interact with NTD domain since it was specific for SI but did not bind to the Sl-RBD ( Figures 2 and 8).
  • VNAR antibodies with a high binding potency to Sl-RBD were further tested in a competition assay.
  • the IC50 values were determined by ELISA as described in Example 4 except that serial dilutions of the VNAR-hFc fusions were premixed with 1.4 nM of purified ACE2 (see Example 1) prior to incubation on the coated microtiter plates.
  • ACE2 binding was measured with an anti-FLAGHRP conjugated antibody (Sigma-Aldrich, A8592) diluted 1:1000.
  • Binding of SI to ACE2 transfected cells was measured with an Alexa Fluor-647-conjugated streptavidin (Invitrogen, S21374) diluted 1:500 using a CytoFLEX flow cytometer (Beckman Coulter). Data presented as normalized median fluorescence intensity (MFI) was used to determine IC50 by 4-parametric non-linear regression analysis using GraphPad Prism 8.0.
  • VNAR antibodies 4 from OSX3 and 6 from OSX6) that blocked ACE2 with both SI and Sl-RBD interaction in cell-based assay (Table 11) were tested for binding to three spike protein variants containing mutations in emerging virus variants. These included two Sl-RBD recombinant proteins with a single E484K or N501Y mutation as well as a quadruple mutant of SI protein containing K417N, E484K, N501Y and D614G mutations.
  • ACE2 binding to Viral Variants As shown in Figure 11, the variants bound to the ACE2 receptor with similar EC50 affinity compared to Sl-RBD when measured by ELISA as described in Example 4 using immobilized SI mutants with serially-diluted recombinant ACE2 receptor. Calculated EC50 values for the SI mutants are presented in
  • VNAR antibody binding to Viral Variants The ten VNAR antibodies were tested in an ELISA as described in Example 4 to determine EC50 values using immobilized SI mutants with serially-diluted VNAR antibodies followed by washes and ACE2 binding detection. Calculated EC50 values for the SI mutants are presented in Table 13. [00188] All the tested VNAR antibodies retained binding to the Sl-RBD N501Y mutant with similar ECso values (cf. Table 13) except for the antibody derived from VNAR clone 25 which showed a stronger ECso to Sl-RBD N501 Y whose binding curves are shown in Figure 12.
  • VNAR antibodies 25, 46, 61, 68, 105, 106, 115, 119, 132 and 135 which blocked ACE2 interaction with both the SI and Sl-RBD in cell-based assay were tested for viral blocking using the live SARS-CoV-2 Wuhan strain as described below. All studies with live virus were conducted in a certified BSL3 laboratory.
  • Vero CCL81 cells were seeded at a cell density of 100,000 cells per well in 48-well plates and incubated at 37° in serum free OptiPro SFM medium (Thermo Fisher Scientific) for 24 hr before infection.
  • the SARS-CoV-2 Wuhan strain propagated in Vero CCL81 cells was preincubated with or without VNAR antibody for 10 min in OptiPro medium before incubation of the mix with prewashed Vero CCL81 cells for 1 hr at 37 °C.
  • Supernatants were transferred to Eppendorf tubes and inactivated with 560 m ⁇ of AVL buffer from QIAamp Viral RNA Mini Kit (Qiagen). The cells were washed and further incubated at 37°C for 48 hr before supernatant was again harvested and the virus inactivated in AVL buffer. Cell death was assessed by phase microscopy at the end of the experiment.
  • Viral RNA was isolated from inactivated viral supernatants using the QIAamp Kit according to manufacturer’s protocol. Briefly, 560 m ⁇ absolute ethanol was added and loaded onto columns. After washes with AW1 and AW2 buffers, RNA was collected using 40 m ⁇ of Ambion nuclease free water (Thermo Fisher Scientific). Total RNA (5 m ⁇ ) was used for cDNA synthesis and qPCR was performed in one step using QuantiTect Probe RT-PCR (Qiagen) on a StepOnePlus System (Applied Biosystems).
  • the qPCR primers (synthesized by Eurofms, Germany) were as follows: N1 forward GAC CCC AAA ATC AGC GAA AT (SEQ ID NO: 171), N1 reverse TCT GGT TAC TGC CAG TTG AAT CTG (SEQ ID NO: 171), N1 reverse TCT GGT TAC TGC CAG TTG AAT CTG (SEQ ID NO: 171), N1 reverse TCT GGT TAC TGC CAG TTG AAT CTG (SEQ ID NO:
  • RNase P Primers were used: RP Forward AGA TTT GGA CCT GCG AGC G (SEQ ID NO: 174), RP Reverse GAG CGG CTG TCT CCA CAA GT (SEQ ID NO: 175), and RP Probe FAM - TTC TGA CCT GAA GGC TCT GCG CG - BHQ-1 (SEQ ID NO: 176).
  • FAM is a dye label and BHQ1 is a quencher.
  • the qPCR primers were used at 0.4 mM with the probe at 0.2 mM and samples were incubated at 50°C for 30 minutes, heated to 95°C for 15 min, followed by 45 cycles of 95°C for 3 seconds and 55°C for 30 seconds. C t values obtained after 48 hr were subtracted from C t values at the time of infection and the data normalized between cells that were neither exposed to the virus nor treated with the antibodies set to 0% and untreated cells exposed to the virus set to 100%.
  • the assay was performed qualitatively using 5 pg/mL (65 nM), 10 pg/mL (130 nM) and 50 pg/mL (650 nM) of VNAR antibody.
  • the ten Sl-RBD binding VNAR antibodies were all able to prevent viral infection at 5 pg/mL ( Figure 14).
  • the Sl-NTD specific VNAR antibody 137 did not show any significant blocking activity until 50 pg/mL ( Figure 15).
  • screening and selection of VNAR clones and VNAR antibodies against the Sl- RBD domain using in vitro and cell-based assays can accurately predict inhibitory potential of the VNARs against the live virus.
  • the OSX6 library generated approximately 50% more blocking antibodies in the ELISA competition assay (13 vs 7, Table 10), the cell-based competition assay (9 vs 6, Table 11) and live virus neutralization assay (6 vs 4, Figure 14).
  • the lower attrition rate during the discovery, screening, and characterization of VNAR antibodies derived from the OSX6 library was a result of improvements in VNAR design, including, independently or in combination, providing optimized scaffolds for the VNAR domains and the improved CDR3 loops of the disclosure.

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Abstract

The present disclosure provides coronavirus S1-fragment specific binding moieties comprising Type II VNAR domains, VNAR antibodies, methods of using those moieties and antibodies to treat COVID-19, and improved Type II VNAR libraries for screening, selecting and/or identifying VNARs that bind specifically to a target molecule of interest. In some embodiments, a VNAR antibody, originally selected from a phage display library as a VNAR clone using S1fragments from the SARS-CoV-2 Wuhan strain, are also effective at specifically binding to and/or neutralizing SARS-CoV-2 and certain SARS-CoV-2 mutants.

Description

SHARK VNARS FOR TREATING COVID-19
CROSS REFERENCE TO RELATED APPLICATION
[0001] This PCT application claims the benefit of non-provisional application U.S. Serial No. 17/343,444, filed June 9, 2021 and of provisional application U.S. Serial No. 63/197,601, filed on June 7, 2021, each of which is incorporated herein by reference in its entirety.
SEQUENCE LISTING
[0002] 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 May 27, 2022, is named 9030_2101-W01_SL.txt and is 1,134,896 bytes in size.
FIELD OF THE DISCLOSURE
[0003] The present disclosure relates to the identification of single domain VNARs derived by bio-panning against the spike protein from the SARS-CoV-2 Wuhan variant. The screen identified ten VNAR Fc fusion proteins (VNAR antibodies) that were shown in biochemical and cells-based assays to be highly effective in blocking the interaction of recombinant spike protein with ACE2 receptor and eight were confirmed to neutralize live Wuhan variant virus using in vitro assays. These ten VNAR antibodies retained high affinity binding and blocking activity against the Sl-RBD N501 Y mutant, and three had activity against the Sl- RBD E484K mutant. The VNAR antibody panel directed against the SARS CoV-2 spike protein expands the molecular toolbox of novel antibody therapeutic approaches directed against COVID-19.
BACKGROUND
[0004] The current COVID-19 pandemic, caused by the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is associated with high infection rates and in some high-risk populations with high mortality rate. Immunological approaches, including vaccines and therapeutic antibodies, have been successfully pursued and are proving immensely helpful in preventing further spread of the virus as well as treating the severely ill. While a high level of protection in immunized populations is observed, establishing long-term safety and efficacy of vaccines will require continuous monitoring of protection especially against newly emerging variants, including B.1.1.7/501 Y. VI (Kent), lineage B.1.351/501 Y.V2 (South African), and lineage P.l (Brazilian). As vaccine-induced immunity can be less effective in older populations and immunocompromised individuals, and can potentially trigger a harmful response in some cases (Jeyanathan, Afkhami et al. 2020), passive immunization via direct administration of purified antibodies may provide a solution to both prevent and treat infections (Yang, Liu et al. 2020).
[0005] The receptor binding domain (Sl-RBD) of the spike protein is the main target for various vaccine and antibody neutralization approaches. However, it is highly protected by being tightly folded within the structure and covered by a glycan shield (Watanabe, Allen et al. 2020). Furthermore, neutralizing antibodies to only a single dominant epitope can result in selective pressure for viral mutants that escape inhibition. Neutralizing antibodies to the Sl- RBD domain have been isolated by cloning human B cells from infected patients and by immunizing humanized mice (Baum, Ajithdoss et al. 2020; Cao, Su et al. 2020; Liu, Wang et al. 2020) but these approaches are not without issues. A major problem with B cell cloning is that many antibodies, and in particular IgMs, will be generated to glycans on the spike protein which impede recognition of neutralizing epitopes. Both approaches suffer from immunodominance which limits epitope coverage and directs the response to viral epitopes more tolerant of mutations. RNA viruses spontaneously evolve as they spread across populations and mutations are already accumulating in the SARS-CoV-2 spike protein both within and outside the Sl-RBD domain (Korber, Fischer et al. 2020), which makes targeting a single immunodominant epitope highly prone to escape upon mutation.
[0006] A potent antibody-evasion strategy employed by viruses is the so-called “glycan shield” present on many viral glycoproteins, which masks neutralizing antibody to antigenically conserved sites (Watanabe, Bowden et al. 2019). Shark VNAR single domain antibodies (also known as IgNARs), which have evolved to compliment conventional antibodies, offer an important alternative with significant advantages for combating viral defenses. Surface-exposed epitopes available to conventional IgGs are generally more tolerant of mutations which allow viral escape (Thyagarajan and Bloom 2014; Doud, Hensley et al. 2017; Doud, Lee et al. 2018). With their small size and long CDR3 loop, VNAR single domain antibodies are ideally designed to access buried epitopes beneath the glycan shield (Stanfield, Dooley et al. 2004; Konning, Zielonka et al. 2017).
[0007] To overcome these shortcomings of conventional antibodies, VNARs have been developed which target the spike protein within Sl-RBD and N-terminal domain (Sl-NTD). The VNAR domains directed against the SARS-CoV-2 spike protein expands the molecular toolbox of antibody therapeutic approaches directed against COVID-19 disease. SUMMARY
[0008] The present disclosure provides coronavirus SI -fragment specific binding moieties comprising Type II VNAR domains, VNAR antibodies, methods of using those moieties and antibodies to treat COVID-19, and improved Type II VNAR libraries for screening, selecting and/or identifying VNARs that bind specifically to a target molecule of interest. In some embodiments, a VNAR antibody, originally selected from a phage display library as a VNAR clone using SI fragments from the SARS-CoV-2 Wuhan strain, are also effective at specifically binding to and/or neutralizing SARS-CoV-2 and certain SARS-CoV-2 mutants. [0009] In one aspect, the SI fragment-binding moieties comprise a Type II VNAR domain represented by the formula, from N to C terminus,
FW 1 -CDR1 -FW2-HV2-FW2’ -HV4-FW3 -CDR3 -FW4, wherein CDR1 comprises or consists essentially of a peptide having an amino acid sequence of one of DSICALSS, DSNCALPS, DSVCALSS, or DSNCALSS (SEQ ID NOS. 150-153, respectively), wherein CDR3 comprises or consists essentially of a peptide having an amino acid sequence of one of VHMEDMNVRD YGGFWGED V, VNLRSVLPCGWPDV, VENLPGSGSCLRYYLSDV, VREWACEDDGRVWGWEDV, V ART S GCE V YT YT GD V, VKNPSGCGVWYSQEDL, SEFKSGCGVFYELTDV, MVFKSVCEDNPYQYGL, or IWAHSGCEVITHAMDL (SEQ ID NOS. 154-162, respectively), and wherein said moiety is capable of specifically binding to an SI fragment comprising amino acids 16-685 of a SARS- CoV-2 spike protein. In some embodiments, HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively). In some embodiments, HV4 is SGSKS or RGSKS (SEQ ID NOS. 167-168, respectively). In embodiments, the VNAR domain comprises one of the CDRls and CDR3s together with any one of the HV2s, with any one of the HV4s, or with both of any one of the HV2s and an HV4s.
[0010] In some embodiments of the moiety, the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRD YGGFWGED V (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 156) (from VNAR 61; the CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and the CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWEDV (SEQ ID NO: 157) (from VNAR 68); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VARTSGCEVYTYTGDV (SEQ ID NO:
158) (from VNAR 105 or 106); the CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and the CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL (SEQ ID NO:
159) (from VNAR 115); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV (SEQ ID NO:
160) (from VNAR 119); the CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and the CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL (SEQ ID NO:
161) (from VNAR 132); or the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL (SEQ ID NO:
162) (from VNAR 135).
[0011] In some embodiments, the moiety comprises any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135).
[0012] In an aspect, any of the moieties of the disclosure further comprise at least one heterologous agent operably linked thereto to thereby form a conjugate. Such heterologous agents, include but are not limited to, one or more of a small molecule diagnostic or therapeutic; a DNA, RNA, or hybrid DNA-RNA; a traceable marker; a radioactive agent; an antibody; a single chain variable domain; or an immunoglobulin fragment.
[0013] In some embodiments the heterologous agent is an immunoglobulin fragment and is operably linked to the VNAR domain to form a fusion protein. In an embodiment, the immunoglobulin fragment is a Fc domain, and preferably a human Fc domain. The human Fc domain can be from any immunoglobulin isotype. In preferred embodiment, the isotype is an IgG. [0014] A further aspect relates to pharmaceutical compositions comprising at least one moiety, conjugate or fusion protein of the disclosure. In embodiments, such compositions can also have, independently, two, three, four, five or more of such moieties, conjugates or fusion proteins.
[0015] In an aspect, the disclosure provides a method of passive immunization against SARS-CoV-2, and variants thereof, which comprises administering a pharmaceutical composition of the disclosure to a subject in need thereof.
[0016] In another aspect, the disclosure provides a method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19. [0017] In some embodiment of these methods, the subject or mammal has tested positive for SARS-CoV-2. In some embodiments of these methods, the subject or mammal has suspected exposure to SARS-CoV-2 and/or tested negative for SARS-CoV-2. In some embodiments of these methods, the composition is administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
[0018] In a further aspect, this disclosure provides VNAR antibodies which comprise a moiety of the disclosure fused to a human Fc domain, which upon expression form a bispecific VNAR antibody. In embodiments of the VNAR antibody, the moiety has a VNAR domain wherein the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 156) (from VNAR 61; the CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and the CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWEDV (SEQ ID NO: 157) (from VNAR 68); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VARTSGCEVYTYTGDV (SEQ ID NO: 158) (from VNAR 105 or 106); the CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and the CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL (SEQ ID NO:
159) (from VNAR 115); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV (SEQ ID NO:
160) (from VNAR 119); the CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and the CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL (SEQ ID NO:
161) (from VNAR 132); or the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL (SEQ ID NO:
162) (from VNAR 135). As indicated, the CDR1 and CDR3 peptides are the cognate pair found in the recited VNAR domain.
[0019] In some embodiments of the VNAR antibody, its VNAR domain is any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135). In an embodiment, a VNAR antibody is capable of neutralizing infection of SARS-CoV-2
[0020] A further aspect relates to pharmaceutical compositions comprising at least one VNAR antibody of the disclosure. In embodiments, such compositions can also have, independently, two, three, four, five or more VNAR antibodies.
[0021] In an aspect, the disclosure provides a method of passive immunization against SARS-CoV-2, and variants thereof, which comprises administering a pharmaceutical composition comprising one or more VNAR antibodies of the disclosure to a subject in need thereof.
[0022] In another aspect, the disclosure provides a method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition comprising one or more VNAR antibodies of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19.
[0023] In some embodiment of these methods, the subject or mammal has tested positive for SARS-CoV-2. In some embodiments of these methods, the subject or mammal has suspected exposure to SARS-CoV-2 and/or tested negative for SARS-CoV-2. In some embodiments of these methods, the composition is administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation. [0024] In yet another aspect, the disclosure provides a coronavirus SI fragment binding moiety comprising a Type II VNAR domain capable of specifically binding to an SI fragment comprising amino acids 16-685 of SARS-CoV-2 spike protein, wherein the said VNAR domain comprises an amino acid sequence of any one of VNAR clones 1-149 in Table 3 or Table 4 (SEQ ID NOS.1-149). In embodiments, these moieties further comprise at least one heterologous agent operably linked to the moiety to thereby form a conjugate.
[0025] As described herein, embodiments include nucleic acids encoding a moiety, conjugate, fusion protein or VNAR antibody of the disclosure. In embodiment, a nucleic acid of the disclosure is in a vector having the nucleic acid operably linked to a promoter to enable expression of the binding moiety, conjugate or VNAR antibody in a host cell. Another aspect provides host cells comprising a nucleic acid or vector of the disclosure.
[0026] In still further aspects, the disclosure provides a synthetic nucleic acid-containing library whose members each encode a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide,
(a) residues 22, 29 and 83 are cysteine;
(b) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg
Wherein Xai and Xa2 are independently any amino acid except cysteine; Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(c) no other residues in said polypeptide are cysteine.
In an embodiment of this library, the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
[XaiMY/L/D/S/G] [D/V/W/Y/G]C [W/E/Y/D/G] [ Y/L/D/V/L] [ Xa2]5 [D/G] [ V/L] .
[0027] In an embodiment, the disclosure provides a synthetic nucleic acid-containing library whose members each comprise a nucleic acid encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide, none of the residues are cysteine except as provided in (a) to (i) and, wherein, (a) FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
(b) CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
(c) FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
(d) HV2 is 9 amino acids in length;
(e) FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
(f) HV4 is 5 amino acids in length;
(g) FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
(h) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine, Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(i) FW4 is 10 amino acids in length and has an amino acid sequence comprising
YG[D/G]GT[A/V]VTVN (SEQ ID NO: 1245).
In an embodiment of this library, the residue at each position of said VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
[0028] In embodiments, any of the nucleic acid libraries of the disclosure are phage display libraries. Such libraries may comprise approximately 109 theoretically distinct nucleic acid sequences.
[0029] In accordance with another aspect of the disclosure, the nucleic acid libraries hereof are used in various methods for identifying polypeptides that bind selectively to target molecules of interest. An embodiment provides a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises: (a) exposing a target molecule of interest to polypeptides produced by expression of a nucleic acid library of the disclosure; and (b) separating polypeptides that selectively bind from those that do not selectively bind the target molecule. In an embodiment, the target molecule of interest is expressed on the surface of a phage, bacterium or cell, or is attached to, tethered to or otherwise associated with a solid support.
[0030] Another embodiment provides a method of screening a library for a polypeptide that selectively binds with high affinity to a target molecule of interest, the library comprising a plurality of polypeptides produced by expression of a nucleic acid library of the disclosure and comprises: (a) incubating a sample of the library with a concentration of a target molecule under conditions suitable for specific binding of the polypeptides to the molecule; (b) incubating a second sample of the library under the same conditions but without target molecule; (c) contacting each of the first and second samples with immobilized target molecule under conditions suitable for binding of the polypeptide to the immobilized target antigen; (d) detecting the polypeptide bound to immobilized target molecule for each sample; (e) determining the affinity of the polypeptide for the target molecule by calculating the ratio of the amounts of bound polypeptide from the first sample over the amount bound polypeptide from the second sample.
[0031] Yet another embodiment provides a method of identifying one or more VNARs that selectively bind to a target molecule of interest which comprises: (a) contacting said target molecule with a phage display library of Claim 40 or 41; (b) separating phage that selectively bind the target molecule from those that do not selectively bind the target molecule to produce an enriched phage library; (c) repeating steps (a) and (b) with the enriched phage library to produce a further enriched phage library; (d) repeating step (c) until the further enriched phage library is enriched from at least about 10- to about 106-fold or more relative to the original phage library; and (e) plating the further enriched phage library and isolating and characterizing individual clones therefrom to thereby identify one or more VNAR polypeptides that selectively bind to the target molecule of interest. In an embodiment of this method, either the target molecule or phage display library can be bound to or attached to a solid support.
[0032] In preferred embodiments for any of these methods, the target molecule is a SARS- CoV-2 spike protein, a domain of the spike protein or a mutant thereof.
[0033] A still further aspect relates to a polypeptide library composition comprising a plurality of synthetic or recombinant polypeptides, each of which encodes a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C- terminus, FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 — CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide,
(a) residues 22, 29 and 83 are cysteine;
(b) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine; Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(c) no other residues in the polypeptide are cysteine.
In an embodiment of this library, the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
[XaiMY/L/D/S/G] [D/V/W/Y/G]C [W/E/Y/D/G] [ Y/L/D/V/L] [ Xa2]5 [D/G] [ V/L] .
[0034] In an embodiment, the disclosure provides a polypeptide library composition whose members each comprise a polypeptide encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide, none of the residues are cysteine except as provided in (a) to (i) and, wherein,
(a) FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
(b) CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
(c) FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
(d) HV2 is 9 amino acids in length;
(e) FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
(f) HV4 is 5 amino acids in length;
(g) FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C; (h) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine, Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(i) FW4 is 10 amino acids in length and has an amino acid sequence comprising
YG[D/G]GT[A/V]VTVN (SEQ ID NO: 1245).
In an embodiment of this library, the residue at each position of the VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
[0035] Yet a further aspect relates to a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises (a) exposing a target molecule of interest to a polypeptide library composition of the disclosure; and (b) separating polypeptides that selectively bind to said target molecule from those that do not selectively bind the target molecule.
BRIEF DESCRIPTION OF THE DRAWINGS
[0036] Figure 1. Schematic representation of VNAR domain variable regions. Variable regions include CDR1 (26-33), HV2 (44-52), HV4 (61-65) and CDR3 (85-100). The OSX6 phage library was generated by random assembly of 1068 synthesized N-terminal fragments designed as provided in Table 1 with approximately lxlO6 C-termini fragments designed as provided in Table 2. The encoded amino acid sequences of the 1068 synthesized N-terminal fragments of Scaffold l to Scaffold_1068 are provided in the Sequence Listing as SEQ ID NOS. 177-1244, respectively.
[0037] Figure 2. Schematic representation of SARS-CoV-2 spike protein and its domains. The SI and S2 fragments are indicated. Protein domains illustrated are: N-terminal domain (NTD), receptor-binding domain (RBD), fusion peptide (FP), heptad repeat 1 (HR1), central helix (CH), connector domain (CD), and transmembrane domain (TM). The SI -RBD recombinant protein contains only the RBD domain, whereas the S 1 recombinant protein contains both the NTD and RBD domains.
[0038] Figure 3. VNAR Binding to Spike Protein Domains. The bar graph depicts antigen binding of VNAR clones isolated from the OSX3 phage library by selection against recombinant Sl-RBD protein and reformatted as VNAR-hFc fusions (VNAR antibodies). VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 (~3 fold over blank) are presented on the graph.
[0039] Figure 4. VNAR Binding to Spike Protein Domains. The bar graph depicts antigen binding of VNAR clones isolated from the OSX3 phage library by selection against recombinant SI protein and reformatted as VNAR-hFc fusions (VNAR antibodies). VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 (~3 fold over blank) are presented on the graph.
[0040] Figure 5. VNAR Binding to Spike Protein Domains. The bar graph depicts antigen binding of VNAR clones isolated from the OSX6 phage library by selection against recombinant Sl-RBD protein and reformatted as VNAR-hFc fusions (VNAR antibodies). VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 (~3 fold over blank) are presented on the graph.
[0041] Figure 6. VNAR Binding to Spike Protein Domains. The bar graph depicts antigen binding of VNAR clones isolated from the OSX6 phage library by selection against recombinant SI protein and reformatted as VNAR-hFc fusions (VNAR antibodies). VNAR antibody binding was determined by ELISA against (a) Sl-RBD, (b) SI and (c) human serum albumin (HSA) as a control, from left to right, respectively. Only clones that showed binding to either Sl-RBD or SI at an OD>0.3 (~3 fold over blank) are presented on the graph.
[0042] Figure 7. ECso binding curves of VNAR antibodies to Sl-RBD for VNARs selected against Sl-RBD. Binding was assessed by ELISA with serial dilutions of diluted VNAR antibody and immobilized recombinant Sl-RBD protein. For the simplicity, the binding curves for eleven VNAR antibodies are shown (VNAR antibodies 7, 19, 20, 22, 25, 26, 103, 104, 105, 106, and 108). Calculated ECso values for all tested VNAR antibodies are presented in Table 8.
[0043] Figure 8. ECso binding curves of VNAR antibody 137 to recombinant Sl-RBD and SI. Binding was assessed by ELISA with serially-diluted VNAR antibody and immobilized recombinant Sl-RBD or SI proteins. VNAR antibody 137 is an example of a specific binder to the NTD domain present in the SI construct which does not bind RBD domain. Its calculated ECso value is provided in Table 9. [0044] Figure 9. ICso curves of three VNAR antibodies (25, 105 and 106) that block the interaction of Sl-RBD with ACE2 protein. ACE2 at a fixed concentration was premixed with serially-diluted VNAR antibodies before incubation with Sl-RBD immobilized on ELISA plates, followed by washing. ACE2 binding was detected by anti- FLAGHRP conjugated antibody. Data presented as normalized OD at 450nm. The calculated IC50 values for the tested VNAR antibodies are presented in Table 10.
[0045] Figure 10. ICso curves of three VNAR antibodies (25, 105 and 106) that block binding of SI to cells overexpressing ACE2. Expi293 cells transiently expressing ACE2 were used for the assay. SI was premixed with serially-diluted VNAR antibodies before incubation with the cells. Binding was measured by flow cytometry and the data presented as normalized median fluorescence intensity (MFI) of the transfected cell population. Calculated IC50 values for the tested VNAR antibodies are presented in Table 11.
[0046] Figure 11. ECso binding curves of SI mutants to ACE2. The mutants included Sl-RBD recombinant protein with a single E484K or N501Y mutation as well as quadruple mutant of SI protein containing K417N, E484K, N501Y and D614G mutations. Binding to immobilized SI mutants with serial dilutions of recombinant ACE2 ectodomain receptor was assessed by ELISA. Calculated EC50 values are presented in Table 12.
[0047] Figure 12. ECso binding curves of VNAR antibody 25 to spike Sl-RBD domain and mutants. Binding was assessed with serially-diluted VNAR antibody on immobilized recombinant spike proteins Sl-RBD (circles), Sl-RBD N501Y (squares), Sl-RBD E484K (upright triangles) and SI K417N, E484K, N501 Y and D614G (inverted triangles).
Calculated EC50 values are presented in Table 13.
[0048] Figure 13. ICso curves of VNAR antibody 25 that blocks Spike protein interactions with ACE2. ACE2 at a fixed concentration was premixed with serially-diluted VNAR antibodies before incubation with recombinant Sl-RBD, Sl-RBD N501Y or Sl-RBD E484K immobilized on ELISA plates. ACE2 binding was detected by anti-FLAG HRP conjugated antibody. Data presented as normalized OD at 450nm. All calculated IC50 values are presented in Table 14.
[0049] Figure 14. Neutralization of SARS-CoV-2 virus by VNAR antibodies. Vero CCL81 cells were exposed to SARS-CoV-2 Wuhan strain preincubated with or without VNAR antibodies at 5 pg/mL (65 nM) for 48 hr using VNAR antibodies 25, 46, 61, 68, 105, 106, 115, 119, 132 and 135. Viral load was determined at the start of the experiment and after 48 hr using RT-qPCR. Infection was assessed relative to cells treated with the virus in the absence of VNAR antibodies. [0050] Figure 15. Neutralization of SARS-CoV-2 virus by VNAR antibody 137. Vero CCL81 cells were exposed to SARS-CoV-2 Wuhan strain preincubated with or without VNAR antibody 137 at 5, 10, 50 pg/mL (65, 130, 650 nM) for 48 hr. Viral load was determined at start of the experiment and after 48 hr using RT-qPCR. Infection was assessed relative to cells treated with the virus in the absence of VNAR antibodies.
[0051] Figure 16. Epitope binning of VNAR antibodies by cross competition ELISA. VNAR antibodies (25, 46, 61, 68, 105, 106, 115, 119, 132 and 135) were used to coat ELISA microplate wells, followed by addition of Sl-RBD or premixed biotinylated Sl-RBD and a competitor VNAR antibody. Binding of biotinylated Sl-RBD to immobilized VNAR antibodies was detected by streptavidin-HRP. Black color indicate competition between two antibodies for the overlapping epitope bin. White color indicates no competition, thus a unique epitope bin.
DETAILED DESCRIPTION Definitions
[0052] In order that the present disclosure may be more readily understood, certain terms are defined below. Additional definitions may be found within the detailed description of the invention.
[0053] Throughout this specification, the word “comprise” or variations such as “comprises” or “comprising” will be understood to imply the inclusion of a stated integer (or components) or group of integers (or components), but not the exclusion of any other integer (or components) or group of integers (or components).
[0054] The singular forms “a,” “an,” and “the” include the plurals unless the context clearly dictates otherwise.
[0055] The term “plurality” as used herein refers to the number of members of a collection, which minimum is at least 10, 20, 30, 50, 75, 100, 1000 or more, and which minimum or maximum number may not be readily ascertainable but which may be indicated by type of collection or the context of its use. For example, a phage display library contains a plurality of phage equal to its titer (which may be the same or different), and by extension encodes a corresponding plurality of polypeptides.
[0056] The term “including” is used to mean “including but not limited to.” “Including” and “including but not limited to” are used interchangeably.
[0057] The terms “patient,” “subject,” and “individual” may be used interchangeably and refer to either a human or a non-human animal. These terms include mammals such as humans, primates, livestock animals ( e.g ., cows, pigs), companion animals (e.g., dogs, cats) and rodents (e.g., mice and rats).
[0058] The term “non-human mammal” means a mammal which is not a human and includes, but is not limited to, a mouse, rat, rabbit, pig, cow, sheep, goat, dog, non-human primate, or other non-human mammals, typically as used in research. As used herein, “mammals” includes the foregoing non-human mammals and humans.
[0059] As used herein, “treating” or “treatment” and grammatical variants thereof refer to an approach for obtaining beneficial or desired clinical results. The term may refer to slowing the onset or rate of development of a condition, disorder or disease, reducing or alleviating symptoms associated with it, generating a complete or partial regression of the condition, or some combination of any of the above. For the purposes of this invention, beneficial or desired clinical results include, but are not limited to, reduction or alleviation of symptoms, diminishment of extent of disease, stabilization (i.e., not worsening) of state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable.
"Treatment" can also mean prolonging survival relative to expected survival time if not receiving treatment. A subject (e.g., a human) in need of treatment may thus be a subject already afflicted with the disease or disorder in question. The term “treatment” includes inhibition or reduction of an increase in severity of a pathological state or symptoms relative to the absence of treatment and is not necessarily meant to imply complete cessation of the relevant disease, disorder or condition.
[0060] As used herein, the terms "preventing" and grammatical variants thereof refer to an approach for preventing the development of, or altering the pathology of, a condition, disease or disorder. Accordingly, "prevention" may refer to prophylactic or preventive measures.
For the purposes of this invention, beneficial or desired clinical results include, but are not limited to, prevention or slowing of symptoms, progression or development of a disease, whether detectable or undetectable. A subject (e.g., a human) in need of prevention may thus be a subject not yet afflicted with the disease or disorder in question. The term “prevention” includes slowing the onset of disease relative to the absence of treatment and is not necessarily meant to imply permanent prevention of the relevant disease, disorder or condition. Thus “preventing” or “prevention” of a condition may in certain contexts refer to reducing the risk of developing the condition or preventing or delaying the development of symptoms associated with the condition. [0061] As used herein, an "effective amount," "therapeutically-effective amount" or "effective dose" is an amount of a composition (e.g., a therapeutic composition or agent) that produces at least one desired therapeutic effect in a subject, such as preventing or treating a target condition or beneficially alleviating a symptom associated with the condition.
[0062] A physiologically-acceptable solution for use in an amount and for a time sufficient to effectively reduce a circulating concentration of the plurality of polypeptides is referred to herein as a perfusate. The amount of perfusate and time of perfusion depends on the non human mammal and can be readily determined by those of skill in the art. For example, with a mouse, using a volume of perfusate approximately lOx the blood volume of the mouse is effective at reducing the circulating concentration of polypeptides. Likewise, any volume of perfusate that reduces the circulating concentration of the plurality of polypeptides by about 10%, 25%, 50% or more (relative to the theoretical concentration of the plurality of polypeptides) being delivered is considered effective at reducing the circulating concentration of that plurality.
[0063] As used herein, a “VNAR domain” or “VNAR” has the general structure, from N to C terminus, given by the formula FW1-CDR1-FW2-HV2-FW2,-HV4-FW3-CDR3-FW4, wherein the FWs are framework regions, CDRs are complementarity determining regions and HVs are hypervariable regions that form the variable domain of a shark IgNAR. The CDR3 region in naturally-occurring VNARs is of heterogeneous size, ranging from about 7 to about 32 amino acid residues in length. The VNAR domains of the invention can optionally have a His-Tag (or other convenient tag for purification purposes). In some cases, such tags are removable. Typical VNAR domains have amino acid residues (aa) 1-25 of the framework 1 (FW1) region; aa 26-33 of the complimentary determining region 1 (CDR1); aa 34-43 of FW2; aa 44-52 of the hypervariable 2 region (HV2); aa 53-84 of FW3; aa 61-65 of HV4; the CDR3 region (of variable length begins with aa 85) and FW4 (11 residues starting immediately after CDR3 at XGXG).
[0064] As used herein, binding to the target of interest is called specific binding, while binding to other sites is called nonspecific binding. As used herein, a binding moiety, specific binding moiety, antibody or VNAR domain that “specifically binds” to its target does so selectively or preferentially. Such moieties, antibodies and VNARS can exhibit specific binding to multiple targets such as occurs when one of these entities exhibits species cross reactivity. [0065] Abbreviations used herein for conventional antibodies include: VL, variable region, light chain; VH, variable region, heavy chain; CL, constant region of light chain; HC, constant region of heavy chain.
SARS-CoV-2 SI Fragment Binding Moieties and Conjugates Thereof [0066] The present invention relates to coronavirus SARS-CoV-2 SI -fragment-specific binding moieties comprising Type II VNAR domains obtained by in vitro selection against recombinant spike protein fragments, including the recombinant SI domain encoded by amino acids 16-685 of the spike protein and the Sl-RBD domain encoded by amino acids 319-541 of the spike protein, using VNAR OSX3 and OSX6 phage display libraries.
[0067] In one aspect, the disclosure provides a coronavirus SI -fragment binding moiety comprising a Type II VNAR domain capable of specifically binding to an SI fragment comprising amino acids 16-685 of SARS-CoV-2 spike protein, wherein the VNAR domain comprises an amino acid sequence of any one of VNAR clones 1-149 in Table 3 and Table 4 (SEQ ID NOS.1-149; see Example 2).
[0068] The CDR1, HV2, HV4 and CDR3 sequences for each of the foregoing VNAR domains identified from the OSX3 and OSX6 libraries are also listed in Tables 5 and 6 for convenience. Each CDR1, HV2, HV4 and CDR3 sequence is a subsequence of its respective VNAR domain set forth in SEQ ID NOS. 1-149. Hence, for each VNAR domain, the CDR1 sequence is found at amino acids 26-33 of the corresponding SEQ ID NO: for that domain; the HV2 sequence at amino acids 44-52; the HV4 sequence at amino acids 61-65; and the CDR3 sequence beginning at amino acid 85 and continuing the length of the particular CDR3.
[0069] In some embodiments, the foregoing moieties further comprise at least one heterologous agent operably linked to the moiety to thereby form a conjugate.
[0070] In a further aspect, the disclosure provides further SI fragment-binding moieties which comprise a Type II VNAR domain represented by the formula, from N to C terminus, FW 1 -CDR1 -FW2-HV2-FW2’ -HV4-FW3 -CDR3 -FW4, wherein CDR1 comprises or consists essentially of a peptide having an amino acid sequence of one of DSICALSS, DSNCALPS, DSVCALSS, or DSNCALSS (SEQ ID NOS. 150-153, respectively), wherein CDR3 comprises or consists essentially of a peptide having an amino acid sequence of one of VHMEDMNVRD YGGFWGED V, VNLRSVLPCGWPDV, VENLPGSGSCLRYYLSDV, VREWACEDDGRVWGWEDV, V ART S GCE V YT YT GD V, VKNPSGCGVWYSQEDL, SEFKSGCGVFYELTDV, MVFKSVCEDNPYQYGL, or IWAHSGCEVITHAMDL (SEQ ID NOS. 154-162, respectively), and wherein said moiety is capable of specifically binding to an SI fragment comprising amino acids 16-685 of a SARS- CoV-2 spike protein. In some embodiments, HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively). In some embodiments, HV4 is SGSKS or RGSKS (SEQ ID NOS. 167-168, respectively). In embodiments, the VNAR domain comprises one of the CDRls and CDR3s together with any one of the HV2s, with any one of the HV4s, or with both of any one of the HV2s and an HV4s.
[0071] In some embodiments of these further moieties, the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 156) (from VNAR 61; the CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and the CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWEDV (SEQ ID NO: 157) (from VNAR 68); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VARTSGCEVYTYTGDV (SEQ ID NO: 158) (from VNAR 105 or 106); the CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and the CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL (SEQ ID NO: 159) (from VNAR 115); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV (SEQ ID NO: 160) (from VNAR 119); the CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and the CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL (SEQ ID NO: 161) (from VNAR 132); or the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL (SEQ ID NO: 162) (from VNAR 135).
[0072] In some embodiments, the FW1, FW2, FW2’, FW3 and FW4 regions of the Type II VNAR domains have naturally occurring VNAR sequences or altered VNAR sequences with amino acid substitutions, insertions or deletions (typically, but not limited to, no more than 1- 10 amino acids changes, insertions or deletions) provided that such alterations maintain the overall primary and tertiary structure of the Type II VNAR, and provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs. In some embodiments, the FW1, FW2, FW2’, FW3 and FW4 regions of the Type II VNAR domains have a sequence for those regions as set forth in Tables 3 and 4 (in any independent combination), and, again, provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs.
[0073] In some embodiments, these further moieties comprise any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135).
[0074] In some embodiments, the VNAR domains of any of the moieties of the disclosure can optionally have a His-Tag (or other convenient tag for purification purposes). In some cases, such tags are removable.
[0075] In an aspect, any of the moieties of the disclosure further comprise at least one heterologous agent operably linked thereto to thereby form a conjugate. Such heterologous agents, include but are not limited to, one or more of a small molecule diagnostic or therapeutic; a DNA, RNA, or hybrid DNA-RNA; a traceable marker; a radioactive agent; an antibody; a single chain variable domain; or an immunoglobulin fragment.
[0076] In some embodiments the heterologous agent is an immunoglobulin fragment and is operably linked to the VNAR domain to form a fusion protein. In an embodiment, the immunoglobulin fragment is a human Fc domain. The human Fc domain can be from any immunoglobulin isotype. In preferred embodiment, the isotype is an IgG, and more preferably IgGl. Fusion proteins are generally monospecific but can be bispecific.
[0077] In yet another aspect of the invention, any of the VNAR domains described herein can form all or part of the variable domain of a single variable domain antibody, a bi- or tri functional VNAR, a conventional antibody, or any fragment or fusion protein of said antibody as well as variable domains with antibody-like backbones. Such constructs can be made by methods known to those of skill in the art.
[0078] Examples of single variable domain antibodies include, but are not limited to, a shark or other cartilaginous fish antibodies, camelid antibodies and nanobodies. Examples of conventional antibodies (and their fragments) include, but are not limited to, immunoglobins having both heavy and light chains, such as IgM’s, IgA’s, IgG’s, IgE’s, single chain Fv’s,
Fab fragments, or any fragment or fusion protein of such antibodies or fragments.
[0079] In embodiments, any of the VNAR domains disclosed herein can be fused to an Fc domain of a conventional antibody to form a VNAR-Fc conjugate. Such fusions can be made at the N terminus or the C terminus of the Fc domain. In some embodiments, the Fc domain is a mammalian Fc domain, including primate Fc domains. More particularly, the Fc domain is a human Fc domain (hFc), a cynomolgus macaque Fc domain (cFc) or a murine Fc domain. Most preferably the Fc domain is an hFc domain. In some embodiments, the Fc domain is from an IgG, and preferably from IgGl. Such fusions are also referred to herein as VNAR antibodies. Methods of making fusion proteins are well known in the art.
[0080] Further, non-limiting examples of antibody -like backbones that may be used according to the disclosure include monospecific and bispecific backbones, such as multimerizing scFv fragments (diabodies, triabodies, tetrabodies), disulfide stabilized antibody variable (Fv) fragments, disulfide stabilized antigen-binding (Fab) fragments consisting of the VL, VH, CL and CH 1 domains, bivalent F(ab’)2 fragments, Fd fragments consisting of the heavy chain and CHI domains, dimeric CH2 domain fragments (CH2D), FC antigen binding domains (Fcabs), single chain FV-CH3 minibodies, bispecific minibodies, isolated complementary determining region 3 (CDR3) fragments, constrained FR3-CDR3- FR4 polypeptides, SMIP domains, and any genetically manipulated counterparts of the foregoing that SI binding function (see e.g., Weiner L, Cell 148: 1081-4 (2012); Ahmad Z et ak, Clin Dev Immunol 2012: 980250 (2012) for reviews).
VNAR Antibodies
[0081] In a further aspect, this disclosure provides VNAR antibodies which comprise an SI -specific binding moiety of the disclosure in which its VNAR domain is fused to a human Fc domain (hFc). When such fusion proteins are expressed, due to the nature of the Fc domain, two chains can associate to form a dimer and thus produce a bispecific molecule, herein referred to as a bispecific VNAR antibody. [0082] The VNAR antibodies of the disclosure are suitable for use in humans, particularly for providing passive immunity against SARS-CoV-2, and variants thereof, and for treating and ameliorating COVID-19 disease and associated symptoms.
[0083] In some embodiments, the VNAR antibodies are capable of blocking the interaction and/or binding of the SARS-CoV-2 spike protein with the ACE2 receptor. In some embodiments, the VNAR antibodies are capable of blocking the interaction and/or binding of mutant SARS-CoV-2 spike protein with the ACE2 receptor. In some embodiments the mutant spike protein has a single mutation, including the E484K or N501 Y mutation. In some embodiments, the mutant spike protein is a quadruple mutant of SI containing K417N, E484K, N501 Y and D614G mutations. These spike mutations are referenced relative to the amino acid sequence of the spike protein from the Wuhan strain, for example, the E484K mutant has the amino acid glutamic acid (E) found at position 484 of the spike protein replaced with the amino acid lysine (K). Similarly, for the N501 Y mutation, the amino acid aspartic acid (N) found at position 501 is replaced with tyrosine (Y), and so on for the quadruple mutant and other mutants.
[0084] In some embodiments, the VNAR antibodies are capable of neutralizing viral infection, including but not limited to the Wuhan strain and mutants thereof, including the mutants single E484K or N501Y mutation as well as a quadruple mutant of SI protein containing K417N, E484K, N501 Y and D614G mutations.
[0085] Methods of making Fc fusion proteins are well known in the art. In some embodiments, the VNAR domain is operably linked via a linker peptide to the C-terminus and/or N-terminus of the Fc domain, and preferably at the N-terminus. In some embodiments, the Fc domain is from an IgG, and preferably from IgGl but other human Fc domain isotype are contemplated.
[0086] Accordingly, preferred embodiments of the VNAR antibody, include but are not limited to SI -specific binding moieties having a Type II VNAR domain represented by the formula, from N to C terminus, FW1-CDR1-FW2-HV2-FW2,-HV4-FW3-CDR3-FW4, wherein the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV (SEQ ID NO: 154) (from VNAR 25); the CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV (SEQ ID NO: 155) (from VNAR 46); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV (SEQ ID NO: 156) (from VNAR 61; the CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and the CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWEDV (SEQ ID NO: 157) (from VNAR 68); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of VARTSGCEVYTYTGDV (SEQ ID NO: 158) (from VNAR 105 or 106); the CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and the CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL (SEQ ID NO: 159) (from VNAR 115); the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV (SEQ ID NO: 160) (from VNAR 119); the CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and the CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL (SEQ ID NO: 161) (from VNAR 132); or the CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and the CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL (SEQ ID NO: 162) (from VNAR 135).
[0087] For some embodiments of the VNAR antibodies, HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively). For some embodiments of the VNAR antibodies, HV4 is SGSKS or RGSKS (SEQ ID NOS. 167- 168, respectively). Additionally, in some embodiments, the VNAR domain comprises the CDR1 and CDR3 pair together with any one of the HV2s, with any one of the HV4s, or with both of any one of the HV2s and an HV4s.
[0088] For the foregoing VNAR domains, the FW1, FW2, FW2’, FW3 and FW4 regions can have naturally occurring VNAR sequences or altered VNAR sequences with amino acid substitutions, insertions or deletions (typically, but not limited to, no more than 1-10 amino acids changes, insertions or deletions) provided that such alterations maintain the overall primary and tertiary structure of a Type II VNAR domain, and provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs. In some embodiments, the FW1, FW2, FW2’, FW3 and FW4 regions of the Type II VNAR domains have a sequence for those regions as set forth in Tables 3 and 4 (in any independent combination), and, again, provided that such VNAR domains have combinations of CDR1, HV2, HV4, and CDR3 regions recited in the preceding two paragraphs.
[0089] In some embodiments of the VNAR antibody, the VNAR domain is any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135). In an embodiment, a VNAR antibody is capable of neutralizing infection of SARS-CoV-2
Additional Conjugates
[0090] The moieties, VNAR domains (VNAR polypeptides) and VNAR antibodies disclosed herein may optionally be conjugated (e.g., using linkers such as chemical linkers and/or linker peptides which are not usually associated with the domains being associated) to one or more additional agents which may include therapeutic and/or diagnostic agents. Such agents include but are not limited to chemotherapeutics such as cytostatic drugs, cytotoxins, radioisotopes, chelators, enzymes, nucleases, nucleic acids such as DNA, RNA or mixed nucleic acid oligonucleotides, including siRNAs, shRNAs, microRNAs, aptamers and the like; immunomodulators such as therapeutic antibodies, antibody and antibody-like fragments, inflammatory and anti-inflammatory cytokines, anti-inflammatory agents, radiotherapeutics, photoactive agents, diagnostic markers and the like. In certain embodiments, the pharmaceutically active moieties comprise at least one scFv molecule that is operably linked via a linker peptide to the C-terminus and/or N-terminus of an Fc region. [0091] In certain embodiments, The moieties, VNAR domains (VNAR polypeptides) and VNAR antibodies disclosed herein are multispecific, i.e., have at least one binding site that binds to a first molecule or epitope of a molecule (i.e., the SI fragment) and one or more other binding sites that bind to at least one heterologous molecule or to an epitope of either SI, another SARS-CoV-2 protein or another molecule. Multispecific binding molecules of the disclosure may comprise at least two binding sites, three binding sites, four binding sites or more.
Nucleic Acid Sequences That Encode an Si-Fragment-Specific Binding Moiety
[0092] In one aspect, the invention provides an isolated nucleic acid which encodes an Sl- fragment-specific binding moiety, conjugate, or VNAR antibody disclosed herein, or a fragment or derivative thereof. The invention also provides an isolated nucleic acid molecule comprising a sequence that hybridizes under stringent conditions to a nucleic acid sequence which encodes a moiety, conjugate, or VNAR antibody of the disclosure , or a fragment or derivative thereof, or the antisense or complement of any such sequence.
[0093] In another aspect, the invention provides an isolated nucleic acid molecule encoding a fusion protein comprising at least two segments, wherein one of the segments comprises a moiety or VNAR domain disclosed herein. In certain embodiments, a second segment comprises a heterologous signal polypeptide, a heterologous binding moiety, an immunoglobulin fragment such as a Fc domain, or a detectable marker.
[0094] A further aspect includes isolated nucleic acid molecules that encode moieties, conjugates, or VNAR antibodies of the disclosure or biologically active portions thereof.
Also included are nucleic acid fragments sufficient for use as hybridization probes to identify SI -fragment binding moieties encoding nucleic acids and fragments for use as polymerase chain reaction (PCR) primers for the amplification or mutation of nucleic acid molecules encoding VNAR domains disclosed herein.
[0095] As used herein, the term “nucleic acid molecule” is intended to include DNA molecules, RNA molecules (e.g., mRNA, shRNA, siRNA, microRNA), analogs of the DNA or RNA generated using nucleotide analogs, and derivatives, fragments and homologs thereof. The nucleic acid molecules of the disclosure may be single-, double-, or triple- stranded. A nucleic acid molecule of the present disclosure may be isolated using sequence information provided herein and well known molecular biological techniques (e.g., as described in Sambrook et ah, Eds., MOLECULAR CLONING: A LABORATORY MANUAL 2ND ED., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; and Ausubel, et ah, Eds., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1993).
[0096] A nucleic acid molecule of the disclosure may be amplified using any form of nucleic acid template and appropriate oligonucleotide primers according to standard PCR amplification techniques. Amplified nucleic acid may be cloned into an appropriate vector and characterized, e.g., by restriction analysis or DNA sequencing. Furthermore, oligonucleotides corresponding to nucleotide sequences that encode a moiety, conjugate, or VNAR antibody of the disclosure may be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
[0097] The term “oligonucleotide” as used herein refers to a series of covalently linked nucleotide (or nucleoside residues, including ribonucleoside or deoxyribonucleoside residues) wherein the oligonucleotide has a sufficient number of nucleotide bases to be used in a PCR reaction. Oligonucleotides comprise portions of a nucleic acid sequence having at least about 10 nucleotides and as many as 50 nucleotides, preferably about 15 nucleotides to 30 nucleotides. Oligonucleotides may be chemically synthesized and may be used as probes. A short oligonucleotide sequence may be used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue.
[0098] Derivatives or analogs of the nucleic acid molecules (or proteins) of the disclosure include, inter alia , nucleic acid (or polypeptide) molecules having regions that are substantially homologous to the nucleic acid molecules or proteins of the invention, e.g., by at least about 45%, 50%, 70%, 80%, 95%, 98%, or even 99% identity (with a preferred identity of 80-99%) over a nucleic acid or amino acid sequence of the same size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art. A percent identity for any candidate nucleic acid or polypeptide relative to a reference nucleic acid or polypeptide may be determined by aligning a reference sequence to one or more test sequences using, for example, the computer program ClustalW (version 1.83, default parameters), which enable nucleic acid or polypeptide sequence alignments across their entire lengths (global alignment) or across a specified length. The number of identical matches in such a ClustalW alignment is divided by the length of the reference sequence and multiplied by 100.
[0099] Also included are nucleic acid molecules capable of hybridizing to the complement of a sequence encoding the proteins of the disclosure under stringent or moderately stringent conditions. See e g. Ausubel, et ah, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1993, and below. An exemplary program is the GAP program (Wisconsin Sequence Analysis Package, Version 8 for UNIX, Genetics Computer Group, University Research Park, Madison, Wis.) using the default settings, which uses the algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482489). Derivatives and analogs may be full length or other than full length, if the derivative or analog contains a modified nucleic acid or amino acid, as described below.
[00100] Stringent conditions are known to those skilled in the art and may be found in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. In certain embodiments, stringent conditions typically permit sequences at least about 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% homologous to each other to remain hybridized to each other. A non-limiting example of stringent hybridization conditions is hybridization in a high salt buffer comprising 6><SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 mg/ml denatured salmon sperm DNA at 65° C. This hybridization is followed by one or more washes in 0.2><SSC, 0.01% BSA at 50° C. The term “stringent hybridization conditions” as used herein refers to conditions under which a nucleic acid probe, primer or oligonucleotide will hybridize to its target sequence, but only negligibly or not at all to other nucleic acid sequences. Stringent conditions are sequence- and length-dependent and depend on % (percent)-identity (or %- mismatch) over a certain length of nucleotide residues. Longer sequences hybridize specifically at higher temperatures than shorter sequences. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.
Methods Of Producing an Si-Fragment-Specific Binding Moiety
[00101] The moieties, conjugates, and VNAR antibodies of the disclosure may be manufactured by standard synthetic methods, by use of recombinant expression systems, or by any other suitable method. Thus, these entities may be synthesized in a number of ways, including, e.g., methods comprising: (1) synthesizing a polypeptide or polypeptide component thereof using standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide compound product; (2) expressing a nucleic acid construct that encodes the polypeptide or polypeptide component thereof in a host cell and recovering the expression product from the host cell or host cell culture; or (3) cell-free in vitro expression of a nucleic acid construct encoding the polypeptide or polypeptide component thereof, and recovering the expression product; or by any combination of the methods of (1), (2) or (3) to obtain fragments of the peptide component, subsequently joining (e.g., ligating) the fragments to obtain the peptide component, and recovering the peptide component.
[00102] It may be preferable to synthesize a polypeptide or polypeptide component of a moiety, conjugate, or VNAR antibody of the disclosure by means of solid-phase or liquid- phase peptide synthesis. Such molecules may suitably be manufactured by standard synthetic methods. Thus, peptides may be synthesized by, e.g., methods comprising synthesizing the peptide by standard solid-phase or liquid-phase methodology, either stepwise or by fragment assembly, and isolating and purifying the final peptide product. In this context, reference may be made to W01998/11125 or, inter alia , Fields, G.B. et al., “Principles and Practice of Solid-Phase Peptide Synthesis”; in: Synthetic Peptides, Gregory A. Grant (ed.), Oxford University Press (2nd edition, 2002) and the synthesis examples herein.
[00103] Accordingly, the present disclosure also relates to methods for producing a moiety, conjugate, or VNAR antibody of the disclosure according to above recited methods; a nucleic acid molecule encoding part or all of such polypeptides, a vector comprising at least one nucleic acid of the disclosure, expression vectors comprising at least one nucleic acid of the disclosure capable of producing a moiety, conjugate, or VNAR antibody of the disclosure when introduced into a host cell, and a host cell comprising a nucleic acid molecule, vector or expression vector of the disclosure invention.
[00104] The moieties, conjugates, and VNAR antibodies of the disclosure may be prepared using recombinant techniques well known in the art. In general, methods for producing such polypeptides by culturing host cells transformed or transfected with a vector comprising the encoding nucleic acid and recovering the polypeptide from cell culture are described in, e.g., Sambrook et ah, Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989); Dieffenbach et ah, PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995).
[00105] A nucleic acid encoding a desired polypeptide may be inserted into a replication vector for further cloning (amplification) of the DNA or for expression of the nucleic acid into RNA and protein. A multitude of cloning and expression vectors are publicly available and suitable for use.
[00106] Expression vectors capable of directing transient or stable expression of genes and having promoters operably linked to such genes are well known in the art. The vector components generally include, but are not limited to, one or more of the following: a heterologous signal sequence or peptide, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence, each of which is well known in the art. Optional regulatory control sequences, integration sequences, and useful markers that can be employed are known in the art.
[00107] Any suitable host cell may be used to produce moieties, conjugates, and VNAR antibodies of the disclosure. Host cells may be cells stably or transiently transfected, transformed, transduced or infected with one or more expression vectors which drive expression of a polypeptide of the invention. Suitable host cells for cloning or expressing nucleic acids of the invention include prokaryote, yeast, or higher eukaryote cells.
Eukaryotic microbes such as filamentous fungi yeast, Arabidopsis, and other plant and animal eukaryotic host cells that may be grown in liquid culture are suitable cloning or expression hosts for vectors. Suitable host cells for the expression of glycosylated polypeptides may also be derived from multicellular organisms.
[00108] Creation and isolation of host cell lines producing a moiety, conjugate, or VNAR antibody of the present disclosure can be accomplished using standard techniques known in the art. Mammalian cells are preferred host cells for expression of polypeptides. Particularly useful mammalian cells include, inter alia , HEK 293, NSO, DG-44, and CHO cells, but any other suitable host cell may be used according to the invention. Preferably, the moieties, conjugates, or VNAR antibodies of the disclosure are secreted into the medium in which the host cells are cultured, from which the moieties, conjugates, or VNAR antibodies of the disclosure may be recovered or purified.
When a polypeptide is produced in a recombinant cell other than one of human origin, it is typically free of polypeptides of human origin. In certain embodiments, it is advantageous to separate a polypeptide away from other recombinant cell components such as host cell polypeptides to obtain preparations that are of high purity or substantially homogeneous. As a first step, culture medium or cell lysates may be centrifuged to remove particulate cell debris and suitable protein purification procedures may be performed. Such procedures include, inter alia , fractionation (e.g., size separation by gel filtration or charge separation by ion-exchange column); ethanol precipitation; Protein A Sepharose columns to remove contaminants such as IgG; hydrophobic interaction chromatography; reverse phase HPLC; chromatography on silica or on cation-exchange resins such as DEAE and the like; chromatofocusing; electrophoretic separations; ammonium sulfate precipitation; gel filtration using, for example, Sephadex beads such as G-75. Any number of biochemical purification techniques may be used to increase the purity of a SI -binding moiety, conjugate, or VNAR antibody of the disclosure.
Methods of Treatment
[00109] In an aspect, the disclosure provides a method of passive immunization against SARS-CoV-2, and variants thereof, which comprises administering a pharmaceutical composition of the disclosure to a subject in need thereof.
[00110] In another aspect, the disclosure provides a method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition of the disclosure to a mammal or a subject for a time and in an amount effect to treat or prevent COVID-19. [00111] Such compositions are described in more detail below but include pharmaceutical compositions comprising at least one SI -specific binding moiety, conjugate or VNAR antibody of the disclosure. In embodiments, such compositions can also have, independently, two, three, four, five or more moieties, conjugates or VNAR antibodies of the disclosure. [00112] In accordance with the foregoing, the moieties, conjugates, and VNAR antibodies of the disclosure can be used the preparation of a medicament to for passive immunization against SARS-CoV-2 and viral variants (mutants) thereof or to treat or prevent COVID-19 in a mammalian subject in need thereof.
[00113] In embodiments of these methods, the subject or mammal has tested positive for SARS-CoV-2. In embodiments of these methods, the subject or mammal has suspected exposure to SARS-CoV-2 and/or tested negative for SARS-CoV-2. In some embodiments of these methods, the composition is preferably administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
Pharmaceutical Compositions, Administration and Dosing
[00114] A further aspect relates to pharmaceutical compositions comprising at least one moiety, conjugate, or VNAR antibody of the disclosure. In embodiments, such compositions can also have, independently, two, three, four, five or more of such moieties, conjugates or VNAR antibodies. The moieties, conjugates and VNAR antibodies may be present as a pharmaceutically acceptable salt or solvate, together with a pharmaceutically acceptable carrier, excipient or vehicle. Certain embodiments of the pharmaceutical compositions of the invention are described in further detail below.
[00115] The moieties, conjugates and VNAR antibodies of the present disclosure (and for convenience may also be referred to as compounds), or salts thereof, may be formulated as pharmaceutical compositions prepared for storage or administration, which typically comprise a therapeutically effective amount of a compound of the disclosure, or a salt thereof, in a pharmaceutically acceptable carrier.
[00116] The therapeutically effective amount of a moiety, conjugate or VNAR antibody of the present disclosure will depend on the route of administration, the type of mammal being treated, and the physical characteristics of the specific mammal under consideration. These factors and their relationship to determining this amount are well known to skilled practitioners in the medical arts. This amount and the method of administration can be tailored to achieve optimal efficacy, and may depend on such factors as weight, diet, concurrent medication and other factors, well known to those skilled in the medical arts. The dosage sizes and dosing regimen most appropriate for human use may be guided by the results obtained by the present invention and may be confirmed by clinical trials. [00117] An effective dosage and treatment protocol may be determined by conventional means, starting with a low dose in laboratory animals and then increasing the dosage while monitoring the effects, and systematically varying the dosage regimen as well. Numerous factors may be taken into consideration by a clinician when determining an optimal dosage for a given subject. Such considerations are known to the skilled person. The term "pharmaceutically acceptable carrier" includes any of the standard pharmaceutical carriers. Pharmaceutically acceptable carriers for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985). For example, sterile saline and phosphate- buffered saline at slightly acidic or physiological pH may be used. pH buffering agents may be phosphate, citrate, acetate, tris/hydroxymethyl)aminom ethane (TRIS), N- Tris(hydroxymethyl)methyl-3-aminopropanesulphonic acid (TAPS), ammonium bicarbonate, diethanolamine, histidine, which is a preferred buffer, arginine, lysine, or acetate or mixtures thereof. The term further encompasses any agents listed in the US Pharmacopeia for use in animals, including humans.
[00118] The term “pharmaceutically-acceptable salt” refers to the salt of the compounds. As used herein a pharmaceutically-acceptable salt retains qualitatively a desired biological activity of the parent compound without imparting any undesired effects relative to the compound. Salts include pharmaceutically acceptable salts such as acid addition salts and basic salts. Acid addition salts include salts derived from nontoxic inorganic acids, such as hydrochloric, nitric, phosphorous, phosphoric, sulfuric, hydrobromic, hydroiodic and the like, or from nontoxic organic acids such as aliphatic mono- and di-carboxylic acids, phenyl- substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like. Examples of basic salts include salts where the cation is selected from alkali metals, such as sodium and potassium, alkaline earth metals such as calcium and magnesium, and ammonium ions +N(R3)3(R4), where R3 and R4 independently designate optionally substituted Ci-6-alkyl, optionally substituted C2-6-alkenyl, optionally substituted aryl, or optionally substituted heteroaryl, and more specifically, the organic amines, such as N, N'-dibenzylethylenediamine, N-methylglucamine, chloroprocaine, choline, diethanolamine, ethylenediamine, procaine and the like. Other examples of pharmaceutically acceptable salts are described in "Remington's Pharmaceutical Sciences", 17th edition. Ed. Alfonso R. Gennaro (Ed.), Mark Publishing Company, Easton, PA, U.S.A., 1985 and more recent editions, and in the Encyclopaedia of Pharmaceutical Technology. [00119] "Treatment" is an approach for obtaining beneficial or desired clinical results. For the purposes of this invention, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. "Treatment" can also mean prolonging survival as compared to expected survival if not receiving treatment. "Treatment" is an intervention performed with the intention of preventing the development or altering the pathology of a disorder. Accordingly, "treatment" refers to both therapeutic treatment and prophylactic or preventative measures in certain embodiments. Those in need of treatment include those already with the disorder as well as those in which the disorder is to be prevented. By treatment is meant inhibiting or reducing an increase in pathology or symptoms when compared to the absence of treatment and is not necessarily meant to imply complete cessation of the relevant condition.
[00120] The pharmaceutical compositions can be in unit dosage form. In such form, the composition is divided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of the preparations, for example, packeted tablets, capsules, and powders in vials or ampoules. The unit dosage form can also be a capsule, cachet, or tablet itself, or it can be the appropriate number of any of these packaged forms. It may be provided in single dose injectable form, for example in the form of a pen. Compositions may be formulated for any suitable route and means of administration.
[00121] Pharmaceutically acceptable carriers or diluents include those used in formulations suitable for oral, rectal, nasal or parenteral (including subcutaneous, intramuscular, intravenous, intradermal, and transdermal) administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. Subcutaneous or transdermal modes of administration may be particularly suitable for the compounds described herein.
[00122] An acceptable route of administration may refer to any administration pathway known in the art, including but not limited to aerosol, enteral, nasal, ophthalmic, oral, parenteral, rectal, vaginal, or transdermal (e.g., topical administration of a cream, gel or ointment, or by means of a transdermal patch). "Parenteral administration” is typically associated with injection at or in communication with the intended site of action, including infraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrastemal, intrathecal, intrauterine, intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal, or transtracheal administration. [00123] In another aspect, the present invention provides a composition, e.g., a pharmaceutical composition, comprising one moiety, conjugate or VNAR antibody of the present disclosure, or a combination of different such or a combination of different such moieties, conjugates or VNAR antibodies, and at least one pharmaceutically acceptable carrier.
[00124] Pharmaceutical compositions of the invention may be administered alone or in combination with one or more other therapeutic or diagnostic agents. A combination therapy may include a moiety, conjugate or VNAR antibody of the present disclosure combined with at least one other therapeutic agent selected based on the particular patient, disease or condition to be treated. Examples of other such agents include, inter alia, a cytotoxic, anti cancer or chemotherapeutic agent, an anti-inflammatory or anti-proliferative agent, an antimicrobial or antiviral agent, growth factors, cytokines, an analgesic, a therapeutically active small molecule or polypeptide, a single chain antibody, a classical antibody or fragment thereof, or a nucleic acid molecule which modulates one or more signaling pathways, and similar modulating therapeutics which may complement or otherwise be beneficial in a therapeutic or prophylactic treatment regimen.
[00125] As used herein, "pharmaceutically acceptable carrier" includes any and all physiologically acceptable, i.e., compatible, solvents, dispersion media, coatings, antimicrobial agents, isotonic and absorption delaying agents, and the like. In certain embodiments, the carrier is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal or epidermal administration (e.g., by injection or infusion). Depending on selected route of administration, the conjugate of the invention may be coated in a material or materials intended to protect the compound from the action of acids and other natural inactivating conditions to which the active conjugate may encounter when administered to a subject by a particular route of administration.
[00126] A pharmaceutical composition of the invention also optionally includes a pharmaceutically acceptable antioxidant. Exemplary pharmaceutically acceptable antioxidants are water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propylgallate, alpha-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
[00127] Examples of suitable aqueous and nonaqueous carriers that may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyloleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
[00128] Pharmaceutical compositions of the disclosure may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of presence of microorganisms may be ensured both by sterilization procedures, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. Isotonic agents, such as sugars, sodium chloride, and the like into the compositions, may also be desirable. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as, aluminum monostearate and gelatin.
[00129] Exemplary pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. Such media and reagents for pharmaceutically active substances are known in the art. The pharmaceutical compositions of the invention may include any conventional media or agent unless any is incompatible with the active conjugate of the invention. Supplementary active compounds may further be incorporated into the compositions.
[00130] Therapeutic compositions are typically sterile and stable under the conditions of manufacture and storage. The composition may be formulated as a solution, microemulsion, liposome, or other ordered structure suitable to high drug concentration. The carrier may be a solvent or dispersion medium containing, for example, water, alcohol such as ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol), or any suitable mixtures. The proper fluidity may be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by use of surfactants according to formulation chemistry well known in the art. In certain embodiments, isotonic agents, e.g., sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride may be desirable in the composition. Prolonged absorption of injectable compositions may be brought about by including in the composition an agent that delays absorption for example, monostearate salts and gelatin.
[00131] Solutions or suspensions used for intradermal or subcutaneous application typically include one or more of: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates; and tonicity adjusting agents such as, e.g., sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide, or buffers with citrate, phosphate, acetate and the like. Such preparations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. [00132] Sterile injectable solutions may be prepared by incorporating a conjugate of the invention in the required amount in an appropriate solvent with one or a combination of ingredients described above, as required, followed by sterilization microfiltration.
Dispersions may be prepared by incorporating the active compound into a sterile vehicle that contains dispersion medium and other ingredients, such as those described above. In the case of sterile powders for the preparation of sterile injectable solutions, the methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient in addition to any additional desired ingredient from a sterile-filtered solution thereof.
[00133] When a therapeutically effective amount of a moiety, conjugate or VNAR antibody of the present disclosure is administered by, e.g., intravenous, cutaneous or subcutaneous injection, the binding agent will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. Methods for preparing parenterally acceptable protein solutions, taking into consideration appropriate pH, isotonicity, stability, and the like, are within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection will contain, in addition to binding agents, an isotonic vehicle such as sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection, or other vehicle as known in the art. A pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives well known to those of skill in the art.
[00134] The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending on a variety of factors, including the subject being treated, and the particular mode of administration. In general, it will be an amount of the composition that produces an appropriate therapeutic effect under the particular circumstances. Generally, out of one hundred percent, this amount will range from about 0.01 per cent to about ninety-nine percent of active ingredient, from about 0.1 per cent to about 70 per cent, or from about 1 percent to about 30 percent of active ingredient in combination with a pharmaceutically acceptable carrier.
[00135] Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic response). For example, a single bolus may be administered, several divided doses may be administered over time, or the dose may be proportionally reduced or increased as indicated by the particular circumstances of the therapeutic situation, on a case by case basis. It is especially advantageous to formulate parenteral compositions in dosage unit forms for ease of administration and uniformity of dosage when administered to the subject or patient. As used herein, a dosage unit form refers to physically discrete units suitable as unitary dosages for the subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce a desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention depend on the specific characteristics of the active compound and the particular therapeutic effect(s) to be achieved, taking into consideration and the treatment and sensitivity of any individual patient.
[00136] For administration of a moiety, conjugate or VNAR antibody of the present disclosure, the dosage range will generally be from about 0.0001 to 100 mg/kg, and more usually 0.01 to 5 mg/kg, of the host body weight. Exemplary dosages may be 0.25 mg/kg body weight, 1 mg/kg body weight, 3 mg/kg body weight, 5 mg/kg body weight or 10 mg/kg body weight or within the range of 1-10 mg/kg. An exemplary treatment regime is a once or twice daily administration, or a once or twice weekly administration, once every two weeks, once every three weeks, once every four weeks, once a month, once every two or three months or once every three to 6 months. Dosages may be selected and readjusted by the skilled health care professional as required to maximize therapeutic benefit for a particular subject, e.g., patient. The moieties, conjugates or VNAR antibodies of the present disclosure will typically be administered on multiple occasions. Intervals between single dosages can be, for example, 2-5 days, weekly, monthly, every two or three months, every six months, or yearly.
[00137] In certain embodiments, two or more moieties, conjugates or VNAR antibodies of the present disclosure with different binding properties may be administered simultaneously or sequentially, in which case the dosage of each administered compound may be adjusted to fall within the ranges described herein.
[00138] In certain embodiments, a moiety, conjugate or VNAR antibody of the present disclosure may be administered as a sustained release formulation, in which case less frequent administration is required. Dosage and frequency vary depending on the half-life of the conjugate in the subject or patient. The dosage and frequency of administration may vary depending on whether the treatment is therapeutic or prophylactic (e.g., preventative), and may be adjusted during the course of treatment. In certain prophylactic applications, a relatively low dosage is administered at relatively infrequent intervals over a relatively long period of time. Some subjects may continue to receive treatment over their lifetime. In certain therapeutic applications, a relatively high dosage at relatively short intervals is sometimes required until progression of the disease is reduced or until the patient shows partial or complete amelioration of symptoms of disease. Thereafter, the patient may be switched to a suitable prophylactic dosing regimen.
[00139] Actual dosage levels of the moiety, conjugate or VNAR antibody of the present disclosure alone or in combination with one or more other active ingredients in the pharmaceutical compositions may be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without causing deleterious side effects to the subject or patient. A selected dosage level will depend upon a variety of factors, such as pharmacokinetic factors, including the activity of the particular conjugate or composition employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the subject or patient being treated, and similar factors well known in the medical arts.
[00140] Therapeutic compounds or compositions of the invention may be administered with one or more of a variety of medical devices known in the art. For example, in one embodiment, a therapeutic conjugate of the invention may be administered with a needleless hypodermic injection device. Examples of well-known implants and modules useful in the present invention are in the art, including e.g., implantable micro-infusion pumps for controlled rate delivery; devices for administering through the skin; infusion pumps for delivery at a precise infusion rate; variable flow implantable infusion devices for continuous drug delivery; and osmotic drug delivery systems. These and other such implants, delivery systems, and modules are known to those skilled in the art.
Improved Type VNAR Libraries and Their Construction
Figure imgf000038_0001
[00141] The VNAR domain has the basic structure of an Ig variable domain with two b sheets held together by two canonical cysteine residues that stabilize the framework. Unlike Ig variable domains, however, VNARs typically have one or two additional disulfide bonds and are classified into four isoforms based on the number and position of these non-canonical cysteines (Zielonka, Empting 2015). Semi -synthetic VNAR libraries based on the Type I and Type II VNAR isoforms are available (W02015/200883, published December 30, 2015) and on the Type IV VNAR isoforms (WO2019/246288). The Type I VNAR contains non- canonical cysteines in CDR3 that form two disulfide bonds with cysteine in the framework and has only been reported in the nurse shark ( Ginglymostoma cirratum) to date. The Type II VNAR, which is the most predominant isoform among the various shark species, is distinguished by a disulfide bond between a cysteine in CDR3 and another cysteine in CDR1. [00142] The additional disulfide bonds in both Type I and Type II VNARs serve to stabilize and orient the CDR3 such that it can protrude into binding pockets and grooves (Diaz 2002). In addition to Types I and II, rarer VNAR variants can be found in the natural repertoire, namely Type lib (Streltsov 2004; Liu 2007) and, more recently reported, Type IV (Kovalenko, Olland 2013). Type IV VNARs contain the framework cysteines that form the Ig fold but lack any additional cysteines.
[00143] The VNAR domain libraries disclosed herein are Type II isoform libraries designed from analysis of the natural diversity found in the VNAR scaffold that occurs during the nurse shark immune response. Using nurse sharks immunized with a variety of immunogens, blood samples were collected pre- and post-immunization at different time points from 6 animals, in total producing 30 individual immune repertoire libraries that were subsequently analyzed by next-generation sequencing (NGS). The most common type II VNAR N-termini were identified and overlapping oligonucleotides encoding selected N-terminal fragments covering residues 1-84 with canonical cysteines in positions 22, 29 and 83 were synthesized containing residue substitutions depicted in Table 1. The CDR1, HV2 and HV4 regions (bolded) cover positions 26-33, 44-52 and 61-65, respectively. The CDR3 region within the C-terminal fragment was designed based on NGS analysis of these immune repertoire libraries, which had the most common lengths for CDR3 as 15, 16 and 17 residues with a canonical cysteine located approximately in the middle of CDR3 (Table 2). [00144] For example, a library was generated by enzymatic ligation of 1068 different N- terminal fragments-encoding oligonucleotides (having the amino acid sequences of SEQ ID NOS. 177-1244) with approximately lxl06of C-terminal fragments-encoding oligonucleotides containing the CDR3 that were synthesized following the residue representation instructions outlined in Table 2. In this library, the CDR3 fragment covered residues 85-100 with a canonical cysteine in position 91.
[00145] Methods to make the libraries disclosed herein include but are not limited to, direct synthesis of nucleic acid libraries and site-directed mutagenesis, and for peptide libraries, direct chemical synthesis. Direct synthesis methods are preferred, in part, because the N- terminal and the randomized C-terminal fragments can be designed to exclude potentially detrimental motifs such as: glycosylation (NxS NxT, where x is not P), asparagine deamidation (NG, NS, NT, NH), aspartate isomerization (DG, DS, DT, DD), lysine glycation (LE, LD, LL), integrin binding a\;b3 (RGD, RYD, KGD, NGR), integrin binding a4b1 (LDV), integrin binding a2b1 (DGE), CD11 c/CD 18 binding (GRP), fragmentation (DP, DQ) and hydrophobicity (FF, FW, WW, WF). A schematic of VNAR domain structure is shown in Figure 1, with the N- and C-terminal fragments indicated below the domain. In any event, the size of the library is sufficiently large enough and diverse enough to produce many suitable VNARs to bind to targets of interest during the screening process.
[00146] Accordingly, one aspect of the present invention relates to improved Type II VNAR libraries based on nurse shark immune repertoire library analysis across the entire VNAR domain. These libraries have optimized VNAR scaffolds (i.e., for the framework regions) and/or improved CDR3 loops in accordance with the disclosures herein.
[00147] Hence, libraries of the disclosure comprise synthetic polypeptide compositions and/or nucleic acid molecules encoding them and may be used in assays, e.g., in phage display libraries, to identify and select sequences within the synthetic library which bind selectively to one or more molecular mammalian target molecules of interest. Libraries of the invention enable the generation of novel therapeutic products, in particular, specific binding moieties which bind selectively and with high affinity to a select cellular target, thereby producing a target antagonist compound or mimicking the activity of a native molecule. Exemplary binding moieties and molecular target antagonist compounds which may be identified and isolated using the libraries of the invention include, inter alia , high affinity polypeptide binding domains specific for wildtype and mutant proteins, such as those described herein against coronavirus SARS-CoV-2 spike protein SI domain and mutants thereof as well as for species cross reactive proteins, such as human and mouse CD98hc and other targets of interest such as human BAFF, human and mouse transferrin receptor hTrR-1, myostatin and other antigens.
[00148] Accordingly, in certain embodiments, the present disclosure is directed to a synthetic nucleic acid-containing library whose members each encode a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C- terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 — CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide,
(a) residues 22, 29 and 83 are cysteine;
(b) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg
Wherein Xai and Xa2 are independently any amino acid except cysteine; Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(c) no other residues in said polypeptide are cysteine.
In an embodiment of this library, the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
[XaiMY/L/D/S/G] [D/V/W/Y/G]C [W/E/Y/D/G] [ Y/L/D/V/L] [ Xa2]5 [D/G] [ V/L] . [00149] In an embodiment, the disclosure provides a synthetic nucleic acid-containing library whose members each comprise a nucleic acid encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide, none of the residues are cysteine except as provided in (a) to (i) and, wherein,
(a) FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
(b) CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
(c) FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y; (d) HV2 is 9 amino acids in length;
(e) FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
(f) HV4 is 5 amino acids in length;
(g) FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
(h) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine, Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(i) FW4 is 10 amino acids in length and has an amino acid sequence comprising
YG[D/G]GT[A/V]VTVN (SEQ ID NO: 1245).
In an embodiment of this library, the residue at each position of said VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
[00150] In embodiments, any of the nucleic acid libraries of the disclosure are phage display libraries. Such libraries may comprise approximately 109 theoretically distinct nucleic acid sequences.
[00151] In accordance with another aspect of the disclosure, the nucleic acid libraries hereof are used in various methods for identifying polypeptides that bind selectively to target molecules of interest. An embodiment provides a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises: (a) exposing a target molecule of interest to polypeptides produced by expression of a nucleic acid library of the disclosure; and (b) separating polypeptides that selectively bind from those that do not selectively bind the target molecule. In an embodiment, the target molecule of interest is expressed on the surface of a phage, bacterium or cell, or is attached to, tethered to or otherwise associated with a solid support.
[00152] Another embodiment provides a method of screening a library for a polypeptide that selectively binds with high affinity to a target molecule of interest, the library comprising a plurality of polypeptides produced by expression of a nucleic acid library of the disclosure and comprises: (a) incubating a sample of the library with a concentration of a target molecule under conditions suitable for specific binding of the polypeptides to the molecule; (b) incubating a second sample of the library under the same conditions but without target molecule; (c) contacting each of the first and second samples with immobilized target molecule under conditions suitable for binding of the polypeptide to the immobilized target antigen; (d) detecting the polypeptide bound to immobilized target molecule for each sample; (e) determining the affinity of the polypeptide for the target molecule by calculating the ratio of the amounts of bound polypeptide from the first sample over the amount bound polypeptide from the second sample.
[00153] Yet another embodiment provides a method of identifying one or more VNARs that selectively bind to a target molecule of interest which comprises: (a) contacting said target molecule with a phage display library of Claim 40 or 41; (b) separating phage that selectively bind the target molecule from those that do not selectively bind the target molecule to produce an enriched phage library; (c) repeating steps (a) and (b) with the enriched phage library to produce a further enriched phage library; (d) repeating step (c) until the further enriched phage library is enriched from at least about 10- to about 106-fold or more relative to the original phage library; and (e) plating the further enriched phage library and isolating and characterizing individual clones therefrom to thereby identify one or more VNAR polypeptides that selectively bind to the target molecule of interest. The number of cycles needed to obtain a sufficiently further enriched phage library to readily isolate the desired, individual clones typically ranges from three to eight rounds of selection and more typically can be done with 3-4 rounds of selection. In this method, either the target molecule or the phage display library can be bound to or attached to a solid support to facilitate selective binding (and simplify wash conditions, which stringency can be varied in successive rounds (see, the Examples). Any method known in the art for eluting and recovering bound phage can be used.
[00154] In preferred embodiments for any of these methods, the target molecule is a SARS- CoV-2 spike protein, a domain of the spike protein or a mutant thereof.
[00155] A still further aspect relates to a polypeptide library composition comprising a plurality of synthetic or recombinant polypeptides, each of which encodes a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C- terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide,
(a) residues 22, 29 and 83 are cysteine; (b) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine; Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(c) no other residues in the polypeptide are cysteine.
In an embodiment of this library, the synthetic nucleic acid-containing library comprises a CDR3 which is 16 amino acids in length and has an amino acid sequence of
[XaiMY/L/D/S/G] [D/V/W/Y/G]C [W/E/Y/D/G] [ Y/L/D/V/L] [ Xa2]5 [D/G] [ V/L] . [00156] In an embodiment, the disclosure provides a polypeptide library composition whose members each comprise a polypeptide encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide, none of the residues are cysteine except as provided in (a) to (i) and, wherein,
(a) FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
(b) CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
(c) FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
(d) HV2 is 9 amino acids in length;
(e) FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
(f) HV4 is 5 amino acids in length;
(g) FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
(h) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine, Xb is Y, L, D, S or G; Xc is D, V, W, Y or G; Xd is W, E, Y, D, or G; Xe is Y, L, D, V or L; Xf is D or G; and Xgis V or L; and
(i) FW4 is 10 amino acids in length and has an amino acid sequence comprising YG[D/G]GT[A/V]VTVN (SEQ ID NO: 1245).
In an embodiment of this library, the residue at each position of the VNAR polypeptide is one of the allowed amino acids for that position as provided in Table 1 and Table 2.
[00157] In some embodiments, a plurality is 50 or more or as defined herein (see above). In those embodiments of the polypeptide compositions produced by a phage display library, the composition can have from 100 to 1010 polypeptides as determined by the phage titer.
[00158] Yet a further aspect relates to a method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises (a) exposing a target molecule of interest to a polypeptide library composition of the disclosure; and (b) separating polypeptides that selectively bind to said target molecule from those that do not selectively bind the target molecule.
[00159] Accordingly, the disclosure provides powerful methods for screening and selecting a synthetic VNAR binding moiety with binding specificity directed to one or more of any number of desired molecular target molecules. VNAR libraries may be screened and clones comprising putative binding moiety sequences (polypeptide and/or nucleic acid) may be enriched, purified and tested in whatever in vitro and in vivo biological assays are known and available to the art for the particular molecular target molecule of interest. Once molecular target-binding clones are isolated, polypeptide and/or nucleic acid molecules encoding the synthetic VNAR binding moieties may be identified and optionally isolated. One of skill in the art can use standard genetic and molecular engineering, e.g., affinity maturation and other well-known techniques to optimize the characteristics of the binding moiety for its intended purpose, e.g., to produce improved diagnostic agents or therapeutic versions by making sequence variants and derivatives expected to be more potent or otherwise more drug-like with respect to half-life, pK, solubility, bioavailability, cellular or tissue targeting, in vivo clearance and the like.
[00160] While some embodiments of the invention have been described by way of illustration, it will be apparent that the invention can be put into practice with many modifications, variations and adaptations, and with the use of numerous equivalents or alternative solutions that are within the scope of persons skilled in the art, without departing from the spirit of the invention or exceeding the scope of the claims. [00161] All publications, patents, and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.
EXAMPLES
[00162] The examples presented herein represent certain embodiments of the present invention. However, it is to be understood that these examples are for illustration purposes only and do not intend, nor should any be construed, to be wholly definitive as to conditions and scope of this invention. The examples were carried out using standard techniques, which are well known and routine to those of skill in the art, except where otherwise described in detail.
Example 1. OSX6 phage library generation.
[00163] The OSX6 library was designed based on natural diversity found in the VNAR scaffold that occurs during the nurse shark immune response. Nurse sharks were immunized with a variety of immunogens and blood samples were collected pre- and post-immunization at different time points from 6 animals in total producing 30 individual immune repertoire libraries that were subsequently analyzed by next-generation sequencing (NGS). The most common type II VNAR N-termini were identified and overlapping oligonucleotides encoding selected N-terminal fragments covering residues 1-84 with canonical cysteines in positions 22, 29 and 83 were synthesized containing residue substitutions depicted in Table 1. The CDR1, HV2 and HV4 regions (bolded) cover positions 26-33, 44-52 and 61-65, respectively. The library was generated by enzymatic ligation of 1068 different N-terminal fragments encoding oligonucleotides (having the amino acid sequences of SEQ ID NOS. 177-1244) with approximately lxlO6 of C-terminal fragments-encoding oligonucleotides containing the CDR3 that were synthesized following residue representation instructions outlined in Table 2. The CDR3 fragment covers residues 85-100 with a canonical cysteine in position 91. [00164] The CDR3 region within C-terminal fragment was designed based on NGS analysis of the immune repertoire libraries, which had the most common lengths for CDR3 as 15, 16 and 17 residues with canonical cysteine located approximately in the middle of CDR3 (Table 2). For the OSX6 library, the amino acid representation in each position for positions 85-100 of the C-terminal fragments was as follows:
X(4) [ Y/L/D/ S/ G] [D/V/W /Y/G] C [W/E/Y/D/ G/] [Y/L/D/V/L]X(5)[D/G] [V/L] . [00165] In addition, the randomized C-terminal fragments were designed to exclude potentially detrimental motifs such as: glycosylation (NxS NxT, where x is not P), asparagine deamidation (NG, NS, NT, NH), aspartate isomerization (DG, DS, DT, DD), lysine glycation (LE, LD, LL), integrin binding aUb3 (RGB, RYD, KGD, NGR), integrin binding a4b! (LDV), integrin binding a2b1 (DGE), GDI 1 c/CD 18 binding (GRP), fragmentation (DP, DQ) and hydrophobicity (FF, FW, WW, WF). A schematic of VNAR domain structure is shown in Figure 1, with the N- and C-terminal fragments indicated below the domain.
[00166] After ligation, the final OSX6 library size and diversity was approximately lxlO9. The full OSX6 library was cloned into the expression vector phagemid pOsD2, a modified version of pSEX81 (Progen) in which a 6XHis tag, (SEQ ID NO: 169), a FLAG tag, and an amber stop codon were inserted between the VNAR domain (inserted into Sfil sites) and the full-length PHI protein of the M13 phage as described in U S Patent No 10,479,990.
[00167] Overall, the OSX6 phage library has a framework as well as a CDR3 loop closely resembling the natural repertoire of VNAR domains found in nurse sharks. The framework diversity included modifications to the germline sequence that spread across the whole VNAR scaffold and were not limited to CDR1, HV2, HV4 and CDR3. Such a design, without being bound to a theory, should increase stability, expression yields and developability, thus increasing the success rate for the discovery of functional antibodies despite reduced diversity in CDR3 loop. In addition, the direct synthesis of the fragments used for generation of the OSX6 library, rather than the use of the degenerate NNK codon method, assured a high level of accuracy and nearly exact match between theoretical and achieved design. The direct synthesis also allowed the removal of know liability motifs including glycosylation, asparagine deamidation, aspartate isomerization, lysine glycation, integrin binding, CD 11 c/CD 18 binding, fragmentation and hydrophobicity patches that further improved developability characteristics of VNAR domains isolated from the OSX6 library.
Table 1. Amino Acid Residues For N-Terminal VNAR Fragments
Figure imgf000046_0001
Figure imgf000047_0001
Figure imgf000048_0001
Table 2. Amino Acid Residues For C-Terminal VNAR Fragments
Figure imgf000049_0001
Example 2. Phage Display Selection to Identify VNARs to SI and Sl-RBD.
[00168] Overview. The phage selection process was performed with two different Type II VNAR semi-synthetic libraries, the OSX3 library described in U.S. Pat. No. 10,479,990, and the OSX6 library prepared as described in Example 1. The OSX3 library contains approximately 1.6 x 1010 unique sequences with CDR3 lengths from 11 to 18 amino acids and a flexible position for the canonical cysteine in the CDR3 loop. The OSX6 library contains a single length CDR3 of 14 amino acid residues with a centrally fixed canonical cysteine within approximately 103 framework variants identified from naive and immune repertoire libraries by NGS. [00169] Expression and Purification of SI, Sl-RBD and ACE2. SARS-CoV-2 spike protein (Accession: YP 009724390.1) SI domain (amino acids 16-685) and Sl-RBD domain (amino acids 319-541) (Figure 2) were synthesized and cloned into the pFUSE expression vector (InvivoGen). Both constructs contained AVI and 6xHis tags (SEQ ID NO: 169) at the C-terminal end separated by G4S linkers (SEQ ID NO: 170). ACE2 (UnitProt entry:
Q9BYF1) ectodomain (amino acids 18-740) was synthesized with FLAG and 6xHis tags (SEQ ID NO: 169) at the C-terminal end separated by G4S (SEQ ID NO: 170) linkers before cloning into the pFUSE vector. SI, Sl-RBD and ACE2 recombinant proteins were expressed in Expi293 cells for 5 days following transient transfection using Expifectamine 293 Transfection Kit (Thermo Fisher Scientific). Cell cultures were centrifuged at 4500 for 40 min, supernatants were collected and filtered on 0.45 pm membranes before being loaded on a HisTrap Excel column (Cytiva). After extensive washing, the proteins were eluted with 500 mM imidazole, concentrated and buffer exchanged to PBS pH 7.4 using HiPrep 26/10 desalting columns. The quality of the purified proteins was assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and analytical size exclusion chromatography (SEC) using a Superdex 200 Increase 10/300 GL analytical column (Cytiva). [00170] Phage selections. Phage selection was performed against the Sl-RBD domain (Trenzyme) and SI subunit of SARS-CoV-2 spike protein, which were biotinylated using EZ-Link Sulfo-NHS-Biotin reagent (Pierce). PEG/NaCl precipitated phage libraries blocked in 5% BSA in PBS were deselected with streptavidin magnetic beads prior to bio-panning against biotinylated SI or Sl-RBD. Phage bound to biotinylated target protein were captured by streptavidin coupled Dynabeads (Thermo Fisher Scientific), washed and eluted in 100 nM triethylamine. Eluted phages were adjusted to neutral pH and propagated in TGI E. coli. M13K07 helper phage was used to induce phage production for subsequent rounds of selection. The amount of antigen used in each subsequent selection round was 100, 50, and 25 nM for round 1, 2 and 3, respectively.
[00171] Phage ELISA. Individual clones were picked from agar plates and grown at 37°C with shaking in a 96-well block in 2YT media supplemented with 2% glucose and 100 pg/ml ampicillin until visible growth occurred. The cultures were super-infected with M13K07 helper phage (New England Biolab) for 1 hr and the media was replaced with 2YT media supplemented with 100 pg/ml ampicillin and 50 pg/ml kanamycin. After 16 hr at 30°C, supernatants were collected by centrifugation and blocked in a final concentration of 2.5% milk in PBS with 0.1% Tween-20 (PBST) for 1 hr at room temperature (RT). High binding, 96 well microplates (Greiner) were coated with 100 pi (5 pg/ml) of purified SI or Sl-RBD or commercial human serum albumin (HSA; Sigma-Aldrich) and incubated overnight at 4°C. Plates were blocked with 2.5% milk in PBST for 1 hr at RT. Blocked phage supernatants were transferred to blocked microplates and incubated for 1 hr followed by washing with PBST on a plate washer (BioTek). Anti-M13-HRP antibody (Sino Biological) was used for detection at 1:4000 dilution in blocking buffer. The reaction was developed with 1-Step Ultra TMB-ELISA Substrate Solution (Thermo Fisher Scientific), stopped with 1% HC1 and absorbance was measured at 450 nm on VarioSkan plate reader (Thermo Fisher Scientific). [00172] Results. Three rounds of selection with the OSX3 and OSX6 libraries produced 149 unique VNAR clones as identified by DNA sequencing. The OSX3 library produced 60 and 40 clones from selection with Sl-RBD and SI, respectively (Table 3). The OSX6 library produced 34 and 15 clones from selection with Sl-RBD and SI, respectively (Table 4). The SEQ ID NO: is also used as the name for the VNAR clone or VNAR domain having that sequence. The CDR1, HV2, HV4 and CDR3 sequences of VNARs identified from the OSX3 and OSX6 libraries, respectively are also listed in Tables 5 and 6.
[00173] The specific binding of all 149 clones to either SI or Sl-RBD was confirmed by phage ELISA. The lower number of unique clones obtained from OSX6 in comparison to OSX3 library was likely a consequence of lower CDR3 diversity in the OSX6 library.
Table 3. VNAR Domains from the OSX3 Type II VNAR library
Figure imgf000051_0001
Figure imgf000052_0001
Figure imgf000053_0001
Figure imgf000054_0001
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Table 4. VNAR Domains from the OSX6 Type II VNAR library
Figure imgf000057_0002
Figure imgf000058_0001
Figure imgf000059_0001
Figure imgf000060_0001
Table 5. The CDR1, HV2, HV4 and CDR3 sequences for the VNARs from the OSX3 library
Sequences in Table 5 are residues of the SEQ ID NO in the left column as follows: CDR1 is residues 26-33, HV2 is residues 44-52, HV4 is residues 61-65, and CDR3 is the residues listed in the far-right column.
Figure imgf000060_0002
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Table 6. The CDR1, HV2, HV4 and CDR3 sequences for the VNARs from the OSX6 library
Sequences in Table 6 are residues of the SEQ ID NO in the left column as follows: CDR1 is residues 26-33, HV2 is residues 44-52, HV4 is residues 61-65, and CDR3 is the residues listed in the far-right column.
Figure imgf000063_0002
Figure imgf000064_0001
[00174] For Table 5 and Table 6 above, the amino acid sequence for CDR1 is found at amino acids 26-33 of the indicated SEQ ID NO: for that domain; for HV2 at amino acids 44- 52; for HV4 sequence at amino acids 61-65; and for CDR3 sequence, it begins at amino acid 85 and continues the length of the particular CDR3 (typically 11- 20 amino acids, as shown).
Example 3. Binding activity of VNAR-hFc fusions (VNAR antibodies).
[00175] VNAR-Fc formatting. The VNAR clones that showed specific binding to the antigen in phage ELISAs from Example 2 were identified by Sanger sequencing and cloned into the pFUSE expression vector containing the IgGl human Fc (hFc) domain to produce VNAR human Fc fusions (VNAR-hFc). The final constructs are bivalent antibodies with the VNAR domain fused to the N-terminus of the hFc domain; these fusions are also referred to herein interchangeably as VNAR antibodies. [00176] Expi293 cells were transiently transfected with a VNAR-hFc following the manufacturer protocol at small scale (0.5 ml). Crude supernatants were tested for binding to SI and Sl-RBD proteins by ELISA. Binding to either SI or Sl-RBD was confirmed for a total of 57 VNAR antibodies (Table 7). This data is also shown graphically in Figures 3-6 in which
• Figure 3 shows antigen binding of VNAR antibodies selected against Sl-RBD isolated from the OSX3 phage library;
• Figure 4 shows antigen binding of VNAR antibodies selected against SI protein isolated from the OSX3 phage library;
• Figure 5 shows antigen binding of VNAR antibodies selected against Sl-RBD isolated from the OSX6 phage library; and
• Figure 6 shows antigen binding of VNAR antibodies selected against SI protein isolated from the OSX6 phage library.
Only clones that showed binding by ELISA to either Sl-RBD or SI are presented on the bar graphs, measured as OD>0.3 (or about 3 -fold over blank). The OD450 values are listed in Table 7 and those OD values >0.3 are in bolded.
[00177] The larger OSX3 library produced 37 VNAR antibodies (with 17 from the Sl-RBD and 20 from the SI selection), whereas 20 antibodies came from OSX6 library (with 14 from the Sl-RBD and 6 from the SI selection).
[00178] The VNAR antibodies that specifically bound to either SI or Sl-RBD were expressed at a larger scale (50ml) and purified to measure their binding potency by ELISA. For larger scale production, after 5 days growth, the transiently-transfected cell cultures were centrifuged at 2,000 rpm for 10 min, supernatants were filtered using 0.22 pm membrane filters and loaded onto HiTrap MabSelect SuRe columns (Cytiva) pre-equilibrated against PBS, pH 7.4. Protein A-bound antibodies were eluted with 0.1 M glycine, pH 3.5 and the buffer exchanged to PBS, pH 7.4 using HiPrep 26/10 desalting column (Cytiva). Purity of the purified protein samples was determined by analytical SEC and SDS-PAGE.
[00179] To determine the binding EC50 of the selected VNAR antibodies, high binding 96 well microplates (Greiner) were coated overnight at 4°C with 100 pi of SI, Sl-RBD or HSA at 5 pg/ml or Sl-RBD E484K or Sl-RBD N501Y at 1 pg/ml. Plates were blocked for 1 hr at RT with 5% bovine serum albumin (BSA) in PBS before a 1 hr incubation with serially diluted VNAR-hFc antibodies or ACE2. The plates were washed, and binding was detected with an anti-human IgG (Fc specific) (1:5000 dilution, Sigma-Aldrich, A0170) or anti-FLAG (1:1000 dilution, Sigma-Aldrich, A8592) HRP-conjugated antibodies for VNAR-hFc antibodies or ACE2, respectively. The signal was developed with 1-Step™ Ultra TMB- ELISA substrate solution (Thermo Fisher Scientific) and the reaction was stopped with 1% HC1. Absorbance measured at 450 nm and EC50 values were calculated by 4-parametric non linear regression using GraphPad Prism 8.0.
[00180] The EC50 values were determined for thirty VNAR antibodies (16 from OSX3 and 14 from OSX6) and showed a binding potency for Sl-RBD in the low nM range (Table 8; Figure 7). None of the clones selected against Sl-RBD regardless of library origin showed a binding EC50 >3E-08 M (Table 8). In addition, eleven VNAR antibodies (9 from OSX3 and 2 from OSX6) selected against SI were assessed. Of those, six VNAR antibodies (4 from OSX3 and 2 from OSX6) bound to either SI or Sl-RBD with high potency (Table 9; Figure 8). One VNAR antibody (derived from clone 137) may interact with NTD domain since it was specific for SI but did not bind to the Sl-RBD (Figures 2 and 8).
Table 7. VNAR Antibody Binding to Sl-RBD or SI by ELISA
(Values are OD450)
Figure imgf000066_0001
Figure imgf000067_0001
Table 8. Binding ECso values for VNAR antibodies to Sl-RBD selected against Sl-RBD
Figure imgf000068_0001
Table 9. Binding ECso values of VNAR antibodies to Sl-RBD and SI selected using SI
Figure imgf000069_0001
Example 5. Blocking activity of VNAR antibodies.
[00181] VNAR antibodies with a high binding potency to Sl-RBD were further tested in a competition assay. The IC50 values were determined by ELISA as described in Example 4 except that serial dilutions of the VNAR-hFc fusions were premixed with 1.4 nM of purified ACE2 (see Example 1) prior to incubation on the coated microtiter plates. ACE2 binding was measured with an anti-FLAGHRP conjugated antibody (Sigma-Aldrich, A8592) diluted 1:1000.
[00182] The IC50 values for the twenty VNAR antibodies tested (7 from OSX3 and 13 from OSX6) ranged from 6.40E-07 to 4.98E-09 M (Table 10). Figure 9 shows the inhibition binding curve of VNAR antibodies 105 (solid circles), 106 (solid squares) and 25 (solid triangles) for ACE2 binding to Sl-RBD. The most potent blocking VNAR antibodies from the ELISA-based competition assay were further evaluated in a cell-based blocking assay. [00183] Cell-based blocking was assessed by flow cytometry. Expi293 cells were transiently transfected with ACE2 cloned into the pCMV3-C-GFP Spark expression vector (Sino Biological). Cells were incubated at 37°C in 8% CO2 shaking at 350 RPM for 48 hr, The collected cells were blocked in 2% BSA in PBS for 30 min at 4°C and then transferred to a 96-well V-shaped microplate (Greiner) at a density of 100,000 cells per well. SI protein was biotinylated at the AVI-tag using the BirA biotin-protein ligase kit (Avidity Biosciences) and premixed at 5 nM with serial dilutions of VNAR antibodies for 1 hr at 4°C. Binding of SI to ACE2 transfected cells was measured with an Alexa Fluor-647-conjugated streptavidin (Invitrogen, S21374) diluted 1:500 using a CytoFLEX flow cytometer (Beckman Coulter). Data presented as normalized median fluorescence intensity (MFI) was used to determine IC50 by 4-parametric non-linear regression analysis using GraphPad Prism 8.0.
[00184] The binding of SI or Sl-RBD to cells transiently transfected with ACE2 showed that a total of fifteen VNAR antibodies (6 from OSX3 and 9 from OSX6) blocked the interaction between SI or Sl-RBD and ACE2 expressed on the cell surface (blocking IC50 values in Table 11). Figure 10 shows the inhibition binding curves of VNAR antibodies 105 (solid circles), 106 (solid squares) and 25 (solid triangles) for SI on cells which overexpress ACE2.
Table 10. ELISA ICso Values of VNAR Antibody Block of S1-RBD-ACE2 Interactions
Figure imgf000070_0001
Table 11. Cell-based ICso values for VNAR Antibody Block of S1-RBD-ACE2 or S1-ACE2 Interactions
Figure imgf000071_0001
Example 6. Activity of VNAR antibodies against Spike variants.
[00185] The ten VNAR antibodies (4 from OSX3 and 6 from OSX6) that blocked ACE2 with both SI and Sl-RBD interaction in cell-based assay (Table 11) were tested for binding to three spike protein variants containing mutations in emerging virus variants. These included two Sl-RBD recombinant proteins with a single E484K or N501Y mutation as well as a quadruple mutant of SI protein containing K417N, E484K, N501Y and D614G mutations.
[00186] ACE2 binding to Viral Variants. As shown in Figure 11, the variants bound to the ACE2 receptor with similar EC50 affinity compared to Sl-RBD when measured by ELISA as described in Example 4 using immobilized SI mutants with serially-diluted recombinant ACE2 receptor. Calculated EC50 values for the SI mutants are presented in
Table 12
[00187] VNAR antibody binding to Viral Variants. The ten VNAR antibodies were tested in an ELISA as described in Example 4 to determine EC50 values using immobilized SI mutants with serially-diluted VNAR antibodies followed by washes and ACE2 binding detection. Calculated EC50 values for the SI mutants are presented in Table 13. [00188] All the tested VNAR antibodies retained binding to the Sl-RBD N501Y mutant with similar ECso values (cf. Table 13) except for the antibody derived from VNAR clone 25 which showed a stronger ECso to Sl-RBD N501 Y whose binding curves are shown in Figure 12. ECso binding affinities were reduced for Sl-RBD E484K as well as for SI K417N, E484K, N501Y, D614G in comparison to Sl-RBD (Table 13) and as shown for VNAR antibody 25 in Figure 12. Moreover, all the tested VNAR antibodies inhibited binding of Sl-RBD N501Y to ACE2 with similar IC50 potency when compared to Sl-RBD (Table 14) and as shown for VNAR antibody 25 in Figure 13. Antibodies derived from clones 25, 68 and 132 were also able to inhibit binding of Sl-RBD E484K binding to ACE2 with the same IC50. None of the tested VNAR antibodies were able to block binding of ACE2 and the SI K417N, E484K, N501Y, D614G mutant (Table 14).
Table 12. ECso Binding Values of ACE2 to SI Mutants
Figure imgf000072_0001
Table 13. ECso Binding Values of VNAR Antibodies to SI Mutants
Figure imgf000072_0002
Table 14. ICso Values of VNAR Antibody Blocking of SI Mutants:ACE2 Interactions
Figure imgf000073_0001
* - approximated value due to poor fit to non-linear regression model; n.d., not determinec .
Example 7. Viral neutralization by VNAR antibodies.
[00189] VNAR antibodies 25, 46, 61, 68, 105, 106, 115, 119, 132 and 135 which blocked ACE2 interaction with both the SI and Sl-RBD in cell-based assay were tested for viral blocking using the live SARS-CoV-2 Wuhan strain as described below. All studies with live virus were conducted in a certified BSL3 laboratory.
[00190] Vero CCL81 cells were seeded at a cell density of 100,000 cells per well in 48-well plates and incubated at 37° in serum free OptiPro SFM medium (Thermo Fisher Scientific) for 24 hr before infection. The SARS-CoV-2 Wuhan strain propagated in Vero CCL81 cells was preincubated with or without VNAR antibody for 10 min in OptiPro medium before incubation of the mix with prewashed Vero CCL81 cells for 1 hr at 37 °C. Supernatants were transferred to Eppendorf tubes and inactivated with 560 mΐ of AVL buffer from QIAamp Viral RNA Mini Kit (Qiagen). The cells were washed and further incubated at 37°C for 48 hr before supernatant was again harvested and the virus inactivated in AVL buffer. Cell death was assessed by phase microscopy at the end of the experiment.
[00191] Viral RNA was isolated from inactivated viral supernatants using the QIAamp Kit according to manufacturer’s protocol. Briefly, 560 mΐ absolute ethanol was added and loaded onto columns. After washes with AW1 and AW2 buffers, RNA was collected using 40 mΐ of Ambion nuclease free water (Thermo Fisher Scientific). Total RNA (5 mΐ) was used for cDNA synthesis and qPCR was performed in one step using QuantiTect Probe RT-PCR (Qiagen) on a StepOnePlus System (Applied Biosystems). The qPCR primers (synthesized by Eurofms, Luxembourg) were as follows: N1 forward GAC CCC AAA ATC AGC GAA AT (SEQ ID NO: 171), N1 reverse TCT GGT TAC TGC CAG TTG AAT CTG (SEQ ID NO:
172), and N1 Probe F AM- ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1 (SEQ ID NO:
173). To assess RNA quality, RNase P Primers were used: RP Forward AGA TTT GGA CCT GCG AGC G (SEQ ID NO: 174), RP Reverse GAG CGG CTG TCT CCA CAA GT (SEQ ID NO: 175), and RP Probe FAM - TTC TGA CCT GAA GGC TCT GCG CG - BHQ-1 (SEQ ID NO: 176). FAM is a dye label and BHQ1 is a quencher.
[00192] The qPCR primers were used at 0.4 mM with the probe at 0.2 mM and samples were incubated at 50°C for 30 minutes, heated to 95°C for 15 min, followed by 45 cycles of 95°C for 3 seconds and 55°C for 30 seconds. Ct values obtained after 48 hr were subtracted from Ct values at the time of infection and the data normalized between cells that were neither exposed to the virus nor treated with the antibodies set to 0% and untreated cells exposed to the virus set to 100%.
[00193] The assay was performed qualitatively using 5 pg/mL (65 nM), 10 pg/mL (130 nM) and 50 pg/mL (650 nM) of VNAR antibody. The ten Sl-RBD binding VNAR antibodies were all able to prevent viral infection at 5 pg/mL (Figure 14). Notably, the Sl-NTD specific VNAR antibody 137 did not show any significant blocking activity until 50 pg/mL (Figure 15). Hence, screening and selection of VNAR clones and VNAR antibodies against the Sl- RBD domain using in vitro and cell-based assays can accurately predict inhibitory potential of the VNARs against the live virus.
Example 8. Cross-competition between VNAR antibodies.
[00194] Epitope binning. Pairwise competition ELISA was used to perform epitope binning. Individual VNAR-hFcs were used as primary antibodies at 50 nM concentration in 100 pi to coat high-binding 96-well microplates overnight at 4°C. After blocking with 5% BSA in PBS for 1 hr, 50 nM biotinylated Sl-RBD alone or premixed with 500 nM secondary (competitor) VNAR-hFc was added to the plate pairwise. Binding of biotinylated Sl-RBD to coated VNAR-hFc was detected by streptavidin-HRP (Merck Millipore, 18-152). The signal intensities were collected for each primary VNAR-hFc without competitor and compared to the signal when a competitor antibody was present. If the signal remained the same, it was defined as non-competitive, whereas if the signal was decreased by at least 20% it was defined as competitive. [00195] Results. In epitope binning experiments, the ten VNAR antibodies that blocked the interaction of SI and Sl-RBD with ACE2 in the cell-based assay were tested against each other for binding to Sl-RBD. The epitope binning ELISA allowed testing of each primary VNAR antibody against each secondary VNAR antibody for competition with Sl-RBD and the results are shown in Figure 16. Competition indicated an overlap in the epitope bin between the VNAR antibodies (black boxes) and the lack of competition suggested a unique bin (white boxes). Overall, two bins were identified, with 9 out of 10 VNAR antibodies (25, 46, 61, 105, 106, 115, 119, 132 and 135) showing a shared overlap bin with VNAR antibody 68 having a unique bin.
Example 9. Performance of the OSX6 library.
[00196] Overall, the antibody discovery campaigns identified numerous antibodies against SARS-CoV-2 spike protein with ability to block its interaction with ACE2 receptor and neutralize the virus. The comparison of the two phage libraries OSX3 and OSX6 indicated that the improved design of OSX6 library resulted in increased success rate in selection of functional antibodies. While the smaller size (approximately 1/10) and the lower CDR3 diversity of the OSX6 versus OSX3 library resulted in approximately a 50% reduction in number of unique hits (100 from OSX3 versus 49 from OSX6), the OSX6 library generated approximately 50% more blocking antibodies in the ELISA competition assay (13 vs 7, Table 10), the cell-based competition assay (9 vs 6, Table 11) and live virus neutralization assay (6 vs 4, Figure 14). The lower attrition rate during the discovery, screening, and characterization of VNAR antibodies derived from the OSX6 library was a result of improvements in VNAR design, including, independently or in combination, providing optimized scaffolds for the VNAR domains and the improved CDR3 loops of the disclosure.
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7(1): 15-25.

Claims

WE CLAIM:
1. A coronavirus SI fragment-binding moiety comprising a Type II VNAR domain represented by the formula, from N to C terminus,
FW 1 -CDR1 -FW2-HV2-FW2’ -HV4-FW3 -CDR3 -FW4, wherein CDR1 comprises or consists essentially of a peptide having an amino acid sequence of one of DSICALSS, DSNCALPS, DSVCALSS, or DSNCALSS (SEQ ID NOS. 150-153, respectively), wherein CDR3 comprises or consists essentially of a peptide having an amino acid sequence of one of VHMEDMNVRD YGGFWGED V, VNLRSVLPCGWPDV, VENLPGSGSCLRYYLSDV, VREWACEDDGRVWGWEDV, V ART S GCE V YT YT GD V, VKNPSGCGVWYSQEDL, SEFKSGCGVFYELTDV, MVFKSVCEDNPYQYGL, or IWAHSGCEVITHAMDL (SEQ ID NOS.154-162, respectively), and wherein said moiety is capable of specifically binding to an SI fragment comprising amino acids 16-685 of a SARS- CoV-2 spike protein.
2. The moiety of Claim 1 wherein HV2 is TNEENISKG, TNEESISKG, RKEESISKG, or TNEENILTG (SEQ ID NOS. 163-166, respectively)., and optionally, wherein HV4 is SGSKS or RGSKS (SEQ ID NOS.167-168, respectively).
3. The moiety of Claim 1 or 2, wherein HV4 is SGSKS or RGSKS (SEQ ID NOS.167- 168, respectively).
4. The moiety of any one of Claims 1-3, wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VHMEDMNVRD YGGFWGED V; (SEQ ID NO: 154); wherein said CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV; (SEQ ID NO: 155); wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV; (SEQ ID NO: 156); wherein said CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO: 151) and said CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWEDV; (SEQ ID NO: 157); wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VARTSGCEVYTYTGDV;
(SEQ ID NO: 158); wherein said CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and said CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL; (SEQ ID NO: 159); wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV; (SEQ ID NO: 160); wherein said CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and said CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL; (SEQ ID NO: 161); or wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL. (SEQ ID NO: 162).
5. The moiety of Claim 1, wherein said moiety comprises VNAR domain 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, 135).
6. The moiety of any one of claims 1-5 which further comprises at least one heterologous agent operably linked to said moiety to thereby form a conjugate.
7. The moiety of Claim 6, wherein said agent is selected from the group consisting of one or more of a small molecule diagnostic or therapeutic; a DNA, RNA, or hybrid DNA- RNA; a traceable marker; a radioactive agent; an antibody; a single chain variable domain; or an immunoglobulin fragment.
8. The moiety of Claim 7, wherein said agent is an immunoglobulin fragment and is operably linked to said VNAR domain to form a fusion protein.
9. The moiety of Claim 8, wherein said immunoglobulin fragment is an Fc domain.
10. A pharmaceutical composition comprising at least one moiety or conjugate of any one of Claims 1-9.
11. The composition of Claim 10, which comprises at least two of independent moieties or conjugates.
12. The composition of Claim 11 which comprises three to five independent moieties or conjugates.
13. A method of passive immunization against SARS-CoV-2, or a variant thereof, which comprises administering a pharmaceutical composition of any one of Claims 10-12 to a subject in need thereof.
14. A method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition of any one of Claims 10-12 for a time and in an amount effect to treat or prevent COVID-19.
15. The method of Claim 13 or 14, wherein said subject has tested positive for SARS-CoV- 2
16. The method of Claim 13 or 14, wherein said subject has suspected exposure to SARS- CoV-2 and/or tested negative for SARS-CoV-2.
17. The method of any one of Claims 13-16, wherein said composition is administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
18. A VNAR antibody comprising the moiety of any one of Claims 1-5 fused to a human Fc domain, which, optionally, upon expression can dimerize to form a bispecific VNAR antibody.
19. The VNAR antibody of Claim 18, wherein the moiety has a VNAR domain wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VHMEDMNVRDYGGFWGEDV; (SEQ ID NO: 154); wherein said CDR1 peptide has the amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VNLRSVLPCGWPDV; (SEQ ID NO: 155); wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO:
150) and said CDR3 peptide has an amino acid sequence of VENLPGSGSCLRYYLSDV; (SEQ ID NO: 156); wherein said CDR1 peptide has an amino acid sequence DSNCALPS (SEQ ID NO:
151) and said CDR3 peptide has an amino acid sequence of VREWACEDDGRVWGWEDV; (SEQ ID NO: 157); wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of VARTSGCEVYTYTGDV;
(SEQ ID NO: 158); wherein said CDR1 peptide has an amino acid sequence of DSVCALSS (SEQ ID NO: 152) and said CDR3 peptide has an amino acid sequence of VKNPSGCGVWYSQEDL; (SEQ ID NO: 159); wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of SEFKSGCGVFYELTDV; (SEQ ID NO: 160); wherein said CDR1 peptide has an amino acid sequence of DSNCALSS (SEQ ID NO: 153) and said CDR3 peptide has an amino acid sequence of MVFKSVCEDNPYQYGL; (SEQ ID NO: 161); or wherein said CDR1 peptide has an amino acid sequence of DSICALSS (SEQ ID NO: 150) and said CDR3 peptide has an amino acid sequence of IWAHSGCEVITHAMDL. (SEQ ID NO: 162).
20. The VNAR antibody of Claim 19, wherein the VNAR domain of said moiety is any one of VNAR domains 25, 46, 61, 68, 105, 106, 115, 119, 132, or 135 (SEQ ID NOS. 25, 46, 61, 68, 105, 106, 115, 119, 132, 135).
21. The VNAR antibody of Claim 20, wherein said VNAR antibody is capable of neutralizing infection of SARS-CoV-2 or a variant thereof.
22. A pharmaceutical composition comprising at least one VNAR antibody of any one of Claims 18-21.
23. The composition of Claim 22 which comprises from two to five different VNAR antibodies.
24. A method of passive immunization against SARS-CoV-2 or a variant thereof which comprises administering a pharmaceutical composition of Claim 22 or 23 to a subject in need thereof.
25. A method of preventing or treating COVID-19 which comprises administering a pharmaceutical composition of Claim 22 or 23 for a time and in an amount effect to treat or prevent COVID-19.
26. The method of Claim 24 or 25, wherein said subject has tested positive for SARS- CoV-2.
27. The method of Claim 24 or 25, wherein said subject has suspected exposure to SARS- C oV-2 and tested negative for SARS-CoV-2.
28. The method of any one of Claims 24-27, wherein said composition is administered intravenously, subcutaneously, intramuscularly, intranasally or by inhalation.
29. A coronavirus SI fragment-binding moiety comprising a Type II VNAR domain capable of specifically binding to an SI fragment comprising amino acids 16-685 of SARS- CoV-2 spike protein, wherein said VNAR domain comprises an amino acid sequence of any one of VNAR clones 1-149 in Table 3 or Table 4 (SEQ ID NOS.1-149).
30. The moiety of Claims 29 which further comprises at least one heterologous agent operably linked to said moiety to thereby form a conjugate.
31. A nucleic acid encoding the moiety of any one of Claims 1-9 and 29, a conjugate thereof, or the VNAR antibody of any one of Claims 18-21.
32. A vector comprising a nucleic acid of Claim 31 operably linked to a promoter to enable expression of said moiety, conjugate or VNAR antibody in a host cell.
33. A host cell comprising the nucleic acid or vector of Claim 32.
34. A nucleic acid molecule or a vector encoding at least one binding moiety of any one of Claims 1-5, or a conjugate thereof, wherein said conjugate is a fusion protein with a heterologous diagnostic or therapeutic agent operably linked to said moiety, wherein said vector further comprises a promoter to enable expression of said binding moiety or conjugate in a host cell.
35. A host cell comprising the nucleic acid or vector of Claim 34.
36. A synthetic nucleic acid-containing library whose members each encode a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N- terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide,
(a) residues 22, 29 and 83 are cysteine;
(b) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine,
Xb is Y, L, D, S or G,
Xc is D, V, W, Y or G,
Xd is W, E, Y, D, or G,
Xe is Y, L, D, V or L,
Xf is D or G, and Xgis V or L; and
(c) no other residues in said polypeptide are cysteine.
37. The synthetic nucleic acid-containing library of Claim 36, wherein CDR3 is 16 amino acids in length and has an amino acid sequence of
[X]4[Y/L/D/S/G][D/V/W/Y/G]C[W/E/Y/D/G] [Y/L/D/V/L] [X]S[D/G] [V/L] .
38. A synthetic nucleic acid-containing library whose members each comprise a nucleic acid encoding a Type II VNAR polypeptide with Type II VNAR framework (FW), hypervariable (HV) and complementary determining region (CDR) regions having a domain structure, from N-terminus to C-terminus,
FW 1 — CDR1 -FW2-HV2-FW2 ’ -HV4-FW3 -CDR3 -FW4 wherein, using the overall residue numbering positions of the polypeptide, none of the residues are cysteine except as provided in (a) to (i) and, wherein,
(a) FW1 is 25 amino acids in length and comprises an amino acid sequence in which residue 1 is A or T, residue 2 is R, residue 3 is V, residue 4 is D, residue 5 is H or Q, residue 6 is T, residue 7 is P, residue 15 is D, G or R, residue 17 is E, L or S, residue 18 is L, T or V, residue 22 is C;
(b) CDR1 is 8 amino acids in length and comprises an amino acid sequence in which residue 29 is C;
(c) FW2 is 10 amino acids in length and comprises an amino acid sequence in which residue 36 is F, W or Y;
(d) HV2 is 9 amino acids in length;
(e) FW2’ is 8 amino acids in length and comprises an amino acid sequence in which residue 53 is L, Q or R;
(f) HV4 is 5 amino acids in length;
(g) FW3 is 19 amino acids in length has an amino acid sequence comprising, residue 68 is F or L, residue 70 is F, I or V, residue 73 is I, L or V, residue 79 is D, G or V, residue 81 is F, W or Y, and residue 83 is C;
(h) CDR3 ranges from 11-23 amino acids in length and has an amino acid sequence of
[Xal]2-8XbXcCXdXe[Xa2]2-8XfXg wherein Xai and Xa2 are independently any amino acid except cysteine,
Xb is Y, L, D, S or G,
Xc is D, V, W, Y or G,
Xd is W, E, Y, D, or G,
Xe is Y, L, D, V or L,
Xf is D or G, and Xgis V or L; and
(i) FW4 is 10 amino acids in length and has an amino acid sequence comprising
YG[D/G]GT[A/V]VTVN (SEQ ID NO: 1245).
39. The nucleic acid library of Claim 38, wherein the residue at each position of said VNAR polypeptide is one of an allowed amino acid for that position as provided in Table 1 and Table 2.
40. The nucleic acid library of any one of Claims 36-39, wherein said library is a phage display library.
41. The nucleic acid library of any one of Claims 36-40, wherein the library comprises approximately 109 theoretically distinct nucleic acid sequences.
42. A method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises: a) exposing a target molecule of interest to polypeptides produced by expression of a nucleic acid library of any one of Claims 36-41; and b) separating polypeptides that selectively bind from those that do not selectively bind the target molecule.
43. The method of claim 42, wherein the target molecule of interest is expressed on the surface of a phage, bacterium or cell, or is attached to, tethered to or otherwise associated with a solid support.
44. A method of screening a library for a polypeptide that selectively binds with high affinity to a target molecule of interest, the library comprising a plurality of polypeptides produced by expression of a nucleic acid library of any one of Claims 36-41, which comprises:
(a) incubating a sample of the library with a concentration of a target molecule under conditions suitable for specific binding of the polypeptides to the molecule;
(b) incubating a second sample of the library under the same conditions but without target molecule;
(c) contacting each of the first and second samples with immobilized target molecule under conditions suitable for binding of the polypeptide to the immobilized target antigen;
(d) detecting the polypeptide bound to immobilized target molecule for each sample;
(e) determining the affinity of the polypeptide for the target molecule by calculating the ratio of the amounts of bound polypeptide from the first sample over the amount bound polypeptide from the second sample.
45. A method of identifying one or more VNARs that selectively bind to a target molecule of interest which comprises:
(a) contacting said target molecule with a phage display library of Claim 40 or 41; and
(b) separating phage that selectively bind said target molecule from those that do not selectively bind said target molecule to produce an enriched phage library;
(c) repeating steps a) and b) with said enriched phage library to produce a further enriched phage library;
(d) repeating step c) until said further enriched phage library is enriched from at least about 10- to about 106-fold or more relative to the original phage library;
(e) plating said further enriched phage library and isolating and characterizing individual clones therefrom and thereby identifying one or more VNAR polypeptides that selectively bind to the target molecule of interest.
46. The method of Claim 45, wherein said target molecule or said phage display library is bound to or attached to a solid support.
47. The method of Claim 45 or 46, wherein said target molecule is a SARS-CoV-2 spike protein, a domain of said spike protein or a mutant thereof.
48. A composition comprising a plurality of synthetic or recombinant polypeptides, each polypeptide comprising a Type II VNAR polypeptide of any one of Claims 36-39.
49. A method of identifying a polypeptide that binds selectively to a target molecule of interest which comprises:
(a) exposing a target molecule of interest to a composition of Claim 48; and
(b) separating polypeptides that selectively bind to said target molecule from those that do not selectively bind the target molecule.
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