WO2024018205A1 - Anticorps dirigés contre le sars-cov-2 et leurs utilisations - Google Patents

Anticorps dirigés contre le sars-cov-2 et leurs utilisations Download PDF

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WO2024018205A1
WO2024018205A1 PCT/GB2023/051898 GB2023051898W WO2024018205A1 WO 2024018205 A1 WO2024018205 A1 WO 2024018205A1 GB 2023051898 W GB2023051898 W GB 2023051898W WO 2024018205 A1 WO2024018205 A1 WO 2024018205A1
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seq
sequence
nos
sequence identity
region
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PCT/GB2023/051898
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Kerry Chester
Martin Pule
Francesco NANNINI
Mathieu FERRARI
Tudor ILCA
Preeta DATTA
Shimobi ONUOHA
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Autolus Limited
Ucl Business Ltd
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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]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • 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
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • 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
    • C07K2317/35—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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • 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

Definitions

  • the present invention relates to monoclonal antibodies (mAbs) targeted against the receptorbinding domain (RBD) of the spike (S) glycoprotein of coronavirus SARS-CoV-2.
  • mAbs monoclonal antibodies targeted against the receptorbinding domain (RBD) of the spike (S) glycoprotein of coronavirus SARS-CoV-2.
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • COVID-19 coronavirus disease
  • Monoclonal antibodies have been advocated as a potential alternative to provide protection to individuals that cannot be vaccinated.
  • the majority of commonly identified antibodies neutralize coronaviruses by binding to the receptor binding motif (RBM) in the Spike (S) protein domain 1 (S1) (also termed receptor-binding domain (RBD)). They are therefore most effective when delivered at the early stages of the disease and function by blocking the interaction between the S protein and the receptor ACE2.
  • RBM receptor binding motif
  • S1 Spike protein domain 1
  • RBD receptor-binding domain
  • EUA Emergency-Use Authorization
  • FDA Food and Drug Administration
  • soluble ACE2 An alternative therapeutic strategy for the treatment of COVID-19 is the administration of soluble ACE2.
  • This approach offers a variant-proof treatment, working to abrogate viral entry through a decoy binding of the ACE2 receptor, diverting the SARS-CoV-2 virus away from the endogenous receptor (73).
  • a further advantage to the soluble ACE2 approach is that novel S1 mutations that increase the affinity of the viral protein to the receptor will also increase affinity to the decoy receptor. Soluble ACE2 alone has been evaluated as a treatment for COVID-19 (14); however this has limitations due to the low circulating half-life and affinity of the receptor in the monovalent form.
  • ACE2 Improvements to ACE2 have been made by fusing the molecule to the Fc portion of an antibody to both enhance the half-life through Fc neonatal receptor binding and increase the apparent affinity though avidity effects (16, 17). Additional engineering of ACE2 molecules has improved potency further by incorporating a self-assembling, tetramerization domain from p53 protein (17). While this approach has led to potencies comparable to approved mAb therapies (78), the large molecular weight and complexities in the production of such molecules may prove a challenge to its widespread adoption as a therapeutic.
  • mAb-based binding molecules in particular biparatopic binding molecules, as therapeutic candidates that are resistant to the prevalent variants of concern.
  • Each candidate is objectively superior to the parental mAb clones from which they were derived, in terms of virus neutralising ability and binding kinetics.
  • the invention relates to isolated antibodies and antigen-binding fragments thereof that bind the SARS-CoV-2 Spike protein RBD region.
  • the invention relates to biparatopic binding molecules that bind non-overlapping epitopes within RBD.
  • the inventors have demonstrated that the biparatopic binding molecules have increased overall affinity for the Spike protein relative to the constituent antibodies and are superior in terms of virus neutralising ability and binding kinetics.
  • the combination of two non-competing antibodies or antigen-binding fragments thereof in a biparatopic format provides an at least additive, in one embodiment synergistic effect with regard to neutralisation potency.
  • the biparatopic binding molecule may have greater resilience to viral mutational drift.
  • the invention relates to an isolated antibody or antigen-binding fragment thereof that specifically binds to the receptor binding domain (RBD) region of the SARS-CoV-2 Spike (S) protein wherein said isolated antibody or antigen-binding fragment thereof comprises i) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively; ii) a heavy chain variable region that comprises HCDR1 , HCDR2, and
  • the isolated antibody or antigen-binding fragment thereof comprises i) a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ii) a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iii) a VH region of SEQ ID NO: 21 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 25 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iv) a VH region of SEQ ID NO: 29 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of
  • the antibody or antigen-binding fragment thereof comprises a human heavy chain constant region.
  • the antibody or antigen-binding fragment thereof comprises a light chain constant region.
  • the antibody or antigen-binding fragment thereof comprises a Fab, Fab', F(ab')2, F(ab')3, Fabc, Fd, single chain FV (scFv), (scFv)2, Fv, scFv-Fc, heavy chain only antibody, diabody, tetrabody, triabody, minibody, or single domain antibody.
  • the antibody or antigen-binding fragment thereof neutralizes SARS-CoV-2.
  • the antibody or antigen-binding fragment thereof is linked to a second antibody or antigen-binding fragment thereof that specifically binds to the receptor binding domain (RBD) region of the SARS-CoV-2 Spike (S) protein.
  • RBD receptor binding domain
  • S SARS-CoV-2 Spike
  • the antibody or antigen-binding fragment thereof binds to a first epitope and the second antibody or antigen-binding fragment binds to a second epitope.
  • the first and second antibody are combined in a dual variable domain (DVD), scFv4-Fc or IgG-scFv format.
  • DVD dual variable domain
  • scFv4-Fc or IgG-scFv format.
  • the invention also relates to a polynucleotide encoding an antibody or antibody fragment as described herein.
  • the invention also relates to a vector comprising a polynucleotide as described herein.
  • the invention also relates to a host cell comprising a polynucleotide or a vector as described herein.
  • the invention also relates to a method of making the antibody or antigen-binding fragment as described herein comprising (a) culturing a cell as described herein; and (b) isolating the antibody or antigen-binding fragment thereof or the protein from the cultured cell.
  • the invention also relates to a binding molecule comprising a) a first antibody or antibody binding fragment thereof directed against a first epitope located in the RBD region of the Spike protein of SARS-CoV-2 and b) a second antibody or antibody fragment thereof directed against a second epitope located in the RBD region of the Spike protein of SARS-CoV-2.
  • the first and/or said second isolated antibody or antigen-binding fragment thereof comprises i) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively; ii) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 10, 11 and 12, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 10, 1 1 and 12, respectively, and a light chain variable region that comprises LCDR1 , LCDR2
  • the first and/or said second isolated antibody or antigen-binding fragment thereof comprises i) a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ii) a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iii) a VH region of SEQ ID NO: 21 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 25 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iv) a VH region of SEQ ID NO: 29 or a sequence with at least 80%, 90% or 95% sequence identity thereto and
  • the first isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively; and said second isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 10, 11 and 12, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 10, 11 and 12, respectively, and a light chain variable region that comprises LCDR1 , LCDR
  • the first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto.
  • the first isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 50, 51 and 52, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 50, 51 and 52, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 54, 55 and 56, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 54, 55 and 56 respectively and said second isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 34, 35 and 36, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 34, 35 and 36, respectively, and a light chain variable
  • the first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 53 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 57 or a sequence with at least 80%, 90% or 95% sequence identity thereto; thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 37 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 41 or a sequence with at least 80%, 90% or 95% sequence identity thereto.
  • the first isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 58, 59 and 60, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 58, 59 and 60, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 62, 63 and 64, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 62, 63 and 64 respectively and said second isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 34, 35 and 36, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 34, 35 and 36,
  • the first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 61 sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 65 or a sequence with at least 80%, 90% or 95% sequence identity thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 37 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 41 or a sequence with at least 80%, 90% or 95% sequence identity thereto.
  • the binding molecule the first and second isolated antibody or antigen-binding fragment thereof are combined in a dual variable domain (DVD), scFv4-Fc or IgG-scFv format.
  • DVD dual variable domain
  • the invention also relates to a pharmaceutical composition comprising one or more isolated antibody or antigen-binding fragment thereof or a binding molecule as described herein.
  • the invention also relates to an isolated antibody or antigen-binding fragment thereof as described herein, a binding molecule as described herein or a pharmaceutical composition as described herein for use as a medicament, in particular in the treatment of a SARS-CoV-2 infection.
  • FIG. 1 Flow cytometry staining of cells expressing Wuhan trimeric Spike protein. Antibody clones obtained from phage display were utilised for cell staining (A). Identification of neutralising antibodies. Binding clones showing 2-fold binding over background (in A) were evaluated for neutralisation of lentivral vectors pseudotyped with spike protein (Wuhan) at a fixed concentration of 50 pg/mL (B). Clones demonstrating a greaterthan 85% neutralisation (black dotted line) were selected for further evaluation
  • FIG. 1 Surface plasmon resonance sensograms for phage display derived clones against SARS-CoV-2 S1 domain (Wuhan). Curved fitted with a Langmuir 1 :1 binding model. Analyte was titrated over a 2-fold serial dilution, with a starting concentration of 250 nM, with double reference subtraction.
  • Figure 4 Kinetic affinity of the interactions of control antibodies REGn10933, REGN10987 and LY-COV555 to Wuhan, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2) and Omicron SARS-CoV-2 S1 variants.
  • Figure 5. Neutralisation of SARS-CoV-2 pseudotyped vectors. Antibodies were tested against lentiviral vector pseudotyped with Spike protein (Wuhan). REGN10933, REGN10987 and LY- CoV555 antibodies were utilised as positive controls.
  • Figure 7 Concentration of half maximal neutralisation observed for different antibody constructs. 2-way ANOVA of variant neutralisation compared to Wuhan for each test compound. ** p ⁇ 0.01 , *** p ⁇ 0.001 , **** p ⁇ 0.0001 .
  • Figure 8 Flow cytometry staining of cells expressing Wuhan trimeric Spike protein.
  • Antibody clones obtained from phage display were utilised for cell staining (A). Identification of neutralising antibodies. Binding clones showing 2-fold binding over background (in A) were evaluated for neutralisation of lentivral vectors pseudotyped with spike protein (Wuhan) at a fixed concentration of 50 pg/mL (B). Clones demonstrating a greaterthan 85% neutralisation (black dotted line) were selected for further evaluation.
  • Figure 9 Surface plasmon resonance sensograms for phage display derived clones against SARS-CoV-2 S1 domain (Wuhan). Curved fitted with a Langmuir 1 :1 binding model. Analyte was titrated over a 2-fold serial dilution, with a starting concentration of 250 nM, with double reference subtraction.
  • FIG. 10 Neutralisation of SARS-CoV-2 pseudotyped vectors. Antibodies were tested against lentiviral vector pseudotyped with Spike protein (Wuhan). REGN10933, REGN10987 and LY- CoV555 antibodies were utilised as positive controls.
  • Figure 1 Kinetic affinity of the interactions of control antibodies REGnl 0933, REGN10987 and LY-COV555 to Wuhan, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2) and Omicron SARS-CoV-2 S1 variants.
  • FIG. 13 A) Representative setup of epitope binning data.
  • Ligand Antibody (REGN10933) was coated on the surface of a sensor chip and then exposed to S1 protein or buffer for (negative control). Following injection of S1 protein the chip was exposed to buffer (red), REGN10933 (competing) and REGN10987 (non-competing).
  • FIG. 14 Schematic representation of designed biparatopic antibody formats. D12C1 (blue) and D13C1 (yellow) binding domains were incorporated into DVD, IgG-scFv and scFv4-Fc formats.
  • Figure 15. Neutralisation of SARS-CoV-2 spike (Wuhan), alpha, beta, gamma, and delta variant pseudotyed vectors with D12C1 , D13C1 , DVD, IgG-scFv and scFv-4 biparatopic antibodies.
  • REGN10933/REGN10987 cocktail and LY-CoV555 antibodies were tested against each variant as a control and are shown compared to each antibody format.
  • Figure 17 Kinetic affinity of the scFv4-Fc biparatopic antibodies to Wuhan, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2) and Omicron SARS-CoV-2 S1 variants.
  • FIG. 1 Neutralisation of SARS-CoV-2 spike (Wuhan), beta and delta variant pseudotyed vectors with 84-152, 152-84, 84-222 and 222-84 scFv4-Fc biparatocpic antibodies.
  • REGN10933/REGN10987 cocktail was tested against each variant as a control.
  • Figure 20 Activity wheel measurement (rotations/day).
  • Figure 21 Macroscopic evaluation showing macroscopic lung score and relative lung weight.
  • Enzymatic reactions and purification techniques are performed according to manufacturer's specifications, as commonly accomplished in the art or as described herein.
  • the nomenclatures used in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Standard techniques are used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients. Suitable assays to measure the properties of the molecules disclosed herein are also described in the examples.
  • Coronaviruses are enveloped positive-stranded RNA viruses that belong to the family Coronaviridae and the order Nidovirales. Coronaviruses frequently infect people around the globe. There are a large number of coronaviruses, most of which circulate among peridomestic animals including pigs, camels, bats and cats. Of the seven coronaviruses identified in human so far, Coronaviruses 229E, NL63 were classified as Group 1 antigenic viruses, OC43 and HKU1 were classified as Group 2 antigenic viruses. They typically infect upper respiratory tract in human, and can bring about acute respiratory syndrome and can be fatal. Coronaviruses may be zoonotic in origin.
  • SARS-CoV, MERS-CoV and 2019 SARS CoV-2 have human transmission and infective capability and have caused major public health concern worldwide over a short period within the century.
  • the expansion of genetic diversity among coronaviruses and their consequent ability to cause disease in human beings is mainly achieved through infecting peridomestic animals, which serve as intermediate hosts, nurturing recombination and mutation events.
  • the spike glycoprotein (S glycoprotein) which attaches the virion to the host cell membrane, is postulated to play a dominant role in host range restriction.
  • MERS-CoV exploits dipeptidyl peptidase 4 (DPP4), a transmembrane glycoprotein, to infect type 2 pneumocytes and unciliated bronchial epithelial cells.
  • DPP4 dipeptidyl peptidase 4
  • the inventors have identified and isolated neutralizing antibodies which can be used to treat an infection with SARS-CoV-2, detect SARS-CoV-2 or monitor the progression of COVID-19 disease.
  • the monoclonal antibodies specifically bind to the SARS-CoV-2 Spike protein RBD region.
  • the binding reaction may be shown by standard methods, for example with reference to a negative control test using an antibody of unrelated specificity.
  • the amino acid sequence of the RBD region of the Spike protein of SARS-CoV-2 (the target antigen) is provided below:
  • SARS-CoV-2 (RBD) SEQ ID NO: 1 :
  • Antibodies and antibody fragments as described herein bind an antigen comprising SEQ ID NO: 1 or variants thereof.
  • a variant of SEQ ID NO:1 has at least 80%, 90% or 95% sequence identity to SEQ ID NO:1.
  • Omicron includes Pango lineage B.1 .1 .529 and descendent Pango lineages BA.1 , BA.1.1 , BA.2 and BA.3.
  • the antibodies and antigen-binding fragments thereof of the present invention can be used to detect and neutralize any other SARS-CoV-2 variants existent at the time of filing or with any future variants.
  • the coronavirus S protein which includes the RBD region may be the S protein of any of these variants.
  • antigen(s) and “epitope(s)” are well established in the art and refer to the portion of a protein or polypeptide which is specifically recognized by a component of the immune system, e.g. an antibody or a T-cell I B-cell antigen receptor.
  • the term “antigen(s)” encompasses antigenic epitopes, e.g. fragments of antigens which are recognized by, and bind to, immune components.
  • Epitopes can be recognized by antibodies in solution, e.g. free from other molecules.
  • Epitopes can also be recognized by T-cell antigen receptors when the epitope is associated with a class I or class II major histocompatibility complex molecule.
  • epitopes or “antigenic determinant” refers to a site on the surface of an antigen to which an immunoglobulin, antibody or antigen-binding fragment thereof specifically binds. Generally, an antigen has several or many different epitopes and reacts with many different antibodies. The term “specifically” includes linear epitopes and conformational epitopes.
  • Epitopes within protein antigens can be formed both from contiguous amino acids (usually a linear epitope) or non-contiguous amino acids juxtaposed by tertiary folding of the protein (usually a conformational epitope). Epitopes formed from contiguous amino acids are typically, but not always, retained on exposure to denaturing solvents, whereas epitopes formed by tertiary folding are typically lost on treatment with denaturing solvents.
  • An epitope typically includes at least 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14 or 15 amino acids in a unique spatial conformation.
  • epitope mapping Methods for determining what epitopes are bound by a given antibody or antigen-binding fragment thereof (i.e., epitope mapping) are well known in the art and include, for example, immunoblotting and immunoprecipitation assays, wherein overlapping or contiguous peptides from are tested for reactivity with a given antibody or antigen-binding fragment thereof.
  • Competition assays can also be used to determine if a test antibody binds to the same epitope as a reference antibody. Suitable competition assays are mentioned elsewhere herein and also shown in the examples.
  • the epitope to which an antibody or antigen-binding fragment thereof binds can be determined by, e.g, NMR spectroscopy, X-ray diffraction crystallography studies, ELISA assays, hydrogen/deuterium exchange coupled with mass spectrometry (e.g., liquid chromatography electrospray mass spectrometry), array-based oligo-peptide scanning assays, and/or mutagenesis mapping (e.g, site-directed mutagenesis mapping).
  • antibody refers to an immunoglobulin protein that is capable of binding an antigen, i.e. SARS-CoV-2.
  • antibody as used herein broadly refers to any polypeptide comprising complementarity determining regions (CDRs) that confer specific binding affinity of the polypeptide for an antigen.
  • CDRs complementarity determining regions
  • the term antibody as used herein encompasses polyclonal and monoclonal antibody preparations.
  • the antibody or antigen-binding fragment thereof described herein "which binds” or is “capable of binding” the antigen of interest, binds the antigen with sufficient affinity such that the antibody or antigen-binding fragment thereof is useful as a therapeutic or diagnostic agent in targeting SARS-CoV-2 as described herein.
  • the term “specific” may refer to the situation in which the antibody molecule will not show any significant binding to molecules other than its specific binding partner.
  • polypeptide(s) and “protein(s)” are used interchangeably throughout the application and denote at least two covalently attached amino acids, thus may signify proteins, polypeptides, oligopeptides, peptides, and fragments thereof.
  • the protein may be made up of naturally occurring amino acids and peptide bonds, or synthetic peptidomimetic structures.
  • amino acid(s) or “peptide residue(s)”, as used herein denote both naturally occurring and synthetic amino acids.
  • the immunoglobulin proteins of the present invention may be synthesized using any in vivo or in vitro protein synthesis technique known in the art.
  • antibody As antibodies can be modified in a number of ways, the term “antigen-binding protein” or “antibody” should be construed as covering antibody fragments, derivatives, functional equivalents and homologues of antibodies, including any polypeptide comprising an immunoglobulin binding domain,
  • each heavy chain is comprised of a heavy chain variable region or domain (abbreviated herein as HCVR, VH or VH) and a heavy chain constant region.
  • the heavy chain constant region is comprised of three domains, CH1 , CH2 and CH3.
  • Each light chain is comprised of a light chain variable region or domain (abbreviated herein as LCVR, VL or VL) and a light chain constant region.
  • the light chain constant region is comprised of one domain, CL.
  • Antibodies may include the kappa (K) and lambda (A) light chains and the alpha (IgA), gamma (lgG1 , lgG2, lgG3, lgG4), delta (IgD), epsilon (IgE) and mu (IgM) heavy chains, or their equivalents in other species.
  • Full-length immunoglobulin “light chains” (usually of about 25 kDa or 214 amino acids long) consist of a variable region of approximately 110 amino acids at the NH2-terminus and a kappa or lambda constant region at the COOH-terminus.
  • Fully-length immunoglobulin “heavy chains” (usually of about 50 kDa or 446 amino acids long), likewise consist of a variable region (of about 116 amino acids) and one of the aforementioned heavy chain constant regions, e.g. gamma (of about 330 amino acids).
  • Light or heavy chain variable regions are generally composed of a “framework” region (FR) interrupted by three hypervariable regions, also called CDRs.
  • the extent of the framework region and CDRs have been precisely defined. The sequences of the framework regions of different light and heavy chains are relatively conserved within a species.
  • the framework region of an antibody i.e. the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs.
  • the CDRs are primarily responsible for binding to an epitope of an antigen.
  • CDR set refers to a group of three CDRs that occur in a single variable region capable of binding the antigen. The exact boundaries of these CDRs can be defined differently according to different systems known in the art.
  • Heavy chain CDRs are designated HCDR1 , HCDR2 and HCDR3.
  • Light chain CDRs are designated LCDR1 , LCDR2 and LCDR3.
  • the antibody is comprised of four polypeptide chains, two heavy (H) chains and two light (L) chains, or any functional fragment, mutant, variant, or derivation thereof, which retains the essential epitope binding features of an Ig molecule.
  • Immunoglobulin molecules can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., lgG1 , lgG2, lgG3, lgG4, lgA1 and lgA2) or subclass.
  • the antibody is of the IgG type.
  • CDRs Different definitions of the CDRs are commonly in use. The method described by Kabat is the most commonly used and CDRs are based on sequence variability (Kabat et al., (1971) Ann. NY Acad. Sci. 190:382-391 and Kabat, et al., (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91- 3242). Chothia refers instead to the location of the structural loops (Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)).
  • the Kabat numbering system is generally used when referring to a residue in the variable domain (approximately residues 1-107 of the light chain and residues 1 - 113 of the heavy chain).
  • Another system is the ImMunoGeneTics (IMGT) numbering scheme (Lefranc et al., Dev. Comp. Immunol., 29, 185-203 (2005)).
  • IMGT ImMunoGeneTics
  • a CDR is a loop region of a variable domain, delimited according to the IMGT unique numbering for V domain.
  • CDR1-IMGT loop BC
  • CDR2-IMGT loop C'C
  • CDR3-IMGT loop FG
  • IMGT system as described above is used herein, unless otherwise stated.
  • IMGT numbering IMGT definitions
  • IMGT labelling are used interchangeably herein, antigenbinding
  • antibody is not only inclusive of antibodies generated by methods comprising immunisation, but also includes any polypeptide, e.g., a recombinantly expressed polypeptide, which is made to encompass at least one CDR capable of specifically binding to an epitope on an antigen of interest. Hence, the term applies to such molecules regardless whether they are produced in vitro, in cell culture, or in vivo. Methods of producing polyclonal and monoclonal antibodies are known in the art and described more fully below.
  • antibody as used herein is meant to specifically include antibody fragments I antigenbinding fragments thereof unless stated otherwise.
  • the antibody fragment I antigen-binding fragments may be selected from any fragment capable of binding the antigen or antigenic fragment of interest.
  • Exemplary antibody fragments include, but are not limited to, Fab, Fab', F(ab')2, F(ab')3, Fabc, Fd, single chain Fv (scFv), (scFv)2, Fv, scFv-Fc, heavy chain only antibody, diabody, tetrabody, triabody, minibody, antibody mimetic protein, single domain antibody, e.g. a VH.
  • the antibody fragment I antigen-binding fragment may comprise or consist of any of these fragments.
  • Antigen-binding fragments derived from an antibody, including single-chain antibodies may comprise the variable region(s) alone or in combination with the entire, or parts of the, following: a heavy chain constant domain, or a portion thereof, e.g. a CH1 , CH2, CH3, transmembrane, and/or cytoplasmic domain, on the heavy chain, and a light chain constant domain, e.g. a Ckappa or Clambda domain, or portion thereof on the light chain. Also included in the present disclosure are any combinations of variable region(s) and CH1 , CH2, CH3, Ckappa, Clambda, transmembrane and cytoplasmic domains.
  • Fv fragments ( ⁇ 25kDa) consist of the two variable domains, VH and VL.
  • VH and VL domain are non-covalently associated via hydrophobic interaction and tend to dissociate.
  • stable fragments can be engineered by linking the domains with a hydrophilic flexible linker to create a single chain Fv (scFv).
  • VH and VL domains respectively are capable of binding to an antigen. They are generally referred to as a “single domain antibody” or “immunoglobulin single variable domain”.
  • a single domain antibody ( ⁇ 12 to 15 kDa) has thus either the VH or VL domain.
  • Antigen-binding single VH domains have also been identified from, for example, a library of murine VH genes amplified from genomic DNA from the spleens of immunized mice and expressed in E. coli (Ward et al., 1989, Nature 341 : 544-546). Ward et al.
  • dAbs for single domain antibodies
  • dAb generally refers to a single immunoglobulin variable domain (VH, VHH or VL) polypeptide that specifically binds antigen.
  • VH, VHH or VL immunoglobulin variable domain
  • human single domain antibodies are preferred over camelid derived VHH, primarily because they are not as likely to provoke an immune response when administered to a patient.
  • the antibody or antigen-binding fragment thereof may be chimeric, human or humanised.
  • a “chimeric antibody” is a recombinant protein that contains the variable domains including the CDRs of an antibody derived from one species, for example a murine antibody, while the constant domains of the antibody molecule are derived from those of a different species, for example a human antibody.
  • Methods to humanise antibodies include CDR grafting based on framework regions homology and antibody resurfacing. Human or humanised antibodies or antigen-binding fragments are most desirable for use in antibody therapies, as such molecules would elicit little or no immune response in the human subject.
  • Amino acid sequences of the antibodies of the invention are set out below.
  • the invention relates to antigen-binding molecules, antibodies or antigen-binding fragments thereof comprising or consisting of the full-length antibody sequence or an antigen-binding fragment thereof, e.g. single chain Fvs or single domains of any one of the antibodies listed in table 2. Also within the scope of the invention are sequence variants as explained below.
  • the invention thus relates to an isolated antibody or antigen-binding fragment thereof that specifically binds to the SARS-CoV-2 Spike protein RBD region wherein said antibody or antigen-binding fragment thereof comprises or consists of any of the sequences listed below in table 2.
  • the isolated antibody or antigen-binding fragment thereof comprises or consists of
  • HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively
  • a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively;
  • HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 10, 11 and 12, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 10, 11 and 12, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 14, 15 and 16, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 14, 15 and 16 respectively;
  • HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 18, 19 and 20, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 18, 19 and 20, respectively
  • a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 22, 23 and 24, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 22, 23 and 24 respectively;
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 26, 27 and 28, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 26, 27 and 28, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 30, 31 and 32, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 30, 31 and 32 respectively; ) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 34, 35 and 36, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 34, 35 and 36, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 38, 39
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 130, 131 and 132, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 130, 131 and 132, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 134, 135 and 136, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 134, 135 and 136, respectively;
  • HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 138, 139 and 140, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 138, 139 and 140, respectively
  • a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 142, 143 and 144, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 142, 143 and 144, respectively or
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 146, 147 and 148, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 146, 147 and 148, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 150, 151 and 152, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 150, 151 and 152, respectively.
  • the present disclosure also includes antibodies comprising one, two, or three heavy chain CDRs of at least 80%, 90% or 95% sequence identity to HCDR1 , HCDR2, and/or HCDR3 as mentioned above. Furthermore, the present invention encompasses antibodies having one, two, or three light chain CDRs of at least 80%, 90% or 95% sequence identity to LCDR1 , LCDR2, and/or LCDR3 as mentioned above. All CDRs may either be derived from the same antibody or be independently selected from the different antibodies described herein.
  • VH and VL CDRs are separated by framework regions (FR1 , 2, 3, and 4). FR sequences are also provided above. Amino acid and nucleic acid sequences for FRs are exemplified by the FRs of the antibodies disclosed herein. Antibodies containing FRs with amino acid sequences that are different from the framework regions disclosed herein and encoded by different nucleic acid sequences than those exemplified herein, are expected to exhibit similar or identical immunological binding properties and are viewed as derivatives or variants of the present invention. Conservative amino acid substitutions may also be contemplated for any amino acid residue of CDRs, framework regions, and/or linker regions as further explained below.
  • the isolated antibody or antigen-binding fragment comprises or consists of ) a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ) a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ) a VH region of SEQ ID NO: 21 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 25 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ) a VH region of SEQ ID NO: 29 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO:
  • the antibody is a fragment or single-chain immunoglobulin, comprising or consisting of the variable region(s) alone as described above or combined with the entire, or parts of the, following: a heavy chain constant domain, or portion thereof, e.g., a CH1 , CH2 or CH3 transmembrane, and/or cytoplasmic domain, on the heavy chain, and a light chain constant domain, e.g., a Ckappa or Clambda domain, or portion thereof, on the light chain.
  • a heavy chain constant domain e.g., a CH1 , CH2 or CH3 transmembrane, and/or cytoplasmic domain, on the heavy chain
  • a light chain constant domain e.g., a Ckappa or Clambda domain, or portion thereof, on the light chain.
  • the antibody is a full length antibody and comprises human constant regions and human light chain regions.
  • Sequence identity as defined in the aspects and embodiments herein, in particular with regard to sequences of Table 2 relating to CDR or variable domain sequences (amino acid or polynucleotide sequences) can be at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%, for example at least 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity.
  • sequence variants with these percentage identities of the antibodies as shown in Table 2 are all within the scope of the invention.
  • sequence “homology” or “identity” generally refers to the percentage of amino acid residues in a sequence that are identical with the residues of the reference polypeptide with which it is compared, after aligning the sequences and in some embodiments after introducing gaps, if necessary, to achieve the maximum percent homology, and not considering any conservative substitutions as part of the sequence identity.
  • percent homology between two amino acid sequences is equivalent to the percent identity between the two sequences.
  • N- or C-terminal extensions, tags or insertions shall be construed as reducing identity or homology. Methods and computer programs for the alignment are well known.
  • the percent identity between two amino acid sequences can be determined using well known mathematical algorithms.
  • GAP Garnier GCG package, Accelerys Inc, San Diego USA.
  • GAP uses the Needleman and Wunsch algorithm to align two complete sequences, maximising the number of matches and minimising the number of gaps. Generally, default parameters are used, with a gap creation penalty equalling 12 and a gap extension penalty equalling 4.
  • Use of GAP may be preferred but other algorithms may be used, e.g. BLAST (which uses the method of Altschul et al. (1990) J. Mol. Biol. 215: 405-410), FASTA (which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444-2448), or the Smith- Waterman algorithm (Smith and Waterman (1981) J. Mol Biol.
  • an isolated antibody or antigen-binding fragment thereof that is a variant of any of the above antibodies or antigen-binding fragments and having one or more amino acid substitutions, deletions, insertions or other modifications, and which retains a biological function of the single domain antibody, that is binding to the target antigen and, thus, variant antibody or antigen-binding fragment thereof can be sequence engineered.
  • Modifications may include one or more substitution, deletion or insertion of one or more codons encoding the single domain antibody or polypeptide that results in a change in the amino acid sequence as compared with the native sequence of the antibody or antigen-binding fragment thereof.
  • Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements.
  • Substitutions, insertions, additions or deletions may optionally be in the range of about 1 to 25 or 1 to 50, for example 1 to 5, 1 to 10, 1 to 15, 1 to 20 amino acids, for example 1 , 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.
  • the substitution e.g. 1 , 2, 3, 4 or 5 amino acid substitutions
  • insertion, addition or deletion is in HCDR1 , HCDR2 and or HCDR3.
  • the substitutions, insertion, addition or deletion is in LCDR1 , LCDR2 and or LCDR3.
  • the substitution, insertion, addition or deletion is in a heavy chain framework region or a light chain framework region.
  • the variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity exhibited by the full-length or mature native sequence.
  • the modification is a conservative sequence modification.
  • conservative sequence modifications is intended to refer to amino acid modifications that do not significantly affect or alter the binding characteristics of the antibody containing the amino acid sequence. Such conservative modifications include amino acid substitutions, additions and deletions. Modifications can be introduced into an antibody of the invention by standard techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis. Conservative amino acid substitutions are ones in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • one or more amino acid residues within the CDR regions of a single domain antibody of the invention can be replaced with other amino acid residues from the same side chain family and the altered antibody can be tested for retained function (i.e. antigen binding) using the functional assays described herein.
  • amino acid changes can typically be made without altering the biological activity, function, or other desired property of the polypeptide, such as its affinity or its specificity for antigen.
  • single amino acid substitutions in nonessential regions of a polypeptide do not substantially alter biological activity.
  • substitutions of amino acids that are similar in structure or function are less likely to disrupt the polypeptides' biological activity.
  • Abbreviations for the amino acid residues that comprise polypeptides and peptides described herein, and conservative substitutions for these amino acid residues are shown in Table 3 below.
  • Binding affinity generally refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g., an antibody or antigen-binding fragment thereof) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, “binding affinity” refers to intrinsic binding affinity which reflects a 1 :1 interaction between members of a binding pair (e.g, antibody or antigen -binding fragment thereof and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (KD).
  • Affinity can be measured and/or expressed in a number of ways known in the art, including, but not limited to, equilibrium dissociation constant (KD), and equilibrium association constant (KA).
  • KD equilibrium dissociation constant
  • KA equilibrium association constant
  • Kon refers to the association rate constant of, e.g, an antibody or antigen-binding fragment thereof to an antigen
  • koff refers to the dissociation of, e.g, an antibody or antigenbinding fragment thereof from an antigen.
  • the affinity can be determined by techniques known to one of ordinary skill in the art, such as surface plasmon resonance (SPR) or KinExA.
  • an antibody or antigen-binding fragment thereof of the invention has an affinity KD of ⁇ 250nM, ⁇ 200nM, ⁇ 1 OOnM, ⁇ 50nM, ⁇ 1 OnM or ⁇ 1 nM for the target antigen.
  • an antibody or antigen-binding fragment thereof ofthe invention has an EC50 value of ⁇ 5pM, ⁇ 1 pM, ⁇ 900nM, ⁇ 800nM, ⁇ 700nM, ⁇ 600nM, ⁇ 500nM, ⁇ 400nM, ⁇ 300nM, ⁇ 200nM, ⁇ 100nM, ⁇ 50nM, ⁇ 10nM, ⁇ 5nM, ⁇ 1 nM, ⁇ 0.5nM, or ⁇ 0.1 nM.
  • the EC50 value may be 0.5nM to 0.98 pM.
  • the EC50 is the concentration of a drug that gives half-maximal response. Suitable methods for determining neutralising EC50 values are described in the examples
  • the antibody may comprise a CH2 domain.
  • the CH2 domain is for example located at the N- terminus of the CH3 domain, as in the case in a human IgG molecule.
  • the CH2 domain of the antibody is in one embodiment the CH2 domain of human lgG1 , lgG2, lgG3, or lgG4, e.g the CH2 domain of human lgG1 .
  • the sequences of human IgG domains are known in the art.
  • the antibody may comprise an immunoglobulin hinge region, or part thereof, at the N-terminus of the CH2 domain.
  • the immunoglobulin hinge region allows the two CH2-CH3 domain sequences to associate and form a dimer.
  • the hinge region, or part thereof is a human lgG1 , lgG2, lgG3 or lgG4 hinge region, or part thereof.
  • the hinge region, or part thereof is an lgG1 hinge region, or part thereof.
  • the sequence of the CH3 domain is not particularly limited.
  • the CH3 domain is a human immunoglobulin G domain, such as a human lgG1 , lgG2, lgG3, or lgG4 CH3 domain, e.g. a human lgG1 CH3 domain.
  • An antibody of the invention may comprise a human lgG1 , lgG2, lgG3, or lgG4 constant region.
  • the sequences of human lgG1 , lgG2, lgG3, or lgG4 CH3 domains are known in the art.
  • An antibody of the invention may comprise a non-human IgG constant region, e.g., a rabbit lgG1 constant region.
  • An antibody of the invention may comprise a human IgG Fc with effector function.
  • Fc receptors are key immune regulatory receptors connecting the antibody mediated (humoral) immune response to cellular effector functions. Receptors for all classes of immunoglobulins have been identified, including FcyR (IgG), FcsRI (IgE), FcaRI (IgA), FcpR (IgM) and FcbR (IgD). There are three classes of receptors for human IgG found on leukocytes: CD64 (FcyRI), CD32 (FcyRlla, FcyRllb and FcyRllc) and CD16 (FcyRllla and FcyRlllb). FcyRI is classed as a high affinity receptor (nanomolar range KD) while FcyRI I and FcyRIII are low to intermediate affinity (micromolar range KD).
  • ADCC antibody dependent cellular cytotoxicity
  • FcvRs on the surface of effector cells Natural killer cells, macrophages, monocytes and eosinophils
  • a signalling pathway is triggered which results in the secretion of various substances, such as lytic enzymes, perforin, granzymes and tumour necrosis factor, which mediate in the destruction of the target cell.
  • the level of ADCC effector function various for IgG subtypes.
  • ADCC effector function is high for human lgG1 and lgG3, and low for lgG2 and lgG4. See below for IgG subtype variation in effector functions, ranked in decreasing potency.
  • FcyRs bind to IgG asymmetrically across the hinge and upper CH2 region. Knowledge of the binding site has resulted in engineering efforts to modulate IgG effector functions
  • Antibodies of the invention may have an Fcwith effector function, with enhanced effector function or with reduced effector function.
  • the potency of antibodies can be increased by enhancement of the ability to mediate cellular cytotoxicity functions, such as antibody-dependent cell-mediated cytotoxicity (ADCC) and antibody-dependent cell-mediated phagocytosis (ADCP).
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • ADCP antibody-dependent cell-mediated phagocytosis
  • a number of mutations within the Fc domain have been identified that either directly or indirectly enhance binding of Fc receptors and significantly enhance cellular cytotoxicity: the mutations S239D/A330L/I332E (“3M”), F243L or G236A.
  • enhancement of effector function can be achieved by modifying the glycosylation of the Fc domain, FcyRs interact with the carbohydrates on the CH2 domain and the glycan composition has a substantial effect on effector function activity.
  • Afucosylated (non- fucosylated) antibodies exhibit greatly enhanced ADCC activity through increased binding to FcyRllla.
  • ADCC and CDC may be desirable for some therapeutic antibodies, however, in some embodiments, an antibody that does not activate effector functions is preferred.
  • an antibody that does not activate effector functions is preferred.
  • lgG4 antibodies are the preferred IgG subclass for receptor blocking without cell depletion.
  • lgG4 molecules can exchange half molecules in a dynamic process termed Fab-arm exchange. This phenomenon can occur between therapeutic antibodies and endogenous lgG4.
  • the S228P mutation has been shown to prevent this recombination process allowing the design of lgG4 antibodies with a reduced propensity for Fab-arm exchange.
  • the CH2 domain of an antibody or fragment of the invention may comprise one or more mutations to decrease or abrogate binding of the CH2 domain to one or more FcyR receptors, such as FcyRI, FcyRlla, FcyRllb, FcyRIII and/or to complement.
  • CH2 domains of human IgG domains normally bind to Fey receptors and complement, decreased binding to FcyR receptors is expected to decrease antibody-dependent cell-mediated cytotoxicity (ADCC) and decreased binding to complement is expected to decrease the complement-dependent cytotoxicity (CDC) activity of the antibody molecule.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • CDC complement-dependent cytotoxicity
  • An antibody molecule of the invention may comprise an Fc with modifications K322A/L234A/L235A or L234F/L235E/P331 S (“TM”), which almost completely abolish FcyR and C1q binding.
  • An antibody molecule of the invention may comprise a CH2 domain, wherein the CH2 domain comprises alanine residues at EU positions 234 and 235 (positions 1.3 and 1.2 by IMGT numbering) ("LALA mutation").
  • complement activation and ADCC can be decreased by mutation of Pro329 (position according to EU numbering), e.g., to either P329A or P329G.
  • the antibody molecule of the invention may comprise a CH2 domain, wherein the CH2 domain comprises alanine residues at EU positions 234 and 235 (positions 1.3 and 1.2 by IMGT numbering) and an alanine (LALA- PA) or glycine (LALA-PG) at EU position 329 (position 114 by IMGT numbering).
  • an antibody molecule of the invention may comprise an alanine, glutamine or glycine at EU position 297 (position 84.4 by IMGT numbering).
  • Modification of glycosylation on asparagine 297 of the Fc domain which is known to be required for optimal FcR interaction may confer a loss of binding to FcRs; a loss of binding to FcRs has been observed in N297 point mutations.
  • An antibody molecule of the invention may comprise an Fc with an N297A, N297G or N297Q mutation.
  • An antibody molecule of the invention with an aglycosyl Fc domain may be obtained by enzymatic deglycosylation, by recombinant expression in the presence of a glycosylation inhibitor or following the expression of Fc domains in bacteria.
  • IgG naturally persists for a prolonged period in the serum due to FcRn-mediated recycling, giving it a typical half-life of approximately 21 days.
  • Half-life can be extended by engineering the pH- dependant interaction of the Fc domain with FcRn to increase affinity at pH 6.0 while retaining minimal binding at pH 7.4.
  • the T250Q/M428L variant conferred an approximately 2-fold increase in IgG half-life (assessed in rhesus monkeys), while the M252Y/S254T/T256E variant ("YTE”), gave an approximately 4-fold increase in IgG half-life (assessed in cynomolgus monkeys). Extending half-life may allow the possibility of decreasing administration frequency, while maintaining or improving efficacy.
  • Immunoglobulins are known to have a modular architecture comprising discrete domains, which can be combined in a multitude of different ways to create multispecific, e.g. bispecific, trispecific, or tetraspecific antibody formats.
  • Exemplary multispecific antibody formats are described in Spiess et ai, (2015) Mol Immunol 67: 95-106 and Kontermann (2012) Mabs 4(2): 182-97, for example.
  • the antibodies or antigen-binding fragments thereof of the invention may be employed in such multispecific formats.
  • the antibodies or antigen-binding fragments thereof of the invention may be employed in biparatopic format thus binding to two different epitopes.
  • the invention thus provides an isolated binding molecule comprising or consisting of a) a first antibody or antigen-binding fragment thereof directed against a first epitope located in the RBD region of the Spike protein of SARS-CoV-2 and b) a second antibody or antigen-binding fragment thereof directed against a second epitope located in the RBD region of the Spike protein of SARS-CoV- 2.
  • the first and second epitope are not identical. In one embodiment, the first and second epitope are overlapping epitopes. In another embodiment, the first and second epitope are not overlapping epitopes. In one embodiment, the biparatopic binding molecule is capable of simultaneously engaging two non-overlapping epitopes within the RBD.
  • the first and/or second isolated antibody or antigen-binding fragment thereof may be selected from Table 2.
  • said first and/or second isolated antibody or antigenbinding fragment thereof comprises
  • HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively
  • a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively;
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 10, 11 and 12, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 10, 11 and 12, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 14, 15 and 16, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 14, 15 and 16 respectively; ) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 18, 19 and 20, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 18, 19 and 20, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 22, 23 and 24, or a sequence with
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 114, 115 and 116, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 1 14, 115 and 116, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 118, 119 and 120, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 1 18, 119 and 120, respectively;
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 122, 123 and 124, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 122, 123 and 124, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 126, 127 and 128, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 126, 127 and 128, respectively;
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 130, 131 and 132, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 130, 131 and 132, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 134, 135 and 136, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 134, 135 and 136, respectively;
  • HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 138, 139 and 140, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 138, 139 and 140, respectively
  • a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 142, 143 and 144, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 142, 143 and 144, respectively or
  • a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 146, 147 and 148, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 146, 147 and 148, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 150, 151 and 152, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 150, 151 and 152, respectively.
  • Combinations where one of 1) to 19) is a first antibody and combined with one a second antibody of 1) to 19) are specifically envisaged.
  • said first and/or second isolated antibody or antigen-binding fragment thereof comprises 1) a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto;
  • said first isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively; and said second isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the
  • said first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto;
  • said first isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 50, 51 and 52, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 50, 51 and 52, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 54, 55 and 56, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 54, 55 and 56 respectively and said second isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 34, 35 and 36, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 34, 35 and 36, respectively, and a light chain variable
  • said first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 53 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 57 or a sequence with at least 80%, 90% or 95% sequence identity thereto; and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 37 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 41 or a sequence with at least 80%, 90% or 95% sequence identity thereto.
  • said first isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 58, 59 and 60, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 58, 59 and 60, respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 62, 63 and 64, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 62, 63 and 64 respectively and said second isolated antibody or antigen-binding fragment thereof comprises a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 34, 35 and 36, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 34, 35 and 36,
  • said first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 61 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 65 or a sequence with at least 80%, 90% or 95% sequence identity thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 37 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 41 or a sequence with at least 80%, 90% or 95% sequence identity thereto.
  • first and second isolated antibody or antigen-binding fragment thereof can be combined in a biparatopic format in different ways.
  • the binding molecule may comprise more than one fragment of the first antibody and more than one fragment of the second antibody.
  • dual variable domain (DVD) or DVD-IgG is one type of bispecific antibody format, which is generated from two parental mAbs by stacking the two variable heavy domains of both parental antibodies onto the heavy chain and the variable light domains of both parental antibodies onto the light chain, forming an IgG-like molecule with a double VH/VL domain.
  • the DVD-IgG retains the antigen-binding specificity, affinity, and biologic activities from its both parental antibodies, therefore, all of its four variable domains are functional (see Wu et al, 2007).
  • the invention also relates to a DVD, scFv4-Fc and IgG-scFv comprising a first and a second isolated antigen-binding fragment as described above.
  • DVD-lg can be manufactured by fusing the VH domain of antibody A to the heavy chain of antibody B, and the VL domain of antibody A to the light chain of antibody B, via a peptide linker.
  • scFv4-Fc can be manufactured by substituting the original VH and VL domains of an IgG with one scFv for each chain. The resulting antibody would comprise one scFv4 (binding domain A) on the heavy CH1-CH2-CH3 chain, and one scFv4 (binding domain B) on the light chain.
  • the biparatopic binding molecule may have an increased overall affinity for the Spike protein relative to the constituent antibodies.
  • the combination of two competing antibodies may provide an additive or synergistic effect with regard to affinity and/or neutralisation potency.
  • Neutralisation potency can be defined as the capacity to block viral mediated infection on target cells.
  • Neutralisation potency assays can be selected from Pseudovirus infectivity assay with reporter marker gene (Ferrari et al ASM Journals Journal of Virology Vol. 95, No. 19); ACE2- Spike/S1/RBD competition ELISA assays; TCID50 replication competent virus titration assay; Replication competent virus plaque reduction neutralisation assay.
  • Increase in potency compared the individual constituents may be improved at least 5, 20 or 20 fold.
  • the biparatopic binding molecule may have greater resilience to viral mutational drift.
  • first and second are used to differentiate between the two antibodies or antigenbinding fragments thereof used in the binding molecules of the invention, but are not understood to designate their orientation in the multivalent molecule with respect to the C and N terminus of the protein.
  • said antibody or antigen-binding fragment thereof is located N-terminally and said second antibody or antigen-binding fragment thereof is located C-terminally.
  • said first single antibody or antigen-binding fragment thereof is located C-terminally and said second antibody or antigen-binding fragment thereof is located N-terminally.
  • a biparatopic construct is one selected from the table below having the sequence shown.
  • Data for biparatopic molecule is shown in the examples, e.g. tables 9 and 10.
  • the molecules as shown in Tables 9 and 10 are specifically part of the invention.
  • the invention also relates to the use of an antibody or antigen-binding fragment as disclosed herein in a biparatopic binding molecule.
  • the present invention further provides an isolated nucleic acid encoding an antibody, antigenbinding fragment thereof or binding molecule of the present invention.
  • nucleic acid(s) or polynucleotide as used herein, denotes either DNA or RNA, or molecules which contain both deoxy- and ribonucleotides. Nucleic acid(s) may be naturally occurring or synthetically made, and as such, may denote analogues of naturally occurring polynucleotides in which one or more nucleotides are artificially modified.
  • a polynucleotide encoding an isolated antibody or antigenbinding fragment thereof that specifically binds to the SARS-CoV-2 Spike protein RBD region wherein said polynucleotide encodes a heavy chain variable region polypeptide that comprises HCDR1 , HCDR2, and HCDR3 sequences as shown in Table 2 or sequences with at least 80%, 90% or 95% sequence identity thereto, and a light chain variable region that encodes a light chain variable region polypeptide that comprises LCDR1 , LCDR2 and LCDR3 sequences as shown in Table 2 or sequences with at least 80%, 90% or 95% sequence identity thereto.
  • polynucleotide encoding an isolated antibody or antigen-binding fragment thereof that specifically binds to the SARS-CoV-2 Spike protein RBD region wherein said polynucleotide encodes a VH polypeptide as shown in Table 2 or a polypeptide with at least 80%, 90% or 95% sequence identity thereto and a VL polypeptide as shown in Table 2 or a polypeptide with at least 80%, 90% or 95% sequence identity thereto.
  • Nucleic acids according to the invention can be selected from the following table
  • nucleic acids as shown in Table 3 can be combined.
  • the invention also provides kits of nucleic acids where more than two nucleic acids are needed to generate the molecule (this includes full-length antibodies).
  • the invention also provides nucleic acid constructs that contain two or more nucleic acids (for light and heavy chain respectively), separated by a nucleic acid encoding a sequence that allows co-expression of both nucleic acids, for example an internal ribosome entry site (IRES) or 2A selfcleaving peptide.
  • a nucleic acid encoding a sequence that allows co-expression of both nucleic acids, for example an internal ribosome entry site (IRES) or 2A selfcleaving peptide.
  • IRS internal ribosome entry site
  • the invention relates to a nucleic acid construct comprising at least one nucleic acid as defined herein.
  • the construct may be in the form of a plasmid, vector, transcription or expression cassette.
  • the invention also relates to an isolated recombinant host cell comprising one or more nucleic acid construct as described above.
  • the host cell may be a bacterial, viral, plant, mammalian or other suitable host cell.
  • Such host cells are well known in the art and many are available from the American Type Culture Collection (ATCC). These host cells include, inter alia, Chinese hamster ovary (CHO) cells, such as ExpiCHO cells, NSO, SP2 cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), A549 cells, 3T3 cells, HEK- 293 cells and a number of other cell lines.
  • CHO Chinese hamster ovary
  • NSO Chinese hamster ovary
  • SP2 cells such as ExpiCHO cells, NSO, SP2 cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), A549 cells, 3T3 cells, HEK- 293 cells and a number of other cell lines.
  • Mammalian host cells include human, mouse, rat, dog, monkey
  • yeast and filamentous fungus cells including, for example, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia minuta (Ogataea minuta, Pichia lindneri), Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia guercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorpha, Kluyveromyces sp., Kluyveromyces lactis, Candida alb
  • the antibodies or antigen-binding fragments thereof of the invention are coupled or conjugated to at least one therapeutic moiety, such as a drug, an enzyme or a toxin, thus forming an immunuconjugate.
  • the therapeutic moiety is a toxin, for example a cytotoxic radionuclide, chemical toxin or protein toxin.
  • conjugation and conjugated refer to chemical linkages, either covalent or non-covalent, which proximally associates one molecule of interest with a second molecule of interest.
  • immunoconjugate refers to an antigen-binding protein, e.g., an antibody or antigen-binding fragment, which is chemically or biologically linked to a radioactive agent, a cytokine, an interferon, a target or reporter moiety, an enzyme, a peptide or protein or a therapeutic agent.
  • the antigen-binding protein may be linked to the radioactive agent, cytokine, interferon, target or reporter moiety, enzyme, peptide or therapeutic agent at any location along the molecule so long as it is able to bind its target.
  • immunoconjugates include antibody-drug conjugates and antibody-toxin fusion proteins.
  • the second moity is a label, for example a fluorescent molecule, 0- galactosidase, luciferase molecules, chemical dyes, fluorophores or a radioisotope.
  • the antibodies or antigen-binding fragments thereof of the invention are modified to increase half-life, for example by a chemical modification, especially by PEGylation, or by incorporation in a liposome, or using a serum albumin protein or an antibody or antibody fragment that binds human serum albumin. Increased half-life can also be conferred by conjugating the molecule to an antibody fragment.
  • half-life refers to the time taken for the serum concentration of the amino acid sequence, compound or polypeptide to be reduced by 50%, in vivo, for example due to degradation of the sequence or compound and/or clearance or sequestration of the sequence or compound by natural mechanisms.
  • Half-life may be increased by at least 1 .5 times, preferably at least 2 times, such as at least 5 times, for example at least 10 times or more than 20 times, greater than the half-life of the corresponding antibodies of the invention.
  • increased half-life may be more than 1 hours, preferably more than 2 hours, more preferably more than 6 hours, such as more than 12 hours, or even more than 24, 48 or 72 hours, compared to the antibody of the invention.
  • the in vivo half-life of an amino acid sequence, compound or polypeptide of the invention can be determined in any manner known per se, such as by pharmacokinetic analysis. Suitable techniques will be clear to the person skilled in the art.
  • Half-life can for example be expressed using parameters such as the t1 /2-alpha t1/2-beta and the area under the curve (AUC).
  • linker for example a polypeptide linker.
  • Other linkers are known in the art, for example cysteine linkers for antibody drug conjugates.
  • Antigen-binding protein e.g. antibody or antigen-binding fragment thereof that competes with an antibody or antigen-binding fragment thereof of the invention
  • the invention also relates to an antigen-binding protein e.g. an antibody or antigen-binding fragment that competes with an antibody or antigen-binding fragment of the invention.
  • the term “competes” as used herein, refers to an antigen-binding protein e.g., antibody or antigen-binding fragment thereof) that binds to the target antigen (e.g., SARS-CoV-2) and inhibits or blocks the binding of another antigen-binding protein (e.g., antibody or antigen-binding fragment thereof) to the antigen.
  • the term also includes competition between two antigen-binding proteins e.g., antibodies, in both orientations, i.e., a first antibody that binds and blocks binding of second antibody and vice versa.
  • the first antigen-binding protein (e.g., antibody) and second antigen-binding protein (e.g., antibody) may bind to the same epitope.
  • the first and second antigen-binding proteins (e.g., antibodies) may bind to different, but, for example, overlapping epitopes, wherein binding of one inhibits or blocks the binding of the second antibody, e.g., via steric hindrance.
  • competition between antigen-binding proteins may be measured by methods known in the art, for example, by a real-time, label-free bio-layer interferometry assay.
  • competition between a first and second anti- SARS-CoV-2 antigenbinding protein is determined by measuring the ability of an immobilized first anti- SARS-CoV-2 antigen-binding protein (e.g., antibody) (not initially complexed with SARS-CoV-2 protein) to bind to soluble SARS-CoV-2 protein complexed with a second anti- SARS-CoV-2 antigen-binding protein (e.g., antibody).
  • first anti- SARS-CoV-2 antigen-binding protein e.g., antibody
  • the degree of competition can be expressed as a percentage of the reduction in binding.
  • Such competition can be measured using a real time, label-free bio-layer interferometry assay, e.g., on an Octet RED384 biosensor (Pall ForteBio Corp.), ELISA (enzyme-linked immunosorbent assays) or SPR (surface plasmon resonance), HTRF; flow cytometry; fluorescent microvolume assay technology (FMAT) assay, Mirrorball, high content imaging based fluorescent immunoassays, radioligand binding assays, bio-layer interferometry (BLI), surface plasmon resonance (SPR) and thermal shift assays.
  • FMAT fluorescent microvolume assay technology
  • An antibody that binds to the same epitope as a reference antibody refers to an antibody that blocks binding of the reference antibody to its binding partner (e.g., an antigen or “target”) in a competition assay by 50% or more, and I or conversely, the reference antibody blocks binding of the antibody to its binding partner in a competition assay by 50% or more.
  • binding partner e.g., an antigen or “target”
  • the reference antibody blocks binding of the antibody to its binding partner in a competition assay by 50% or more.
  • Such antibodies are said to compete for binding to an epitope of interest.
  • the present disclosure includes an antibody or antigen-binding fragment thereof or binding molecule as described in previous aspects of the invention may be produced in/by murine, mammal or other animal models, by using hybridoma technology or other methods known in the art.
  • nucleic acids encoding the antibody or antigen-binding fragment thereof or binding molecule as described in previous aspects of the invention may be inserted into a plasmid and expressed in a suitable expression system.
  • the present invention includes methods for expressing an antibody or antigen-binding fragment thereof or immunoglobulin chain thereof in a host cell (e.g., bacterial host cell such as E.
  • a bacterial host cell such as an E. coli, includes a polynucleotide encoding the T7 RNA polymerase gene operably linked to a lac promoter and expression of the polymerase and the chain is induced by incubation of the host cell with IPTG (isopropyl-beta-D-thiogalactopyranoside).
  • Transformation can be by any known method for introducing polynucleotides into a host cell.
  • Methods for introduction of heterologous polynucleotides into mammalian cells are well known in the art and include dextran-mediated transfection, calcium phosphate precipitation, polybrene- mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, biolistic injection and direct microinjection of the DNA into nuclei.
  • nucleic acid molecules may be introduced into mammalian cells by viral vectors. Methods of transforming cells are well known in the art.
  • the present invention also includes recombinant methods for making an antibody or antigen-binding fragment thereof or binding molecule of the present invention comprising (i) introducing one or more polynucleotides (e.g., including the nucleotide sequence disclosed herein) encoding light and/or heavy immunoglobulin domains of the antigen-binding protein, for example, wherein the polynucleotide is in a vector; and/or integrated into a host cell chromosome and/or is operably linked to a promoter; (ii) culturing the host cell (e.g., E.
  • the polynucleotide under condition favorable to expression of the polynucleotide and, (iii) optionally, isolating the antigen-binding protein, (e.g., antibody orfragment) or chain from the host cell and/or medium in which the host cell is grown.
  • antigen-binding protein e.g., antibody orfragment
  • an antigen-binding protein e.g., antibody or antigen-binding fragment
  • coexpression of the chains in a single host cell leads to association of the chains, e.g., in the cell or on the cell surface or outside the cell if such chains are secreted, so as to form the antigen-binding protein (e.g., antibody or antigen-binding fragment).
  • the methods include those wherein only a heavy immunoglobulin chain or only a light immunoglobulin chain (e.g., any of those discussed herein including mature fragments and/or variable domains thereof) is expressed.
  • Such chains are useful, for example, as intermediates in the expression of an antibody or antigen-binding fragment that includes such a chain.
  • Eukaryotic and prokaryotic host cells including mammalian cells, may be used as hosts for expression of an anti-TMPRSS2 antigen-binding protein. Such host cells are mentioned elsewhere herein,
  • the disease is a viral infection, i.e. SARS-CoV-2 infection.
  • Methods of treatment are also envisaged.
  • a pharmaceutical composition comprising an antibody or antigen-binding fragment thereof or a binding molecule as described herein and optionally a pharmaceutically acceptable carrier or excipient.
  • the pharmaceutical composition may comprise one or more antibody or antigen-binding fragment thereof as shown in Table 2 and described herein. All combinations of these antibodies or fragments are envisaged.
  • the pharmaceutical composition may comprise only one antibody or antigen-binding fragment thereof as shown in Table 2 and described herein.
  • the pharmaceutical composition may comprise two or more antibodies or antigen-binding fragments thereof as shown in Table 2 and described herein.
  • the pharmaceutical composition may comprise two or more binding molecules as described herein.
  • the antibody or antigen-binding fragment thereof or binding molecule as described herein or the pharmaceutical composition of the invention can be administered by any convenient route, including but not limited to oral, topical, parenteral, sublingual, rectal, vaginal, ocular, intranasal, pulmonary, intradermal, intravitreal, intramuscular, intraperitoneal, intravenous, subcutaneous, intracerebral, transdermal, transmucosal, by inhalation, or topical, particularly to the ears, nose, eyes, or skin or by inhalation.
  • Parenteral administration includes, for example, intravenous, intramuscular, intraarterial, intraperitoneal, intranasal, rectal, intravesical, intradermal, topical or subcutaneous administration.
  • the pharmaceutically acceptable carrier or vehicle can be particulate, so that the compositions are, for example, in tablet or powder form.
  • carrier refers to a diluent, adjuvant or excipient, with which an antibody or antigen-binding fragment thereof or binding molecule of the present invention is administered.
  • Such pharmaceutical carriers can be liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
  • the carriers can be saline, gum acacia, gelatin, starch paste, talc, keratin, colloidal silica, urea, and the like.
  • auxiliary, stabilizing, thickening, lubricating and coloring agents can be used.
  • the antibody or antigen-binding fragment thereof or binding molecule of the present invention or compositions and pharmaceutically acceptable carriers are sterile.
  • Water is a preferred carrier when the antibody or antigen-binding fragment thereof or binding molecule of the present invention are administered intravenously.
  • Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions.
  • Suitable pharmaceutical carriers also include excipients such as starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
  • excipients such as starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
  • the present compositions if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.
  • the pharmaceutical composition of the invention can be in the form of a liquid, e.g., a solution, emulsion or suspension.
  • the liquid can be useful for delivery by injection, infusion (e.g., IV infusion) or sub-cutaneously.
  • composition When intended for oral administration, the composition is preferably in solid or liquid form, where semi-solid, semi-liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid.
  • the composition can be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like form.
  • a solid composition typically contains one or more inert diluents.
  • binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, or gelatin; excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, corn starch and the like; lubricants such as magnesium stearate; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; a flavoring agent such as peppermint, methyl salicylate or orange flavoring; and a coloring agent.
  • a liquid carrier such as polyethylene glycol
  • the composition can be in the form of a liquid, e. g. an elixir, syrup, solution, emulsion or suspension.
  • the liquid can be useful for oral administration or for delivery by injection.
  • a composition can comprise one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer.
  • a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent can also be included.
  • compositions can take the form of one or more dosage units.
  • the composition can be desirable to administer the composition locally to the area in need of treatment, or by injection, intravenous injection or infusion.
  • the composition is part of a device which includes an injector pen.
  • the composition may be provided as a pre-filled syringe or other self-administration device.
  • the term “effective amount” means an amount of antibody or antigen-binding fragment thereof of the invention, that when administered alone or in combination with an additional therapeutic agent to a cell, tissue, or subject, is effective to achieve the desired therapeutic or prophylactic effect under the conditions of administration.
  • the term “effective amount” of a composition, as used herein, is intended to denote a non-lethal but sufficient amount of the composition to provide the desired effect.
  • the effective amount is the one which eliminates or diminishes the symptoms associated with the disorder, e.g. so as to provide control over SARS-Cov-2 infection by eliminating viral particles.
  • An effective amount may be determined by one of ordinary skill in the art, using routine experimentation.
  • in vitro or in vivo assays can optionally be employed to help identify optimal dosage ranges.
  • the precise dose to be employed in the compositions will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Factors like age, body weight, sex, diet, time of administration, rate of excretion, condition of the host, drug combinations, reaction sensitivities and severity of the disease shall be taken into account.
  • the amount is at least about 0.01 % of a the antibody or antigen-binding fragment thereof of the present invention by weight of the composition.
  • this amount can be varied to range from about 0.1 % to about 80% by weight of the composition.
  • Preferred oral compositions can comprise from about 4% to about 50% of the single domain antibody of the present invention by weight of the composition.
  • compositions of the present invention can be prepared so that a parenteral dosage unit contains from about 0.01 % to about 2% by weight of the single domain antibody of the present invention.
  • the composition can comprise from about typically about 0.1 mg/kg to about 250 mg/kg of the subject’s body weight, forexample, between about 0.1 mg/kg and about 20 mg/kg of the animal's body weight, for example about 1 mg/kg to about 10 mg/kg of the animal's body weight.
  • the composition is administered at a dose of about 1 to 30 mg/kg, e.g., about 5 to 25 mg/kg, about 10 to 20 mg/kg, about 1 to 5 mg/kg, or about 3 mg/kg.
  • the dosing schedule can vary from e.g., once a week to once every 2, 3, or 4 weeks.
  • the antibody or antigen-binding fragment thereof or binding molecule of the present invention can be administered at an initial dose, followed by one or more secondary doses.
  • the initial dose may be followed by administration of a second or a plurality of subsequent doses of antibody or antigen-binding fragment thereof in an amount that can be approximately the same or less than that of the initial dose, wherein the subsequent doses are separated by at least 1 day to 3 days; at least one week, at least 2 weeks; at least 3 weeks; at least 4 weeks; at least 5 weeks; at least 6 weeks; at least 7 weeks; at least 8 weeks; at least 9 weeks; at least 10 weeks; at least 12 weeks; or at least 14 weeks.
  • the invention provides methods of treating SARS-CoV-2-mediated diseases or disorders in a mammal, e.g., a human patient or subject, comprising administering an effective amount of an antibody or antigen-binding fragment thereof or binding molecule of the present invention to a mammal in need thereof.
  • the invention furthermore relates to a method for the prevention and/or treatment of SARS-CoV-2 infection said method comprising administering, to a subject in need thereof, a pharmaceutically active amount of an antibody or antigen-binding fragment thereof or binding molecule of the invention or pharmaceutical composition of the invention.
  • treat means inhibiting or relieving a disease or disorder.
  • treatment can include a postponement of development of the symptoms associated with a disease or disorder, and/or a reduction in the severity of such symptoms that will, or are expected, to develop with said disease.
  • the terms include ameliorating existing symptoms, preventing additional symptoms, and ameliorating or preventing the underlying causes of such symptoms.
  • the terms denote that a beneficial result is being conferred on at least some of the mammals, e.g., human patients, being treated. Many medical treatments are effective for some, but not all, patients that undergo the treatment.
  • a subject refers to an animal which is the object of treatment, observation, or experiment.
  • a subject includes, but is not limited to, a mammal, including, but not limited to, a human or a non-human mammal, such as a non-human primate, murine, bovine, equine, canine, ovine, or feline.
  • the subject may have a viral infection, e.g., a SARS-CoV-2 infection, or be predisposed to developing an infection.
  • Subjects predisposed to developing an infection, or subjects who may be at elevated risk for contracting an infection include subjects with compromised immune systems because of autoimmune disease, subjects receiving immunosuppressive therapy (for example, following organ transplant), subjects afflicted with human immunodeficiency virus (HIV) or acquired immune deficiency syndrome (AIDS), subjects with forms of anemia that deplete or destroy white blood cells, subjects receiving radiation or chemotherapy, or subjects afflicted with an inflammatory disorder. Additionally, subjects of old age (e.g., 65 years of age or older) are at increased risk.
  • the invention also relates to an antibody or antigen-binding fragment thereof or binding molecule as described herein that binds to the SARS-CoV-2 Spike protein RBD region, or pharmaceutical composition of the invention for use in the treatment or prevention of a disease.
  • the invention relates to an antibody or antibody or antigen-binding fragment thereof or binding molecule as described herein that binds to the SARS-CoV-2 Spike protein RBD region or a pharmaceutical composition of the invention for use in the treatment or prevention of a SARS-CoV-2 infection.
  • the invention relates to an antibody or antigen-binding fragment thereof or binding molecule as described herein that binds to the SARS-CoV-2 Spike protein RBD region or a pharmaceutical composition of the invention for use in the manufacture of a medicament for the treatment or prevention of a SARS-CoV-2 infection.
  • the invention in another aspect, relates to an immunotherapy comprising an antibody or antigenbinding fragment thereof or binding molecule as described herein that binds to the SARS-CoV-2 Spike protein RBD region or a pharmaceutical composition of the invention.
  • This may include the step of administering the antibody, antigen-binding fragment thereof, binding molecule or pharmaceutical composition to a subject in need thereof.
  • the invention in another aspect, relates to a method of treating or preventing prevention of a SARS-CoV-2 infection comprising administering an antibody or antigen-binding fragment thereof or binding molecule as described herein that binds to the SARS-CoV-2 Spike protein RBD region or administering a pharmaceutical composition of the invention.
  • immunotherapy refers to the treatment of a disease (e.g. of a viral infection) by modulating, directing or supplementing the immune response to an antigen associated with, or produced during, the disease (e.g. an antigen of the infectious agent).
  • immunotherapy refers to blocking or diminishing the infection and/or intercellular spreading of the virus in any given subject by administering one or more of the monoclonal antibodies of the invention.
  • the SARS-CoV-2 infection may be caused by a variant, for example as shown in Table 1 .
  • the variant is omicron.
  • the antibody, antigen-binding fragment thereof, binding molecule or pharmaceutical composition of the invention may be administered as the sole active ingredient or in combination with one or more other therapeutic agent.
  • a therapeutic agent is a compound or molecule which is useful in the treatment of a disease. Examples of therapeutic agents include antibodies, antibody fragments, drugs, toxins, nucleases, hormones, immunomodulators, pro-apoptotic agents, anti- angiogenic agents, boron compounds, photoactive agents or dyes and radioisotopes.
  • An antibody molecule includes a full antibody or fragment thereof as mentioned elsewhere herein, e.g., a Fab, F(ab')2, Fv, a single chain Fv fragment (scFv) or a single domain antibody, for example a VH domain, or antibody mimetic protein.
  • the antibody or antigen-binding fragment thereof or binding molecule may be administered alone or in combination, e.g. one of the antibodies or antibody fragments listed in Table 2 may be administered followed by administration of one, two or three other antibodies or antibody fragments listed in Table 2.
  • the invention also relates to a combination therapy comprising at least two of the antibodies or antigen-binding fragment thereof listed in Table 2.
  • one or more antibody or antigen-binding fragment thereof or binding molecule or pharmaceutical composition as described herein is used in combination with an existing therapy ortherapeutic agent, for example an anti-viral compound, an antibody therapy that targets SARS-CoV-2, a vaccine, an immunomodulator or an anti-inflammatory.
  • the invention also relates to a combination therapy comprising administration of one or more antibody, or antigen-binding fragment thereof, binding molecule or pharmaceutical composition described herein and an anti-viral therapy.
  • the combination therapy may comprise one of more of antibodies or antigenbinding fragments thereof listed in Table 2. In one embodiment, the combination therapy may comprise one antibody or antigen-binding fragment thereof listed in Table 2. In another embodiment, the combination therapy may comprise two or more antibodies or antigen-binding fragments thereof listed in Table 2.
  • a further anti-viral therapy may be administered concurrently or sequentially with one or more of antibody or antigen-binding fragment thereof listed in Table 2.
  • a number of therapies that treat and prevent COVID-19 are known or being developed and the antibody or antibody fragment of the invention and any of these therapies may be used in conjunction with the antibodies of the invention.
  • these therapies include: i) Antivirals, e.g. Remdesivir, Chloroquine/hydroxychloroquine, Lopinavir/ritonavir combination, Favipiravir, Umifenovir, Ribavirin, EIDD-2801 , Niclosamide and Oseltamivir; ii) Immune modulators, e.g.
  • Colchicine Angiotensin-converting-enzyme inhibitors/angiotensin II receptor blockers, Statins, Aspirin, Clopidogrel, Anticoagulants, Bemcentinib, Omeprazole, Famotidine, Zilucoplan, Ascorbic acid/vitamin C, Aviptadil, Opaganib, Tradipitant, AZD1656, Nitric oxide and Razuprotafib or iv) Antibodies that neutralise SARS-CoV-2, e.g. asirivimab and imdevimab. bamlanivimab, etesevimab, casirivimab, imdevimab, sotrovimab, tixagevimab plus cilgavimab: or combinations thereof.
  • a viral entry inhibitor or a viral attachment inhibitor is administered.
  • administration of the antibody, antigen-binding fragment thereof, binding molecule pharmaceutical composition of the invention with the therapeutic agent; e.g. anti-viral therapy is concurrent or sequential.
  • the antibody, antigen-binding fragment thereof, binding molecule or pharmaceutical composition of the invention is administered prior or subsequent to administration of the therapeutic agent, e.g. at least an hour, five hours, 12 hours, a day, a week, a month, for example several months (e. g. up to three months), prior or subsequent to administration of composition of the present invention.
  • the invention provides a kit for the treatment or prevention of Covid-19 and/or for detecting SARS-CoV-2 for diagnosis, prognosis or monitoring disease comprising an antibody, antigen-binding fragment thereof, binding molecule or pharmaceutical composition of the invention; e.g. one or more antibody or antigen-binding fragment thereof listed in Table 2.
  • a kit may contain other components, packaging, instructions, or material to aid in the detection of SARS-CoV-2 protein.
  • the kit may include a labeled antibody, antigen-binding fragment thereof, binding molecule or pharmaceutical composition of the invention and one or more compounds for detecting the label.
  • the invention in another aspect provides an antibody, antigen-binding fragment thereof, binding molecule or a pharmaceutical composition of the invention packaged in lyophilized form or packaged in an aqueous medium.
  • an antibody, antigen-binding fragment thereof, , e.g. as shown in Table 2, or binding molecule of the invention is used for non-therapeutic purposes, such as diagnostic tests and assays, for example immunoassays for the detection or quantification of SARS-Cov-2 virus.
  • the immunoassays per se are well-known and any of the well-known immunoassays may be employed. That is, classifying the known immunoassays according to the reaction type, known immunoassays include sandwich immunoassays, competition immunoassays, agglutination immunoassays, Western blot and the like.
  • known immunoassays include fluorescence immunoassays, enzyme immunoassays, radio immunoassays, biotin immunoassays and the like. Any of these immunoassays may be employed. Further, diagnosis may be attained by immunohistostaining. In cases where a labeled antibody antigen-binding fragment thereof or binding molecule is used in the immunoassay, the methods per se for labeling an antibody are well-known, and any of the well-known methods may be employed.
  • the antibody, antigen-binding fragment thereof or binding molecule of the present invention is immobilized on a solid phase as a first antibody, first antigen-binding fragment thereof or first binding molecule.
  • the first antibody first antigenbinding fragment thereof or first binding molecule is then reacted with a sample, and after washing the solid phase, the resultant is then reacted with a second antibody which reacts with the enzyme of the present invention by antigen-antibody reaction. After washing the solid phase, the second antibody bound to the solid phase is measured.
  • the second antibody bound to the solid phase is measured.
  • the above-mentioned measurement is conducted for a plurality of standard samples each containing a known concentration of the enzyme, and the relationship between the concentrations of the enzyme in the standard samples and the measured amounts of the label is plotted to prepare a calibration curve.
  • the enzyme in a test sample may be quantified by applying the measured amount to the calibration curve.
  • detecting is used herein in the broadest sense to include both qualitative and quantitative measurements of a target molecule. Detecting includes identifying the mere presence of the target molecule in a sample as well as determining whether the target molecule is present in the sample at detectable levels. Detecting may be direct or indirect.
  • the above-mentioned first antibody and the above-mentioned second antibody may be exchanged.
  • the antibody according to the present invention or an antigen-binding fragment thereof is immobilized on particles such as latex particles, and the particles are reacted with a sample, followed by measurement of the absorbance.
  • the above-mentioned measurement is conducted for a plurality of standard samples each containing a known concentration of the enzyme, and the relationship between the concentrations of the enzyme in the standard samples and the measured absorbance is plotted to prepare a calibration curve.
  • the enzyme in a test sample may be determined by applying the measured absorbance to the calibration curve.
  • a method for detecting the presence of SARS-Cov-2 particles or SARS- Cov-2 viral components in a test subject comprising contacting a test sample with an isolated antibody, antigen-binding fragment thereof or binding molecule of the invention.
  • the method may further comprise i) determining the degree of binding of the antibody, antigenbinding fragment thereof or binding molecule to the test sample (ii) contacting a control sample with an isolated antibody, antigen-binding fragment thereof or binding molecule according to any of claims 1 to x and determining the degree of binding to the control sample; and (iii) comparing the degree of binding obtained in steps (i) and (iii, wherein, an effective amount obtained in step (i) which is higher than the effective amount obtained in step (ii), is considered positive for the presence of SARS-Cov-2.
  • the degree of binding of the antibody, antigen-binding fragment thereof or binding molecule to the test sample is compared to a pre-determined value indicating a healthy value.
  • the method may further comprise the step of obtaining a test sample from a subject.
  • the test sample may be a healthy subject or a diseased subject, e.g. a subject showing symptoms of CoVID-19 disease.
  • the control sample is from a subject that does not have CoVID-19 disease, i.e. a healthy subject.
  • patients may be tested before receiving any treatment.
  • patients may be tested following treatment, after a certain period or periodically, to monitor their response to therapy.
  • the method also includes the additional step of treating the patient with a COVID-19 therapy.
  • a method for monitoring the progression of COVID -19 disease in a test subject that suffers from infection comprising contacting a test sample with an isolated antibody, antigen-binding fragment thereof or binding molecule of the invention and detecting the presence of SARS-CoV-2 particles or SARS-CoV-2 viral components in a test subject.
  • the method may further comprise i) determining the degree of binding of the antibody, antigenbinding fragment thereof or binding molecule to the test sample (ii) contacting a control sample with an isolated antibod , antigen-binding fragment thereof or binding molecule as described herein determining the degree of binding to the control sample; and (iii) comparing the degree of binding obtained in steps (i) and (ii), wherein, an effective amount obtained in step (i) which is higher than the effective amount obtained in step (ii), is considered to indicate progression of disease.
  • the degree of binding of the antibody, antigen-binding fragment thereof or binding molecule to the test sample is compared to a pre-determined value indicating a certain stage of disease.
  • the method may further comprise the step of obtaining a test sample from a subject.
  • the test sample is from a subject which has previously been diagnosed as having COVID-19.
  • patients may be at an early stage of COVID-19 disease, exhibiting few and mild symptoms.
  • patients may be at a more advanced stage of COVID-19 disease, exhibiting more severe symptoms.
  • patients may be tested before receiving any treatment.
  • patients may be tested following treatment, after a certain period or periodically, to monitor their response to therapy.
  • the method also includes the additional step of treating the patient with a COVID-19 therapy.
  • the control sample may be a sample from the same subject taken at an earlier timepoint.
  • Samples used in the methods above may be used include, but are not limited to, nasal I nasopharyngeal swabs I washes I aspirates, nasal mucosal fluid, oral I oropharyngeal swabs I washes I aspirates, biological fluids such as serum, saliva plasma, whole I peripheral I capillary blood, sputum and cough secretions, isolated / separated cells / cell populations, cultured cells of any origin and cell extracts, as well as tissue material such as fresh / frozen biopsies and formalin- fixed I paraffin-embedded biopsies.
  • the invention also relates to a method for detecting the presence of SARS- Cov-2 particles or SARS-Cov-2 viral components on solids and in fluids of any type including, but not limited to, surfaces and objects in medical I hospital environments, schools, recreational facilities and households, hotels, drinking I washing I irrigation water supplies, and sewage reservoirs.
  • the method comprises contacting a test solid or fluid sample with an isolated antibody or antigen-binding fragment of the invention and detecting the presence of SARS-Cov-2 particles or SARS-Cov-2 viral components in test solid or fluid sample.
  • the test sample is not from a subject.
  • the method may further comprise i) determining the degree of binding of the antibody or antibody fragment to the test sample (ii) contacting a control sample with an isolated antibody or antigenbinding fragment thereof as described herein determining the degree of binding to the control sample; and (iii) comparing the degree of binding obtained in steps (i) and (ii), wherein, an effective amount obtained in step (i) which is higher than the effective amount obtained in step (ii), is considered to indicate progression of disease.
  • the degree of binding of the antibody, antigen-binding fragment thereof or binding molecule to the test sample is compared to a pre-determined value indicating test sample free of SARS-Cov-2 particles or SARS-Cov-2 viral components.
  • Suitable detectable labels which may be conjugated to antigen-binding proteins are known in the art and include radioisotopes such as iodine-125, iodine-131 , yttrium- 90, indium-1 11 and technetium-99; fluorochromes, such as fluorescein, rhodamine, phycoerythrin, Texas Red and cyanine dye derivatives for example, Cy7, Alexa750 and Alexa Fluor 647; chromogenic dyes, such as diaminobenzidine; latex beads; enzyme labels such as horseradish peroxidase; phospho or laser dyes with spectrally isolated absorption or emission characteristics; electro-chemiluminescent labels, such as SULFO-TAG which may be detected via stimulation with electricity in an appropriate chemical environment; and chemical moieties, such as biotin, which may be detected via binding to a specific cognate detectable moiety, e.g. labelled avidin or streptavidin.
  • the high sensitivity exhibited by the antibody, antigen-binding fragment thereof or binding molecule of the invention is particularly advantageous in facilitating detection of virus even in low viral titer biological fluids such as might be self-sampled by a consumer relatively non-invasively, e.g., by swabbing mucosal fluids such as nasal fluids or saliva.
  • the antibody, antigen-binding fragment thereof or binding molecule according to the present invention as at least one of the solid phase antibody, antigen-binding fragment thereof or binding molecule and labeled antibody, antigen-binding fragment thereof or binding molecule, a reagent for measuring SARS-Cov-2 virus may be produced.
  • the solid phase on which the above-described antibody, antigen-binding fragment thereof or binding molecule is immobilized various solid phases used in conventional immunoassays may be used.
  • solid phases examples include various solid phases such as ELISA plates, latices, gelatin particles, magnetic particles, polystyrenes and glasses, insoluble carriers such as beads and matrices through which liquid can be transported and the like.
  • the labeled antibody, antigenbinding fragment thereof or binding molecule may be produced by labeling an antibody, antigenbinding fragment thereof or binding molecule with an enzyme, colloidal metal particle, colored latex particle, luminescent substance, fluorescent substance, radioactive substance or the like.
  • reagents such as these solid phase antibodies, antigen-binding fragment thereof or binding molecule and/or labeled antibodies, antigen-binding fragment thereof or binding molecule, reagents used in enzyme immunoassays, radioimmunoassays, fluoroimmunoassays or the like may be produced.
  • These measurement reagents are the reagents for measuring an antigen of interest present in the test sample by sandwich immunoassay or competitive binding immunoassay.
  • the immunoassay device of the present invention for measuring SARS-Cov-2 virus utilizes the principle of immunochromatography.
  • the device comprises a detection zone having the monoclonal antibody of the present invention immobilized on a matrix through which liquid can be transported, and a labeled reagent zone having a labeled anti- SARS-Cov-2 virus monoclonal antibody of the present invention spotted movably on the above-described matrix.
  • the invention relates to a solid support comprising an isolated antibody, antigen-binding fragment thereof or binding molecule according to the invention.
  • the solid support may be selected from a polystyrene plate, polystyrene beads, nitrocellulose test strip, a nanoparticle or microfluidic chip.
  • the invention relates to a lateral flow immunoassay for detecting SARS-Cov-2 particles or SARS-Cov-2 viral components in a sample, comprising:
  • a mobile phase comprising a detection antibody conjugated or otherwise associated with a detectible signal, said detection antibody being capable of binding SARS-Cov-2 particles or SARS-Cov-2 viral components to form a binary complex;
  • a stationary phase comprising a substrate comprising immunochromatographic material having immobilized thereon a capture antibody or fragment as described herein, said capture antibody being capable of binding said SARS-Cov-2 of the binary complex to form a ternary complex, whereby a detectible signal generated by said ternary complex is indicative of the presence of SARS-Cov-2 in the sample.
  • lateral flow refers to capillary flow through a material in a horizontal direction, but will be understood to apply to the flow of a liquid from a point of application of the liquid to another lateral position even if, for example, the device is vertical or on an incline. Lateral flow depends upon properties of the liquid/substrate interaction (surface wetting orwicking action) and does not require application of outside forces, e.g., vacuum or pressure applications by the user.
  • the mobile phase typically comprises the sample, liquid diluents and a detection antibody-signal conjugate
  • the immobile phase typically comprises the capture antibody immobilized at the test and control lines, both detection and capture antibodies being specific for the analyte.
  • the liquid biological sample is absorbed onto the sample pad, and the sample progresses by capillary action into the conjugate pad, where it rehydrates detection antibody particles labelled with a detectable moiety such as a colored label, allowing for the mixing of these particles with the absorbed liquid sample.
  • the labelled antibody interacts with the specific analyte contained in the sample, thereby initiating the intermolecular interactions which are dependent on the affinity and avidity of the reagents.
  • the binary complex of the labelled antibody and its specific analyte migrate along the strip toward the capture antibody immobilized in the reaction zone (typically in a line transverse, for example perpendicular, to the sample flow to form a "test line” across the strip), which recognizes and captures the complex, where it becomes immobilized and produces a distinct signal, for example, in the form of a colored line.
  • This technique may be used to obtain quantitative or semi- quantitative results.
  • solutions or suspensions of labelled antibody and biological sample are combined under conditions to form a binary complex of the labelled antibody with the analyte, prior to application to a test strip.
  • the chromatographic strip is "dipped into” or otherwise contacts the liquid, so that the complex of labelled antibody and target analyte is drawn across the strip as described above, toward the capture antibody at the test line.
  • the invention relates to the use of the antibodies, antigen-binding fragment thereof or binding molecule according to the invention as detection agents for SARS-Cov-2 particles or SARS-Cov-2 viral components or therapeutic agents.
  • the invention relates to the following aspects
  • An isolated antibody or antigen-binding fragment thereof that specifically binds to the receptor binding domain (RBD) region of the SARS-CoV-2 Spike (S) protein wherein said isolated antibody or antigen-binding fragment thereof comprises i) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively; ii) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 10, 1 1 and 12, or a sequence with at least 80%, 90% or 9
  • the isolated antibody or antigen-binding fragment thereof according to aspect 1 comprising i) a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ii) a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iii) a VH region of SEQ ID NO: 21 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 25 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iv) a VH region of SEQ ID NO: 29 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL
  • the antigen-binding fragment comprises a Fab, Fab', F(ab')2, F(ab')3, Fabc, Fd, single chain FV (scFv), (scFv)2, Fv, scFv-Fc, heavy chain only antibody, diabody, tetrabody, triabody, minibody, or single domain antibody,.
  • the antibody or antigen-binding fragment thereof according to any preceding aspect which is linked to a second antibody or antigen-binding fragment thereof that specifically binds to the receptor binding domain (RBD) region of the SARS-CoV-2 Spike (S) protein.
  • RBD receptor binding domain
  • S SARS-CoV-2 Spike
  • a vector comprising a polynucleotide according to aspect 16.
  • a host cell comprising a polynucleotide according to aspect 16 or a vector according to aspect 17.
  • a method of making the antibody or antigen-binding fragment according to any one of aspects 1 to 16 comprising (a) culturing a cell according to aspect 18; and (b) isolating the antibody or antigen-binding fragment thereof or the protein from the cultured cell.
  • a binding molecule comprising a) a first antibody or antibody binding fragment thereof directed against a first epitope located in the RBD region of the Spike protein of SARS-CoV-2 and b) a second antibody or antibody fragment thereof directed against a second epitope located in the RBD region of the Spike protein of SARS-CoV-2.
  • the binding molecule according to aspect 20 wherein said first and/or said second isolated antibody or antigen-binding fragment thereof comprises i) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 2, 3 and 4, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 2, 3 and 4 respectively, and a light chain variable region that comprises LCDR1 , LCDR2 and LCDR3 comprising the amino acid sequences of SEQ ID NOs: 6, 7 and 8, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 6, 7 and 8 respectively; ii) a heavy chain variable region that comprises HCDR1 , HCDR2, and HCDR3 comprising the amino acid sequences of SEQ ID NOs: 10, 1 1 and 12, or a sequence with at least 80%, 90% or 95% sequence identity to SEQ ID NOs: 10, 11 and 12, respectively, and a light chain variable region that
  • the binding molecule according to aspect 20 or 21 wherein said first and/or said second isolated antibody or antigen-binding fragment thereof comprises i) a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto; ii) a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iii) a VH region of SEQ ID NO: 21 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 25 or a sequence with at least 80%, 90% or 95% sequence identity thereto; iv) a VH region of SEQ ID NO: 29 or a sequence with at least 80%
  • binding molecule according to any of aspects 20 to 23 wherein said first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 5 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 9 or a sequence with at least 80%, 90% or 95% sequence identity thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 13 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 17 or a sequence with at least 80%, 90% or 95% sequence identity thereto;
  • binding molecule according to any of aspects 20 to 22 or 27 wherein said first isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 61 a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 65 or a sequence with at least 80%, 90% or 95% sequence identity thereto and said second isolated antibody or antigen-binding fragment thereof comprises a VH region of SEQ ID NO: 37 or a sequence with at least 80%, 90% or 95% sequence identity thereto and a VL region of SEQ ID NO: 41 or a sequence with at least 80%, 90% or 95% sequence identity thereto.
  • binding molecule according to any of aspects 20 to 28 wherein the first and second isolated antibody or antigen-binding fragment thereof are combined in a dual variable domain (DVD), scFv4-Fc or IgG-scFv format.
  • DVD dual variable domain
  • a combination therapy comprising at least two antibodies or antigen-binding fragments according to any of aspects 1 to 15, a binding molecule according to any of aspects 20 to 29 or a pharmaceutical composition according to aspect 31 .
  • a pharmaceutical composition comprising one or more isolated antibody or antigen-binding fragment thereof according to any of aspects 1 to 15 or a binding molecule according to any of aspects 20 to 29.
  • a method of treatment of a patient suffering from a SARS-CoV-2 infection comprising administering an isolated antibody or antigen-binding fragment thereof according to any of aspects 1 to 15, a binding molecule according to any of aspects 20 to 29 or a pharmaceutical composition according to aspect 31 to said patient.
  • a method for diagnosing a SARS-CoV-2 infection comprising detecting SARS-CoV-2 particles or SARS-CoV-2 viral components in a sample using an isolated antibody or antigenbinding fragment thereof according to aspects 1 to 15.
  • a method for monitoring disease progression comprising detecting SARS-Cov-2 particles or SARS-CoV-2 viral components in a sample using an isolated antibody or antigen-binding fragment thereof according to aspects 1 to 15.
  • a method for detecting the presence of SARS-CoV-2 particles or SARS-CoV-2 viral components in a test subject comprising contacting a test sample with an isolated antibody or antigen-binding fragment thereof according to any of aspects 1 to 15.
  • a kit comprising an isolated antibody or antigen-binding fragment thereof according to any of aspects 1 to 15, a binding molecule according to any of aspects 20 to 29 or a pharmaceutical composition according to aspect 31 and optionally instructions for use.
  • Immune phage-display libraries were generated from cDNA derived from PBMCs of two convalescent donors and RNA from 5x10 6 cells extracted then purified using the I llustra RNAspin Mini kit (GE healthcare, 25-055-71), according to manufacturer’s instructions. cDNA was then amplified from the extracted RNA using oligo dT and the Superscript IV First-Strand Synthesis System (Thermo Fisher) with RiboLock RNase inhibitor (Thermo Fisher), in accordance with manufacturer’s instructions. Heavy chain VDJ and light chain VJ region amplification was performed by PCR on each donor cDNA separately, using KOD Xtreme Hot Start DNA Polymerase Kit (Sigma-Aldrich) to manufacturer’s instructions.
  • the generated phage display libraries were electroporated in E.coli and subsequently used for the biopanning process. A library size of 10 8 was determined for both libraries used. Phage particles were obtained by superinfection with helper phage (M13K07, New England Biolabs, N0315). The libraries were initially selected against the full-length Spike protein (Aero biosystems, SPN-C52H9) and a further round of biopanning was carried out against the RBD only domain (Aero biosystems, SPD-C52H3). Briefly, immunotubes were coated at 4°C overnight using the SARS-CoV2 antigens at 5 and 2 pg/ml, respectively, in sterile PBS (Lonza, BE17-513F).
  • variable regions of the identified chains were formatted into full length IgG antibodies, then expressed, purified, and subjected to biophysical and flow cytometry analysis.
  • Antibody clones were assayed for binding against SupT1 cells expressing Spike protein (Wuhan).
  • a total of 24 unique Spike binding clones were identified via phage display approach (Fig. 1A).
  • the neutralisation capacity of clones capable of binding to Spike protein was evaluated against an engineered replication-deficient lentiviral vector pseudotyped with the Wuhan Spike glycoprotein (76).
  • Spike-binding clones were each mixed in a 1 :1 ratio with 1x10 5 IU/ml of pseudotyped lentivirus (PsV), at a fixed concentration of 50 pg/ml.
  • PsV pseudotyped lentivirus
  • Clones D12C1 , D12C3 and D13C1 were analysed via surface plasmon resonance (SPR) for binding kinetics to SARS-CoV-2 S1 domain ( Figure 2). Binders were captured on flow cell 2 of a Series S Protein A sensor chip (Cytiva - 29127555) to a density of 75 RU, using a Biacore 8K instrument (Cytiva). HBS-P + buffer was used as running buffer in all experimental conditions. Recombinant S1 at 250 nM with 2-fold serial dilutions, was used as the ‘analyte’ and injected over the flow channels with 150s contact time and 300s dissociation. All experiments were performed at 25°C with a flow rate of 30 pl/ml.
  • SPR surface plasmon resonance
  • Flow cell 1 was unmodified and used for reference subtraction.
  • a ‘0 concentration’ sensogram of buffer alone was used as a double reference subtraction to factor for drift.
  • Data were fit to a 1 :1 Langmuir binding model using Biacore insight evaluation software (Cytiva). Since a capture system was used, a local Rmax parameter was used for the data fitting in each case.
  • Clones D12C1 and D13C1 were screened via SPR for binding kinetics to SARS-CoV-2 S1 domain of variants Wuhan, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2) and omicron (Figure 3).
  • control antibodies LY-CoV555, REGN10933 and REGN10987 were tested on the same variants ( Figure 4). Binders were captured on flow cell 2 of a Series S Protein A sensor chip (Cytiva - 29127555) to a density of 75 RU, using a Biacore 8K or Biacore T200 instrument (Cytiva). HBS-P + buffer was used as running buffer in all experimental conditions.
  • Recombinant S1 at 250 nM with 2-fold serial dilutions was used as the ‘analyte’ and injected over the flow channels with 150s contact time and 300s dissociation. All experiments were performed at 25°C with a flow rate of 30 pl/ml.
  • Flow cell 1 was unmodified and used for reference subtraction.
  • a ‘0 concentration’ sensogram of buffer alone was used as a double reference subtraction to factor for drift.
  • Data were fit to a 1 :1 Langmuir binding model using Biacore insight evaluation software (Cytiva). Since a capture system was used, a local Rmax parameter was used for the data fitting in each case.
  • the D12C1 , D12C2, D12C3, D13C1 , D13C27, D13C32 and D13C37 neutralising antibodies were tested in a more stringent neutralisation assay by titrating against 1x10 6 lU/ml PsV (described above) and compared to the control antibodies REGN10933, REGN10987 and Ly-CoV555 (Figure 5).
  • Clones identified through phage display demonstrated varying levels of neutralisation with four antibodies showing ECso values ranging from 6.5 nM to 0.98 pM and three failing to show appreciable activity.
  • Clones D12C1 and D13C1 were tested in neutralization assays against SARS-CoV-2 pseudotyped lentiviral vectors carrying the spike protein of Wuhan, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2) variants.
  • Antibodies were tested at a range of concentrations with 4-fold serial dilutions. Each antibody dilution was mixed 1 :1 with lentiviral vectors normalised to 1x10 5 physical particle of vectors pseudotyped with WT Wuhan glycoprotein, to a final volume of 200 pL and incubated at 37 °C for 1 h.
  • Antibody-virus mixtures were added to 3x10 4 HEK-293T (ACE2 + , TMPRSS2 + ) in 48-well plates and incubated for 72 h. Viral titers were then quantified by eGFP expression in target cells using BD LSRFORTESSA X- 20 cell analyser and infectivity of all fractions was determined as a percentage of viral titers in the PBS only control.
  • a 1 :1 antibody cocktail of REGN10933 and REGN10987, and the clone LY- CoV555 were used as controls (Figure 6). Clone D13C1 showed sustained neutralisation capacity over all variants tested.
  • Activated and memory B cells that bound S1-tetramer were FACS-purified from PBMCs and partitioned into single B cell V(D)J libraries using the 10x genomics platform.
  • the libraries were sequenced, and the native IgA and IgG heavy and light chains identified and paired for each cell using the 10x barcodes.
  • the variable regions of the identified chains from each approach were formatted into full length IgG antibodies, then expressed, purified, and subjected to biophysical and flow cytometry analysis.
  • Antibody clones were assayed for binding against SupT 1 cells expressing Spike protein (Wuhan) (Fig. 8A). A total of 213 unique Spike binding clones were identified, of which 131 demonstrated appreciable binding to the spike protein.
  • the neutralisation capacity of clones capable of binding to Spike protein were evaluated against an engineered replication-deficient lentiviral vector pseudotyped with the Wuhan Spike glycoprotein.
  • Spike-binding clones were each mixed in a 1 :1 ratio with 1x10 5 lU/ml of pseudotyped lentivirus, at a fixed concentration of 50 pg/ml.
  • a total of 24 antibodies demonstrated over 85% neutralisation capacity (Fig. 8B).
  • Antibody-virus mixtures were added to 3x10 4 HEK-293T (ACE2 + , TMPRSS2 + ) in 48-well plates and incubated for 72 h. Viral titers were then quantified by eGFP expression in target cells using BD LSRFORTESSA X-20 cell analyser and infectivity of all fractions was determined as a percentage of viral titers in the PBS only control. Clones demonstrated varying levels of neutralisation with four antibodies showing ECso values ranging from 0.7 nM to 212 nM.
  • Clones S4A_84 (84), S4B_56 (56), S4B_152 (152) and S4B_222 (222) were screened via SPR for binding kinetics to SARS-CoV-2 S1 domain of variants Wuhan, alpha (B.1 .1 .7), beta (B.1 .351), gamma (P.1), delta (B.1.617.2) and omicron ( Figure 11 , Table 3). Binders were captured on flow cell 2 of a Series S Protein A sensor chip (Cytiva - 29127555) to a density of 75 RU, using a Biacore 8K instrument (Cytiva). HBS-P + buffer was used as running buffer in all experimental conditions.
  • Recombinant S1 at 250 nM with 2-fold serial dilutions was used as the ‘analyte’ and injected over the flow channels with 150s contact time and 300s dissociation. All experiments were performed at 25°C with a flow rate of 30 pl/ml.
  • Flow cell 1 was unmodified and used for reference subtraction.
  • a ‘0 concentration’ sensogram of buffer alone was used as a double reference subtraction to factor for drift.
  • Data were fit to a 1 :1 Langmuir binding model using Biacore insight evaluation software (Cytiva). Since a capture system was used, a local Rmax parameter was used for the data fitting in each case. Antibodies tested showed high affinity interactions against the spike variants tested. Clones 84 and 56 showed impaired binding to omicron variant.
  • Clones 84, 56, 152 and 222 were tested at a range of concentrations with 4-fold serial dilutions. Each antibody dilution was mixed 1 :1 with lentiviral vectors normalised to 1x10 5 physical particle of vectors pseudotyped with WT Wuhan glycoprotein, to a final volume of 200 pL and incubated at 37 °C for 1 h. SARS-CoV-2 spike variants tested were Wuhan, Beta (1.351) and Delta (B.1.617.2) as these were the ones shoving more challenging conditions among the available Variants of concern. Antibody-virus mixtures were added to 3x10 4 HEK-293T (ACE2 + , TMPRSS2 + ) in 48-well plates and incubated for 72 h.
  • Viral titers were then quantified by eGFP expression in target cells using BD LSRFORTESSA X-20 cell analyser and infectivity of all fractions was determined as a percentage of viral titers in the PBS only control.
  • a 1 :1 antibody cocktail of REGN10933 and REGN10987 was used as control ( Figure 12).
  • Clone D13C1 showed sustained neutralisation capacity over all variants tested. All clones showed consistent neutralisation against Wuhan, Beta and delta variants.
  • the binding epitope for these binders has already been precisely determined based on their solved co-crystal structures (PDB 6XDG and 7L3N) and would therefore serve as reference for mapping our own candidates. Simultaneous binding of two antibodies to S1 would indicate targeting non-overlapping regions of the S1 protein and would therefore fall into separate bins; while two antibodies binding to the same or overlapping epitopes would show limited secondary binding events and would be grouped into the same bin (Fig. 13A). Mapping the data highlighted a number of antibodies with unique binding epitopes (Fig. 13B).
  • Antibodies were selected based on ability to co-operatively binding to S1 , as well as showing competition with ACE2-Fc.
  • To LY-CoV555 was assigned the Bin 1 , to REGN10933 the Bin 2, to REGN10987 the Bin 3 and to ACE2-Fc the Bin 4.
  • Bin 1 and Bin 3 are overlapping or in close proximity epitopes and clones LY-CoV555 and REGN10987 do compete with each other.
  • ACE2- Fc bin (bin 4) comprises all 3 bins. Clones D12C3, D13C1 and S4B_177 bound to a distinct epitope not occupied by LY-CoV-555 (Bin 1), REGN10933 (Bin 2) or REGN10987 (Bin 3).
  • Clones S4A_16, S4A_54, S4A_60 and S4A_79 also mapped to a distinct epitope but lied outside of the ACE2 epitope.
  • Clone D12C1 mapped in the Bin 1 and Bin 3.
  • Clones S4A_84 and S4B_56 mapped in Bin 3.
  • Clones S4B_156, S4B_222 and S4B_276 mapped in Bin 1 and Bin 2.
  • Clones D13C27, D13C32, D13C37, S4A_18, S4B_39, S4B109B and S4B_142 mapped on a broad epitope encompassing Bin 1 , 2, 3 and 4 ( Figure 13B).
  • Two antibody clones, D12C1 and D13C1 were clones in the dual variable domain (DVD) architecture (Fig. 14).
  • Each antibody dilution was mixed 1 :1 with lentiviral vectors normalised to 1x10 5 physical particle of vectors pseudotyped with WT Wuhan glycoprotein, to a final volume of 200 pL and incubated at 37 °C for 1 h.
  • Antibody-virus mixtures were added to 3x10 4 HEK-293T (ACE2 + , TMPRSS2 + ) in 48-well plates and incubated for 72 h. Viral titers were then quantified by eGFP expression in target cells using BD LSRFORTESSA X- 20 cell analyser and infectivity of all fractions was determined as a percentage of viral titres in the PBS only control. As a control, the REGN10933/10987 cocktail and LY-CoV555 were evaluated against the same variants.
  • the D12C1 and D13C1 antibodies were able to neutralise SARS-CoV- 2 (Wuhan), with a dose-response curve demonstrating an EC50 of 4.7 and 7 nM, respectively.
  • a reduction in neutralisation was observed for D12C1 against the beta and delta variants, indicating susceptibility to the current mutational landscape.
  • a similar effect was observed with the REGN10933/10987 antibody cocktail.
  • D13C1 proved to be resistant to mutational drift in spike (Fig. 15B).
  • the DVD consistently showed better EC50 values across the variants, with a 61- and 21 -fold improvement over D12C1 for the beta and gamma variants, respectively, while maintaining neutralisation capacity against the delta variant.
  • IgG-scFv and scFv4-Fc two additional biparatopic antibody architectures: IgG-scFv and scFv4-Fc (Fig. 14).
  • the IgG-scFv, and scFv4-Fc constructs showed significantly improved EC50 values, compared to the DVD molecule, ranging between 0.9-5.1 and 0.5-2.7 nM against the Wuhan, alpha, beta and delta variants, respectively.
  • the scFv4-Fc construct showed the highest overall neutralisation, comparable to the REGN10933/10987 cocktail, against the Wuhan, alpha and gamma variants.
  • Binding affinities of the biparatopic constructs were further evaluated to recombinant S1 protein domains of the different variants. Binders were captured on flow cell 2 of a Series S Protein A sensor chip (Cytiva - 29127555), using a Biacore 8K instrument (Cytiva). HBS-P + bufferwas used as running buffer in all experimental conditions. Recombinant S1 at 250 nM with 2-fold serial dilutions, was used as the ‘analyte’ and injected over the flow channels with 150s contact time and 300s dissociation. All experiments were performed at 25°C with a flow rate of 30 pl/ml. Flow cell 1 was unmodified and used for reference subtraction.
  • the binding kinetics data indicates that the DVD biparatopic antibody construct was capable of consistently increasing the overall affinity to the Spike protein relative to the constituent antibodies, with a 4.4-fold increase for the delta variant compared to the parental D12C1 antibody, to 6.7 nM (Fig. 16, Table 7).
  • the IgG-scFv and the scFv4-Fc formats also showed greatly improved affinities for the SARS- CoV-2 S1 variants compared to the parental D12C1 and D13C1 IgG antibody formats, with up to 6.3-fold affinity increase for the IgG-scFv format and up to 9.7-fold improvement for the scFv4-Fc format (Table 9).
  • all biparatopic formats (DVD, IgG-scFv and scFv4-Fc) showed a greatly improved affinity profile for the omicron variant.
  • ScFv4-Fc biparatopic format of combinations of clone 84 and 152 (84-152 and 152-84 orientations) or 84 and 222 (84-222 and 222-84 orientations) also showed a greatly improved affinities towards Wuhan, alpha, beta gamma and delta S1 variants, with affinity improvements in excess of 10-fold and in the pM range ( Figure 17, Table 10).
  • Biparatopic formats also showed nM affinities for the Omicron variant, despite the loss of binding for the parental clone 84, highlighting the resistance to mutational escape (Figure 17 and Table 10).
  • Neutralisation efficiency of scFv4-Fc 84-152, 152-84, 84-222 and 222-84 against SARS-CoV-2 Wuhan, beta and delta pseudotyped lentiviral vectors was performed as described above. Each antibody dilution was mixed 1 :1 with lentiviral vectors normalised to 1x10 5 physical particle of vectors pseudotyped with WT Wuhan glycoprotein, to a final volume of 200 pL and incubated at 37 °C for 1 h. Antibody-virus mixtures were added to 3x10 4 HEK-293T (ACE2 + , TMPRSS2 + ) in 48-well plates and incubated for 72 h.
  • Viral titres were then quantified by eGFP expression in target cells using BD LSRFORTESSA X-20 cell analyser and infectivity of all fractions was determined as a percentage of viral titers in the PBS only control.
  • a 1 :1 antibody cocktail of REGN10933 and REGN10987 was used as control ( Figure 18). All biparatopic antibodies showed efficient neutralisation of pseudotyped viral infection with consistent performance across all variants tested. Of note, the scFv4-Fc biparatopic antibodies showed > 5-fold improvement in EC50 compared to the REGN cocktail for the beta variant.
  • Clones D12C1 , D13C1 , 84, 56, 152, 222 IgG antibodies, D12C1/D13C1 biparatopic antibody (DVD, IgG-Fc and scFv4-Fc) and scFv4-Fc antibodies 84-152, 152-84, 84-222 and 222-84 are tested at a range of concentrations with 4-fold serial dilutions in a SARS-CoV-2 pseudotyped lentiviral vector neutralisation assay against Wuhan and Omicron variants.
  • Each antibody dilution is mixed 1 :1 with lentiviral vectors normalised to 1x10 5 physical particle of vectors pseudotyped with WT Wuhan glycoprotein, to a final volume of 200 pL and incubated at 37 °C for 1 h.
  • Antibodyvirus mixtures are added to 3x10 4 HEK-293T (ACE2 + , TMPRSS2 + ) in 48-well plates and incubated for 72 h.
  • Viral titres are then quantified by eGFP expression in target cells using BD LSRFORTESSA X-20 cell analyser and infectivity of all fractions is determined as a percentage of viral titres in the PBS only control.
  • a 1 :1 antibody cocktail of REGN10933 and REGN10987 and the Ly-CoV555 antibody are used as control.
  • the total area of consolidated lung tissue was evaluated (dorsal and ventral perspective) with a photograph of the lungs and drawing during necropsy by a veterinary pathologist or trained veterinarian. A second evaluation was performed after the necropsy with the drawing and photos. The score represents mean of both evaluations.
  • the whole left side (one lobe) was evaluated and the percentage of affected lung tissue of the left lobe was graded (objective 2.5x or 5x in duplicate):
  • Swabs collected at DPI -4 were all negative for viral RNA.
  • sgRNA levels were significantly lower for D12/D13 scFv4-Fc group compared to PBS at DPI 9 and for D12C1/D13C1 antibody cocktail DP1 10 (two-way ANOVA with Dunnett’s post-test versus PBS group, * P ⁇ 0.05, ** P ⁇ 0.01).
  • CDRs are according to IMGT. CDRs are underlined
  • LCDR3 SEQ ID NO: 32 QVWDSSSDHPV
  • VH SEQ ID NO: 69 QITLKESGPTLVKPTQTLTLACTVSGFSLSTSGVGVGWIRQPPGKALEWLALIYWDDDQRYSPS
  • LCDR1 SEQ ID NO: 70 QNIGDY
  • VH SEQ ID NO: 77 QVTLRESGPALVKPTQTLTLTCTFSGFSLSTSGMCVNWIRQPPGKALEWLARIDWDDAKYYST
  • LCDR3 SEQ ID NO: 96 GTWDNSLSAGV
  • LCDR1 SEQ ID NO: 102 QDINHY
  • HCDR2 SEQ ID NO: 35 ISGNGGAI HCDR3 SEQ ID NO: 36 AKGYYYDDGGYSGREDAFDI
  • LCDR1 SEQ ID NO: 38 QGISNF
  • HCDR1 SEQ ID NO: 106 GITVSSNY HCDR2 SEQ ID NO: 107 IYSGGST
  • LCDR1 SEQ ID NO: 110 QSVSSSS

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Abstract

L'invention concerne des anticorps ou des fragments de liaison à l'antigène de ceux-ci qui se lient spécifiquement à la région de domaine de liaison au récepteur (RBD) de la protéine de spicule (S) du SARS-CoV-2. L'invention concerne en outre des méthodes de traitement ou de prévention d'une infection par le SARS-CoV-2 et des utilisations médicales associées des anticorps ou des fragments de liaison à l'antigène de ceux-ci.
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Citations (3)

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WO2021205184A1 (fr) * 2020-04-09 2021-10-14 Autolus Limited Polypeptide
WO2022122788A1 (fr) * 2020-12-09 2022-06-16 Institute For Research In Biomedicine Anticorps multispécifiques contre le coronavirus du syndrome respiratoire aigu sévère 2
WO2022136685A1 (fr) * 2020-12-23 2022-06-30 Vib Vzw Compositions d'anticorps pour traiter une infection par le virus corona

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Publication number Priority date Publication date Assignee Title
WO2021205184A1 (fr) * 2020-04-09 2021-10-14 Autolus Limited Polypeptide
WO2022122788A1 (fr) * 2020-12-09 2022-06-16 Institute For Research In Biomedicine Anticorps multispécifiques contre le coronavirus du syndrome respiratoire aigu sévère 2
WO2022136685A1 (fr) * 2020-12-23 2022-06-30 Vib Vzw Compositions d'anticorps pour traiter une infection par le virus corona

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