WO2023094980A1 - Antibodies to coronavirus - Google Patents

Antibodies to coronavirus Download PDF

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Publication number
WO2023094980A1
WO2023094980A1 PCT/IB2022/061257 IB2022061257W WO2023094980A1 WO 2023094980 A1 WO2023094980 A1 WO 2023094980A1 IB 2022061257 W IB2022061257 W IB 2022061257W WO 2023094980 A1 WO2023094980 A1 WO 2023094980A1
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WIPO (PCT)
Prior art keywords
sars
cov
seq
antibody
protein
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PCT/IB2022/061257
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French (fr)
Inventor
Emanuele ANDREANO
Ida PACIELLO
Noemi MANGANARO
Piero Pileri
Elisa PANTANO
Valentina ABBIENTO
Concetta DE SANTI
Claudia SALA
Rino Rappuoli
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Fondazione Toscana Life Sciences
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Publication of WO2023094980A1 publication Critical patent/WO2023094980A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • 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
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • 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
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • 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
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • Human monoclonal antibodies are provided by the present invention that have a potent neutralizing activity against SARS-CoV-2.
  • human monoclonal antibodies recognizing SARS-CoV-2 have been isolated from memory B cells of people previously exposed to SARS-CoV-2 infection and subsequently vaccinated with the COVID-19 BNT162b2 mRNA vaccine.
  • the invention relates to human monoclonal antibodies recognizing SARS-CoV-2 for their use in therapy, prophylaxis, and diagnosis of SARS-CoV-2 dependent diseases.
  • mAbs Human monoclonal antibodies
  • mAbs Human monoclonal antibodies
  • isolating and screening memory B cells allowed identification of highly potent neutralizing mAbs and further improvement of their potency. This possibility resulted in a decreased quantity of antibodies necessary for therapy thus making non- intravenous delivery of potent neutralizing mAbs possible.
  • mAbs have the possibility to become one of the first drugs that can be used for immediate therapy of any patient testing positive for the virus, and even to provide immediate protection from infection in high-risk populations.
  • Preliminary evidences show that plasma from infected subjects improves the outcome of patients with severe disease, therefore it is possible that a mAb-based therapy and/or prophylaxis be highly effective.
  • vaccination strategies inducing neutralizing antibodies have already shown to protect non-human primates from infection.
  • mAbs offer a series of advantages.
  • they are the ones that can be developed in the shortest period of time.
  • the extensive clinical experience with the safety of more than 50 commercial mAbs approved to treat cancer, inflammation and autoimmunity provides high confidence on their safety, support the possibility of having an accelerated regulatory pathway.
  • the long industrial experience in developing and manufacturing mAbs decreases the risks usually associated with technical development of investigational products.
  • the enormous technical progress in the field allows to shorten the conventional timelines and go from discovery to proof of concept trials in 5-6 months.
  • Several candidates are presently under development in the field of HIV, pandemic influenza, RSV and many other infectious diseases.
  • SARS-CoV-2 entry into host cells is mediated by the interaction between S-protein and the human angiotensin converting enzyme 2 (ACE2).
  • ACE2 human angiotensin converting enzyme 2
  • the S-protein is a trimeric class I viral fusion protein which exists as a metastable pre-fusion conformation and as a stable post-fusion conformation.
  • Each S-protein monomer is composed of two distinct regions, the SI and S2 subunits. Structural rearrangement occurs when the receptor binding domain (RBD) present in the SI subunit binds to the host cell membrane. This interaction destabilizes the pre-fusion state of the S-protein triggering the transition into the post-fusion conformation which in turn results in the entry of the virus particle into the host cell.
  • RBD receptor binding domain
  • Singlecell RNA-seq analyses evaluating the expression levels of ACE2 in different human organs has shown that SARS-CoV-2, through S-protein binding, can invade human cells in different major physiological systems including the respiratory, cardiovascular, digestive and urinary systems, enhancing the possibility of spreading and infection. Therefore, it is important to produce neutralizing mAbs or antigen-binding portion thereof that are effective to block the entry process of the virus. Accordingly, there remains an urgent need for potent, broad spectrum antibody therapeutics for use in treatment, prophylaxis, and diagnosis of Coronavirus, in particular SARS-CoV-2, dependent diseases. In particular, there remains an urgent need for monoclonal antibodies able to neutralize also the SARS-CoV-2 variants such as alpha, beta, gamma and delta variants.
  • the new isolated antibodies show a potent neutralization activity not only with the Wuhan variant, but also with all the emerging variants such as the Alpha, Beta, Gamma and Delta variants.
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein, wherein said antibody or antigenbinding portion thereof showing 100% inhibitory concentration (ICioo) of less than 25 ng/ml, preferably of less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS- CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma, preferably said in vitro neutralization assay is the CPE-MN assay.
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof according to claim 1, having an equilibrium dissociation constant (KD) of less than 6 pM against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Gamma, Delta and Kappa as measured by surface plasmon resonance (SPR).
  • KD equilibrium dissociation constant
  • S Spike
  • SPR surface plasmon resonance
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein said VH and VL comprise the following complementarity-determining regions (CDRs):
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof, comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein said VH having SEQ ID NO:7 and said VL having SEQ ID NO:8; or wherein said VH having SEQ ID NO:25 and said VL having SEQ ID NO:26; or wherein said VH having SEQ ID NO:43 and said VL having SEQ ID NO:44 or wherein said VH having SEQ ID NO:61 and said VL having SEQ ID NO:62.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof, wherein said VL and said VH is at least 90% identical in amino acid sequence, preferably at least 95%, more preferably at least 99% of
  • VH having SEQ ID NO:7 and said VL having SEQ ID NO:8;
  • VH having SEQ ID NO:25 and said VL having SEQ ID NO:26;
  • VH having SEQ ID NO:43 and said VL having SEQ ID NO:44 or VH having SEQ ID NO:61 and said VL having SEQ ID NO:62 in particular showing 100% inhibitory concentration (ICioo) of less than 25 ng/ml, preferably of less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS-CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma, wherein said in vitro neutralization assay is measured for example using the CPE-MN assay and/or having an equilibrium dissociation constant (KD) of less than 6 pM against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Gamma, Delta and Kappa as measured by surface plasmon resonance (SPR).
  • ICioo inhibitory concentration
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to a severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein wherein said antibody or antigen-binding portion thereof has one or more of the following characteristics: (a) neutralizing one or more of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and Delta with an IC100 of less than 25 ng/ml; (b) having an equilibrium dissociation constant (KD) against the Spike (S) protein of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and/or Delta of less than 6 E" 10 M; and/or (c) comprises three heavy chain complementarity determining regions (CDRs) (CDR-H1, CDR-H2, and CDR-H3) contained within a heavy chain variable region (VH) comprising an amino acid sequence having at least about 90% sequence identity to a VH of a monoclonal antibody selected
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the light chain variable domain (VL) and heavy chain variable domain (VH) of a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • VL light chain variable domain
  • VH heavy chain variable domain
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the CDRs of a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the VL and VH domains that are at least 85%, 90%, 95%, 97%, 98% or 99% identical in amino acid sequence to the VL and VH domains, respectively, of a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01
  • the invention provides human monoclonal antibodies or antigen-binding portion thereof that compete for the SARS-CoV-2 S-protein with any of the antibodies herein disclosed.
  • the invention provides human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed, for use in a prophylactic or therapeutic treatment of a viral infection or conditions or disorders resulting from such infection.
  • the invention provides human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed, for use in a prophylactic or therapeutic treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19).
  • the invention provides a method of preventing or treating the SARS-CoV- 2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19), comprising administering a human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed, to a subject in need thereof.
  • the invention further provides human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed for use in the diagnosis, prophylaxis and/or treatment of a subject having, or at risk of developing, a virus infection, in particular a coronavirus infection, more in particular SARS-CoV-2 infection, more in particular an infection of the SARS-CoV-2 variant Alpha, Beta, Delta or Gamma.
  • a virus infection in particular a coronavirus infection, more in particular SARS-CoV-2 infection, more in particular an infection of the SARS-CoV-2 variant Alpha, Beta, Delta or Gamma.
  • the invention pertains to the use of the human binding molecules and/or the nucleic acid molecules of the invention in the diagnosis/detection of such viral infections.
  • the invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising at least one or more human monoclonal antibodies or antigen-binding portions thereof according to any one of the embodiments herein disclosed and a pharmaceutically acceptable carrier and its use in the prevention and/or treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19).
  • the invention provides an isolated cell line that produces the antibody or antigen-binding portion thereof according to any one of the embodiments herein disclosed.
  • the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes the antibody or antigen-binding portion thereof according to any one of the embodiments herein disclosed.
  • the invention provides a vector comprising the nucleic acid molecule encoding the antibody or antigen-binding portion thereof embodiments according to any one of the embodiments herein disclosed, wherein the vector optionally comprises an expression control sequence operably linked to the nucleic acid molecule.
  • the invention provides a non-human transgenic animal or transgenic plant comprising the nucleic acid according to any one of the preceding embodiments, wherein the non- human transgenic animal or transgenic plant expresses said nucleic acid.
  • said non-human transgenic animal is a mammal.
  • the invention provides the use of the human monoclonal antibody or an antigen-binding portion thereof according to any one of the embodiments herein disclosed in the diagnosis of the SARS-CoV-2 infection.
  • the invention provides an in vitro method for revealing the presence of the SARS-CoV-2 in a sample comprising the following steps: i) Contacting the antibody or an antigen-binding portion thereof according to any one of the embodiments herein disclosed; ii) Detecting the binding of said antibody or an antigen-binding portion thereof to the S-protein of the SARS-CoV-2.
  • the invention provides an in vitro method for the diagnosis of the SARS- CoV-2 infection in a subject comprising the following steps: i) Contacting the antibody or an antigen-binding portion thereof according to any one of the embodiments herein disclosed with a biological sample of said subject; ii) Detecting the binding of said antibody or an antigen-binding portion thereof to the S-protein of the SARS-CoV-2.
  • the invention contemplates combinations of any of the foregoing aspects and embodiments of the invention.
  • the invention provides a method for the prevention or treatment a viral infection or conditions or disorders resulting from such infection in a subject, comprising administering a therapeutically effective amount of one or more of any of the antibodies or an antigen-binding portion thereof herein disclosed to said subj ect in need thereof.
  • a viral infection or conditions or disorders resulting from such infection in particular Coronavirus disease 2019 (COVID-19).
  • FIG. 1 Neutralization activity against SARS-CoV-2 and emerging variants.
  • A-D Graphs show the ability of mAbs 02M04 (A), 2H05 (B), 01023 (C), 01E15 (D) and S309 (E) to neutralize SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the CPE-MN assay. All experiments were performed in technical duplicates.
  • F The table summarizes the IC100 obtained for all tested antibodies.
  • FIG. 1 Binding affinity of 02M04 antibody to SARS-CoV-2 spike proteins.
  • A-E Graphs show the ability of mAbs 02M04 to bind the spike protein of the SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the surface plasmon resonance (SPR) assay.
  • SPR surface plasmon resonance
  • Figure 3 Binding affinity of 02H05 antibody to SARS-CoV-2 spike proteins.
  • A-E Graphs show the ability of mAbs 02H05 to bind the spike protein of the SARS-CoV-2 Wuhan, B.
  • A-E Graphs show the ability of mAbs 01E15 to bind the spike protein of the SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the surface plasmon resonance (SPR) assay.
  • SPR surface plasmon resonance
  • polypeptide encompasses native or artificial proteins, protein fragments and polypeptide analogues of a protein sequence.
  • a polypeptide may be monomeric or polymeric.
  • isolated protein is a protein, polypeptide or antibody that by virtue of its origin or source of derivation (1) is not associated with naturally associated components that accompany it in its native state, (2) is free of other proteins from the same species, (3) is expressed by a cell from a different species, or (4) does not occur in nature.
  • a polypeptide that is chemically synthesized or synthesized in a cellular system different from the cell from which it naturally originates will be “isolated” from its naturally associated components.
  • a protein may also be rendered substantially free of naturally-associated components by isolation, using protein purification techniques well known in the art.
  • isolated antibodies include an anti- SARS- CoV-2 S-protein antibody that has been affinity purified using SARS-CoV-2 S-protein or a portion thereof, an anti- SARS-CoV-2 S-protein antibody that has been synthesized by a hybridoma or other cell line in vitro, and a human anti- SARS-CoV-2 S-protein antibody derived from a transgenic animal.
  • a protein or polypeptide is "substantially pure", “substantially homogeneous", or “substantially purified” when at least about 60 to 75% of a sample exhibits a single polypeptide.
  • the polypeptide or protein may be monomeric or multimeric.
  • a substantially pure polypeptide or protein will typically comprise about 50%, 60%, 70%, 80% or 90% W/W of a protein sample, more usually about 95%, and preferably will be over 99% pure. Protein purity or homogeneity may be indicated by a number of means well known in the art, such as polyacrylamide gel electrophoresis of a protein sample, followed by visualizing a single polypeptide band upon staining the gel with a stain well known in the art. For certain purposes, higher resolution may be provided by using HPLC or other means well known in the art for purification.
  • polypeptide fragment refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion, but where the remaining amino acid sequence is identical to the corresponding positions in the naturally occurring sequence.
  • fragments are at least 5, 6, 8 or 10 amino acids long.
  • the fragments are at least 14, at least 20, at least 50, or at least 70, 80, 90, 100, 150 or 200 amino acids long.
  • polypeptide analogue refers to a polypeptide that comprises a segment that has substantial identity to a portion of an amino acid sequence and that has at least one of the following properties: (1) specific binding to SARS-CoV-2 S-protein under suitable binding conditions, (2) ability to inhibit SARS-CoV-2 S-protein.
  • polypeptide analogues comprise a conservative amino acid substitution (or insertion or deletion) with respect to the native sequence.
  • Analogues typically are at least 20 or 25 amino acids long, preferably at least 50, 60, 70, 80, 90, 100, 150 or 200 amino acids long or longer, and can often be as long as a full- length polypeptide.
  • polypeptide fragments or polypeptide analogue antibodies with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 substitutions from the germline amino acid sequence.
  • amino acid substitutions to an anti- SARS-CoV-2 S-protein antibody or antigen-binding portion thereof are those which: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity to form protein complexes, and (4) confer or modify other physicochemical or functional properties of such analogues, but still retain specific binding to SARS-CoV-2 S-protein.
  • Analogues can include various muteins of a sequence other than the normally occurring peptide sequence.
  • single or multiple amino acid substitutions may be made in the normally occurring sequence, preferably in the portion of the polypeptide outside the domain(s) forming intermolecular contacts.
  • a conservative amino acid substitution should not substantially change the structural characteristics of the parent sequence; e.g., a replacement amino acid should not alter the anti-parallel [beta]-sheet that makes up the immunoglobulin binding domain that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence.
  • glycine and proline would not be used in an anti-parallel [beta]-sheet.
  • SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2), the type of coronavirus that causes coronavirus disease 2019 (COVID-19), where an "antibody” is referred to herein with respect to the invention, it is normally understood that an antigen-binding portion thereof may also be used.
  • An antigen-binding portion competes with the intact antibody for specific binding. See generally, Fundamental Immunology, Ch. 7 (Paul, W., ed., second ed. Raven Press, N.Y. (1989)) (incorporated by reference in its entirety for all purposes).
  • Antigen-binding portions may be produced by recombinant DNA techniques or by enzymatic or chemical cleavage of intact antibodies.
  • antigen-binding portions include Fab, Fab', F(ab')2, Fd, Fv, dAb, and complementarity determining region (CDR) fragments, single-chain antibodies (scFv), chimeric antibodies, diabodies, nanobodies and any polypeptides that contain at least a portion of an antibody that is sufficient to confer specific antigen binding to the polypeptide.
  • CDR complementarity determining region
  • an antibody that is referred to by number is the same as a monoclonal antibody that is obtained from the human peripheral blood mononuclear cells (PBMCs) isolated from the donor of the same number.
  • PBMCs peripheral blood mononuclear cells
  • MAD1005M04 or abbreviated as 02M04 is the same antibody as one obtained from PBMCs isolated from subject identified by the code, or a subclone thereof.
  • a Fd fragment means an antibody fragment that consists of the VH and CH 1 domains; an Fv fragment consists of the VL and VH domains of a single arm of an antibody; and a dAb fragment (Ward et al, Nature 341 :544-546 (1989)) consists of a VH domain.
  • the antibody is a single-chain antibody (scFv) in which a VL and VH domains are paired to form a monovalent molecule via a synthetic linker that enables them to be made as a single protein chain.
  • scFv single-chain antibody
  • the antibodies are diabodies, i.e., are bivalent antibodies in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites.
  • a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites.
  • the CDR(s) may be incorporated as part of a larger polypeptide chain, may be covalently linked to another polypeptide chain, or may be incorporated noncovalently.
  • the binding sites may be identical to one another or may be different.
  • human antibody means any antibody in which the variable and constant domain sequences are human sequences or any of the CDRs of the variable domain sequences are human sequences.
  • the term encompasses antibodies with sequences derived from human genes, but which have been changed, e.g. to decrease possible immunogenicity, increase affinity, eliminate cysteine that might cause undesirable folding, etc.
  • the term encompasses such antibodies produced recombinant in non-human cells, which might impart glycosylation not typical of human cells.
  • chimeric antibody as used herein means an antibody that comprises regions from two or more different antibodies.
  • epitope includes any protein determinant capable of specific binding to an immunoglobulin or T-cell receptor or otherwise interacting with a molecule.
  • Epitopes or antigenic determinants generally consist of chemically active surface groupings of molecules such as amino acids or carbohydrate or sugar side chains and generally have specific three- dimensional structural characteristics, as well as specific charge characteristics.
  • An epitope may be "linear” or “conformational.” In a linear epitope, all of the points of interaction between the protein and the interacting molecule (such as an antibody) occur linearly along the primary amino acid sequence of the protein. In a conformational epitope, the points of interaction occur across amino acid residues on the protein that are separated from one another.
  • a “neutralizing antibody”, an antibody with “neutralizing activity”, as used herein means an antibody that neutralizes a biological effect that its target (e.g., a pathogen or an infectious particle) may have.
  • a “neutralizing antibody”, an antibody with “neutralizing activity”, as used herein is for example an antibody or antigen-binding portion thereof showing a 100% inhibitory concentration (ICioo) of at least less than 25 ng/ml, preferably less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS-CoV-2 virus. ICioo is measured preferably using the CPE-MN assay as disclosed for example in Andreano et al. Cell 184, 1821- 1835.el816 (2021).
  • an antibody is said to specifically bind an antigen when the dissociation constant is for example ⁇ 1 mM, preferably ⁇ 100 nM and most preferably ⁇ 10 nM.
  • the dissociation constant may be measured by any of the methods available in the state of the art as for example using enzyme-linked immunosorbent assay (ELISAs), radioimmunoassay (RIAs), flow cytometry, surface plasmon resonance, such as BIACORE(TM).
  • polynucleotide as referred to herein means a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxyribonucleotides or a modified form of either type of nucleotide.
  • the term includes single and double stranded forms.
  • isolated polynucleotide as used herein means a polynucleotide of genomic, cDNA, or synthetic origin or some combination thereof, which by virtue of its origin the "isolated polynucleotide” (1) is not associated with all or a portion of a polynucleotides with which the "isolated polynucleotide” is found in nature, (2) is operably linked to a polynucleotide to which it is not linked in nature, or (3) does not occur in nature as part of a larger sequence.
  • nucleotides as used herein includes deoxyribonucleotides and ribonucleotides.
  • modified nucleotides as used herein includes nucleotides with modified or substituted sugar groups and the like.
  • oligonucleotide linkages referred to herein includes oligonucleotides linkages such as phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phoshoraniladate, phosphoroamidate, and the like. See e.g., LaPlanche et al., Nucl. Acids Res.
  • oligonucleotide can include a label for detection, if desired.
  • “Operably linked” sequences include both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
  • expression control sequence means polynucleotide sequences that are necessary to affect the expression and processing of coding sequences to which they are ligated. Expression control sequences include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance protein secretion.
  • control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include promoter, ribosomal binding site, and transcription termination sequence; in eukaryotes, generally, such control sequences include promoters and transcription termination sequence.
  • control sequences is intended to include, at a minimum, all components whose presence is essential for expression and processing, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences.
  • vector as used herein, means a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • the vector is a plasmid, i.e., a circular double stranded piece of DNA into which additional DNA segments may be ligated.
  • the vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome.
  • the vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • the vectors e.g., non-episomal mammalian vectors
  • certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply, "expression vectors").
  • recombinant host cell means a cell into which a recombinant expression vector has been introduced. It should be understood that "recombinant host cell” and “host cell” mean not only the particular subject cell but also the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein.
  • sequence identity in the context of nucleotide or aminoacidic sequences means the residues in two sequences that are the same when aligned for maximum correspondence.
  • the length of sequence identity comparison may be over a stretch of at least about nine nucleotides, usually at least about 18 nucleotides, more usually at least about 24 nucleotides, typically at least about 28 nucleotides, more typically at least about 32 nucleotides, and preferably at least about 36, 48 or more nucleotides.
  • polynucleotide sequences can be compared using FASTA, Gap or Bestfit, which are programs available, provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences (Pearson, Methods Enzymol. 183:63-98 (1990); Pearson, Methods Mol. Biol. 132: 185-219 (2000); Pearson, Methods Enzymol. 266:227-258 (1996); Pearson, J Mol. Biol 276:71-84 (1998); incorporated herein by reference).
  • nucleic acid or fragment thereof, or aminoacidic when referring to a nucleic acid or fragment thereof, or aminoacidic means that when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 85%, preferably at least about 90%, and more preferably at least about 95%, 96%, 97%, 98% or 99% of the nucleotide bases, as measured by any well-known algorithm of sequence identity, such as FASTA, BLAST or Gap, as discussed above.
  • the term "substantial identity” means that two peptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights as supplied with the programs, share at least 70%, 75% or 80% sequence identity, preferably at least 90% or 95% sequence identity, and more preferably at least 97%, 98% or 99% sequence identity.
  • residue positions that are not identical differ by conservative amino acid substitutions.
  • a "conservative amino acid substitution” is one in which an amino acid residue is substituted by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or hydrophobicity). In general, a conservative amino acid substitution will not substantially change the functional properties of a protein.
  • the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well- known to those of skill in the art. See, e.g., Pearson, Methods Mol. Biol. 243 :307-31 (1994).
  • Examples of groups of amino acids that have side chains with similar chemical properties include 1) aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine; 2) aliphatic- hydroxyl side chains: serine and threonine; 3) amide-containing side chains: asparagine and glutamine; 4) aromatic side chains: phenylalanine, tyrosine, and tryptophan; 5) basic side chains: lysine, arginine, and histidine; 6) acidic side chains: aspartic acid and glutamic acid; and 7) sulphur-containing side chains: cysteine and methionine.
  • Conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, glutamate-aspartate, and asparagine-glutamine.
  • a conservative replacement is any change having a positive value in the PAM250 log-likelihood matrix disclosed in Gonnet et al, Science 256: 1443-45 (1992), incorporated herein by reference.
  • a “moderately conservative” replacement is any change having a nonnegative value in the PAM250 log-likelihood matrix. Sequence identity for polypeptides is typically measured using sequence analysis software.
  • Protein analysis software matches sequences using measures of similarity assigned to various substitutions, deletions and other modifications, including conservative amino acid substitutions.
  • GCG contains programs such as "Gap” and "Bestfit” which can be used with default parameters as specified by the programs to determine sequence homology or sequence identity between closely related polypeptides, such as homologous polypeptides from different species of organisms or between a wild type protein and a mutein thereof.
  • the terms “label” or “labelled” refers to incorporation of another molecule in the antibody.
  • the label is a detectable marker, e.g., incorporation of a radiolabelled amino acid or attachment to a polypeptide of biotinyl moieties that can be detected by marked avidin (e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods).
  • the label or marker can be therapeutic, e.g., a drug conjugate or toxin.
  • Various methods of labelling polypeptides and glycoproteins are known in the art and may be used.
  • variant of SARS-CoV-2 refers to viruses with one or more mutations that differentiate it from other variants of the SARS-CoV-2 viruses.
  • SARS-CoV-2 variant are Wuhan virus, B.l.1.7 (alpha, isolated in the United Kingdom), B.1.351 (beta, isolated in South Africa), B.1.1.248 (gamma, isolated in Brazil) and B.1.617.2 (delta, isolated in India).
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein characterized in that is capable of neutralizing one or more of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and Delta with an ICioo of less than 25 ng/ml, preferably the ICioo is measured by CPE-MN assay.
  • SARS severe acute respiratory syndrome
  • SARS-CoV-2 Corona Virus 2
  • S Spike
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein characterized in that having an equilibrium dissociation constant (KD) against the Spike (S) protein of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and Delta of less than 6 E' 10 M, preferably of less than 4, 3, 2, 1 E' 10 M, the KD is measured for example by surface plasmon resonance assay.
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein characterized in that is capable of neutralizing the SARS-CoV-2 variant Alpha with an ICioo of less than 6.0 ng/ml and/or the SARS-CoV-2 variant Beta with an ICioo of less than 4.0 ng/ml and/or the SARS-CoV-2 variant Gamma with an ICioo of less than 3.0 ng/ml and/or the SARS-CoV-2 variant Delta with an ICioo of less than 7.0 ng/ml, preferably the ICioo is measured by CPE-MN assay, more preferably said human monoclonal antibody or antigen-binding portion thereof having a VL and VH with at least 90% identical in amino acid sequence, preferably at least 95%, more preferably at least 99% with the VH
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof having an equilibrium dissociation constant (KD) of less than 6 pM6 E' 10 M, preferably of less than 4, 3, 2, 1 E' 10 M, against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma as measured by surface plasmon resonance (SPR).
  • KD equilibrium dissociation constant
  • S Spike
  • SPR surface plasmon resonance
  • the amino acidic sequence of the VH and VL of said human monoclonal antibody or antigen-binding portion thereof is at least 90% identical in amino acid sequence, preferably at least 95%, more preferably at least 99% of the VH an VL of the sequence of the antibody selected from MAD1005M04 or MAD1005H05 or MAD 1009023 or MAD1006E15.
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising: (a) a heavy chain variable domain amino acid sequence that comprises the amino acid sequence of the heavy chain variable domain of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); (b) a light chain variable domain amino acid sequence that comprises the amino acid sequence of the light chain variable domain of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); (c) a heavy chain variable domain of (a)
  • the invention provides a monoclonal antibody or an antigen-binding portion thereof that specifically binds human SARS-CoV-2 S-protein, comprising: (a) a heavy chain variable domain amino acid sequence that comprises the heavy chain CDR1 , CDR2 and CDR3 amino acid sequences of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); (b) a light chain variable domain amino acid sequence that comprises the light chain CDR1 , CDR2 and CDR3 amino acid sequences of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED
  • the invention provides a monoclonal antibody or an antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein, wherein the antibody comprises FR1, FR2, FR3 and FR4 amino acid sequences from an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the invention provides a monoclonal antibody that specifically binds SARS-CoV-2 S-protein, wherein said antibody comprises a heavy chain of an antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the invention provides a monoclonal antibody that specifically binds SARS-CoV-2 S-protein, wherein said antibody comprises a light chain of an antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the invention provides a monoclonal antibody that specifically binds SARS-CoV-2 S-protein, wherein said antibody comprises a heavy chain and a light chain of the same antibody which is selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising VL and VH domains that are at least 85%, 90%, 95%, 97%, 98% or 99% identical in amino acid sequence to the VL and VH domains, respectively, of a monoclonal antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • a monoclonal antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15)
  • the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the light chain and the heavy chain that are at least 85%, 90%, 95%, 97%, 98% or 99% identical in amino acid sequence to the light chain and the heavy chain, respectively, of a monoclonal antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • a monoclonal antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15)
  • One type of amino acid substitution that may be made is to change one or more cysteines in the antibody, which may be chemically reactive, to another residue, such as, without limitation, alanine or serine.
  • the substitution can be made in a CDR or framework region of a variable domain or in the constant domain of an antibody.
  • the cysteine is canonical.
  • Another type of amino acid substitution that may be made is to change any potential proteolytic sites in the antibody. Such sites may occur in a CDR or framework region of a variable domain or in the constant domain of an antibody.
  • substitution of cysteine residues and removal of proteolytic sites may decrease the risk of any heterogeneity in the antibody product and thus increase its homogeneity.
  • Another type of amino acid substitution is to eliminate asparagine-glycine pairs, which form potential deamidation sites, by altering one or both of the residues.
  • the C-terminal lysine of the heavy chain of the anti SARS-CoV-2 S-protein antibody of the invention is cleaved.
  • the heavy and light chains of the anti-SARS-CoV-2 S-protein antibodies may optionally include a signal sequence.
  • the class and subclass of anti-SARS-CoV-2 S-protein antibodies may be determined by any method known in the art.
  • the class and subclass of an antibody may be determined using antibodies that are specific for a particular class and subclass of antibody. Such antibodies are commercially available.
  • the class and subclass can be determined by ELISA, or Western blot (immunoblot) as well as other techniques.
  • the class and subclass may be determined by sequencing all or a portion of the constant domains of the heavy and/or light chains of the antibodies, comparing their amino acid sequences to the known amino acid sequences of various class and subclasses of immunoglobulins, and determining the class and subclass of the antibodies.
  • the human anti-SARS-CoV-2 S-protein antibody is an IgG, an IgM, an IgE, an IgA, or an IgD molecule.
  • the human anti-SARS-CoV-2 S- protein antibody is an IgG and is an IgGl, IgG2, IgG3, IgG4 subclass. In still another embodiment, the human antibody subclass is IgGl.
  • the anti-SARS-CoV-2 S-protein antibodies bind to SARS-CoV-2 S-protein with high affinity. In some embodiments, the anti-SARS-CoV-2 S- protein antibodies bind with high affinity to the SI domain of SARS-CoV-2 S-protein. In some embodiments, the anti-SARS-CoV-2 S-protein antibodies bind to the S2 domain of SARS-CoV-2 S-protein. In another embodiment, the anti-SARS-CoV-2 S-protein antibody binds to SARS-CoV S-protein.
  • the binding affinity and dissociation rate of an anti-SARS- CoV-2 S-protein antibody to SARS-CoV-2 S-protein can be determined by methods known in the art.
  • the binding affinity can be measured by ELISAs, RIAs, flow cytometry, surface plasmon resonance, such as BIACORE(TM).
  • the dissociate rate can be measured by surface plasmon resonance.
  • the binding affinity and dissociation rate is measured by surface plasmon resonance. More preferably, the binding affinity and dissociation rate are measured using BIACORE(TM).
  • Example V exemplifies a method for determining affinity constants of anti-SARS-CoV- 2 S-protein monoclonal antibodies.
  • the invention provides a human anti-SARS-CoV-2 S-protein monoclonal antibody that binds to SARS-CoV-2 S-protein and competes or cross-competes with and/or binds the same epitope as an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) . If two antibodies reciprocally compete with each other for binding to SARS-CoV-2 S-protein, they are said to crosscompete.
  • test antibody if the test antibody is not able to bind to SARS-CoV-2 S-protein at the same time, then the test antibody binds to the same epitope, an overlapping epitope, or an epitope that is in close proximity to the epitope bound by the human anti-SARS-CoV-2 S-protein antibody, or the binding of the human anti-SARS-CoV-2 S-protein antibody may induce a conformational change in the SARS-CoV-2 S-protein that prevents or reduces binding of the test antibody.
  • This experiment can be performed using ELISA, RIA, BIACORE(TM), flow cytometry or other methods known in the art.
  • the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases SARS-CoV-2 S-protein binding to a receptor, in particular, to angiotensin-converting enzyme 2 (ACE2).
  • ACE2 angiotensin-converting enzyme 2
  • the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases SARS-CoV-2 S- protein-mediated viral entry into cells.
  • the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases fusion of viral and cell membranes.
  • the invention provides an anti-SARS-CoV-2 S- protein antibody that decreases viral load.
  • the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases in severity for any period of time symptoms or conditions resulting from SARS-CoV-2 infection.
  • the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases in severity for a day, a week, a month, 6 months, a year, or for the remainder of the subjects’ life symptoms or conditions resulting from SARS-CoV-2 infection by 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%.
  • the invention provides an anti-SARS-CoV-2 S-protein antibody that may perform any combination of the preceding embodiments.
  • the mAb constant region of the antibodies is modified for half-life extension and reduced risk of Antibody-Dependent Enhancement (ADE) of disease.
  • AD Antibody-Dependent Enhancement
  • two different and alternative sets of mutations into their constant domains may be applied.
  • mutations that abrogate binding to Fc receptors will be introduced in the Fc part of the IgGl molecule as previously described (L234A/L235A as in Hezareh et al., 2001; Beltramello et al., 2010; P329G LALA as in Schlothauer et al., 2016). All of these modifications may be carried out by means of site-directed mutagenesis, for example using the Agilent Quick-Change II Site-Directed Mutagenesis Kit, according to the manufacturer’s recommendations.
  • the antibody comprises the variable regions of an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) and a mutant IgGl constant region backbone, which contains one or more of the following groups of mutations: L234A/L235A (as in Hezareh et al., 2001; Beltramello et al., 2010), P329G (as in Schlothauer et al., 2016); M428L/N434S (as in Zalevsky et al., 2010).
  • the antibody comprises the variable regions of an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) and a mutant IgGl constant region backbone, which contains all three groups of such mutations.
  • the present invention also encompasses nucleic acid molecules encoding anti- SARS-CoV- 2 S-protein antibodies or antigen-binding portions thereof.
  • different nucleic acid molecules encode a heavy chain and a light chain of an anti-SARS-CoV-2 S- protein immunoglobulin.
  • the same nucleic acid molecule encodes a heavy chain and a light chain of an anti-SARS-CoV-2 S-protein immunoglobulin.
  • the nucleic acid encodes a SARS-CoV-2 S-protein antibody, or antigenbinding portion thereof, of the invention.
  • the nucleic acid molecule comprises a nucleotide sequence that encodes a VL amino acid sequence comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 conservative amino acid substitutions and/or 1, 2, or 3 non- conservative substitutions compared to germline. Substitutions may be in the CDR regions, the framework regions, or in the constant domain.
  • the nucleic acid molecule encodes a VL amino acid sequence comprising one or more variants compared to germline sequence that are identical to the variations found in the VL of one of the antibodies selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the nucleic acid molecule encodes at least three amino acid substitutions compared to the germline sequence found in the VL of one of the antibodies selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • the nucleic acid molecule comprises a nucleotide sequence that encodes the VL amino acid sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or a variant or portion thereof.
  • the nucleic acid encodes an amino acid sequence comprising the light chain CDRs of one of said above-listed antibodies.
  • said portion is a contiguous portion comprising CDR1-CDR3.
  • the nucleic acid encodes the amino acid sequence of the light chain CDRs of said antibody. In some embodiments, said portion encodes a contiguous region from CDR1-CDR3 of the light chain of an anti-SARS-CoV-2 S-protein antibody.
  • the nucleic acid molecule encodes a VL amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to a VL amino acid sequence of a VL region of any one of antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • Nucleic acid molecules of the invention include nucleic acids that hybridize under highly stringent conditions, such as those described above, to a nucleotide sequence encoding the amino acid sequence of a VL region.
  • the nucleic acid encodes a full-length light chain of an antibody selected MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or a light chain comprising a mutation, such as one disclosed herein.
  • the nucleic acid molecule encodes the variable domain of the heavy chain (VH) that comprises a human VH1, VH3 or VH4 family gene sequence or a sequence derived therefrom.
  • the nucleic acid molecule encodes one or more amino acid mutations compared to the germline sequence that are identical to amino acid mutations found in the VH of one of monoclonal antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15).
  • the nucleic acid molecule comprises a nucleotide sequence that encodes at least a portion of the VH amino acid sequence of a monoclonal antibody selected from monoclonal antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) all three CDR regions, a contiguous portion including CDR1 -CDR3, or the entire VH region, with or without a signal sequence.
  • a monoclonal antibody selected from monoclonal antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) all three CDR regions, a contiguous portion including C
  • the nucleic acid molecule comprises a nucleotide sequence that encodes the amino acid sequence of one of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or said sequence lacking the signal sequence.
  • the nucleic acid molecule comprises at least a portion of the nucleotide sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or said sequence lacking the signal sequence.
  • said portion encodes the VH region (with or without a signal sequence), a CDR3 region, all three CDR regions, or a contiguous region including CDR1-CDR3.
  • the nucleic acid molecule encodes a VH amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the VH amino acid sequences of any one of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
  • Nucleic acid molecules of the invention include nucleic acids that hybridize under highly stringent conditions, such as those described above, to a nucleotide sequence encoding the amino acid sequence ofMAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or that encodes a VH region thereof.
  • the nucleic acid encodes a full-length heavy chain of an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or a heavy chain having the amino acid sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) with or without a signal sequence, or a heavy chain comprising a mutation, such as one of the variants discussed herein.
  • the nucleic acid may comprise the nucleotide sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) with or without a signal sequence, or a nucleic acid molecule encoding a heavy chain comprising a mutation, such as one of the variants discussed herein.
  • a nucleic acid molecule encoding the heavy or light chain of an anti-SARS-CoV-2 S-protein antibody or portions thereof can be isolated from any source that produces such antibody.
  • the nucleic acid molecules are isolated from a B cell isolated from an animal immunized with SARS-CoV-2 S-protein or from an immortalized cell derived from such a B cell that expresses or encodes an anti-SARS-CoV-2 S-protein antibody.
  • Methods of isolating mRNA encoding an antibody are well known in the art. See, e.g., Sambrook et al. The mRNA may be used to produce cDNA for use in the polymerase chain reaction (PCR) or cDNA cloning of antibody genes.
  • the nucleic acid molecule is isolated from a hybridoma that has as one of its fusion partners a human immunoglobulin- producing cell from a non-human transgenic animal.
  • the human immunoglobulin producing cell is isolated from a XENOMOUSE animal.
  • the human immunoglobulin-producing cell is from a non-human, nonmouse transgenic animal, as described above.
  • the nucleic acid is isolated from a non-human, non-transgenic animal.
  • the nucleic acid molecules isolated from a non-human, non-transgenic animal may be used, e.g., for humanized antibodies.
  • a nucleic acid encoding a heavy chain of an anti-SARS-CoV-2 S-protein antibody of the invention can comprise a nucleotide sequence encoding a VH domain of the invention joined in-frame to a nucleotide sequence encoding a heavy chain constant domain from any source.
  • a nucleic acid molecule encoding a light chain of an anti-SARS- CoV-2 S-protein antibody of the invention can comprise a nucleotide sequence encoding a VL domain of the invention joined in-frame to a nucleotide sequence encoding a light chain constant domain from any source.
  • nucleic acid molecules encoding the variable domain of the heavy (VH) and/or light (VL) chains are "converted" to full-length antibody genes.
  • nucleic acid molecules encoding the VH or VL domains are converted to full-length antibody genes by insertion into an expression vector already encoding heavy chain constant (CH) or light chain constant (CL) domains, respectively, such that the VH segment is operatively linked to the CH segment(s) within the vector, and/or the VL segment is operatively linked to the CL segment within the vector.
  • CH heavy chain constant
  • CL light chain constant
  • nucleic acid molecules encoding the VH and/or VL domains are converted into full-length antibody genes by linking, e.g., ligating, a nucleic acid molecule encoding a VH and/or VL domains to a nucleic acid molecule encoding a CH and/or CL domain using standard molecular biological techniques.
  • Nucleotide sequences of human heavy and light chain immunoglobulin constant domain genes are known in the art. See, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed., NIH Publ. No. 91- 3242, 1991.
  • Nucleic acid molecules encoding the full-length heavy and/or light chains may then be expressed from a cell into which they have been introduced and the anti-SARS-CoV- 2 S-protein antibody isolated.
  • the nucleic acid molecules may be used to recombinantly express large quantities of anti- SARS-CoV-2 S-protein antibodies.
  • the nucleic acid molecules also may be used to produce chimeric antibodies, bispecific antibodies, single chain antibodies, immunoadhesins, diabodies, mutated antibodies and antibody derivatives, as described further below. If the nucleic acid molecules are derived from a non-human, non-transgenic animal, the nucleic acid molecules may be used for antibody humanization, also as described below.
  • a nucleic acid molecule of the invention is used as a probe or PCR primer for a specific antibody sequence.
  • the nucleic acid can be used as a probe in diagnostic methods or as a PCR primer to amplify regions of DNA that could be used, inter alia, to isolate additional nucleic acid molecules encoding variable domains of anti- SARS-CoV-2 S-protein antibodies.
  • the nucleic acid molecules are oligonucleotides. In some embodiments, the oligonucleotides are from highly variable domains of the heavy and light chains of the antibody of interest.
  • the oligonucleotides encode all or a part of one or more of the CDRs of antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or variants thereof as described herein.
  • the nucleic acid molecules herein disclosed may be DNA or RNA molecules.
  • the invention provides vectors comprising nucleic acid molecules that encode the heavy chain of an anti-SARS-CoV-2 S-protein antibody of the invention or an antigen-binding portion thereof.
  • the invention also provides vectors comprising nucleic acid molecules that encode the light chain of such antibodies or antigen-binding portion thereof.
  • the invention further provides vectors comprising nucleic acid molecules encoding fusion proteins, modified antibodies, antibody fragments, and probes thereof.
  • the anti- SARS-CoV-2 S-protein antibodies or antigen-binding portions of the invention are expressed by inserting DNAs encoding partial or full-length light and heavy chains, obtained as described above, into expression vectors such that the genes are operatively linked to necessary expression control sequences such as transcriptional and translational control sequences.
  • Expression vectors include plasmids, retroviruses, adenoviruses, adeno- associated viruses (AAV), plant viruses such as cauliflower mosaic virus, tobacco mosaic virus, cosmids, YACs, EBV derived episomes, and the like.
  • the antibody gene is ligated into a vector such that transcriptional and translational control sequences within the vector serve their intended function of regulating the transcription and translation of the antibody gene.
  • the expression vector and expression control sequences are chosen to be compatible with the expression host cell used.
  • the antibody light chain gene and the antibody heavy chain gene can be inserted into separate vectors. In one embodiment, both genes are inserted into the same expression vector.
  • the antibody genes are inserted into the expression vector by standard methods (e.g., ligation of complementary restriction sites on the antibody gene fragment and vector, or blunt end ligation if no restriction sites are present).
  • a convenient vector is one that encodes a functionally complete human CH or CL immunoglobulin sequence, with appropriate restriction sites engineered so that any VH or VL sequence can easily be inserted and expressed, as described above.
  • splicing usually occurs between the splice donor site in the inserted J region and the splice acceptor site preceding the human C domain, and also at the splice regions that occur within the human CH exons. Polyadenylation and transcription termination occur at native chromosomal sites downstream of the coding regions.
  • the recombinant expression vector also can encode a signal peptide that facilitates secretion of the antibody chain from a host cell.
  • the antibody chain gene may be cloned into the vector such that the signal peptide is linked in-frame to the amino terminus of the immunoglobulin chain.
  • the signal peptide can be an immunoglobulin signal peptide or a heterologous signal peptide (i.e. a signal peptide from a non -immunoglobulin protein).
  • the recombinant expression vectors of the invention carry regulatory sequences that control the expression of the antibody chain genes in a host cell.
  • regulatory sequences for mammalian host cell expression include viral elements that direct high levels of protein expression in mammalian cells, such as promoters and/or enhancers derived from retroviral LTRs, cytomegalovirus (CMV) (such as the CMV promoter/enhancer), Simian Virus 40 (SV40) (such as the SV40 promoter/enhancer), adenovirus, (e.g.
  • CMV cytomegalovirus
  • SV40 Simian Virus 40
  • adenovirus e.g.
  • AdMLP adenovirus major late promoter
  • polyoma adenovirus major late promoter
  • strong mammalian promoters such as native immunoglobulin and actin promoters.
  • AdMLP adenovirus major late promoter
  • Methods for expressing antibodies in plants, including a description of promoters and vectors, as well as transformation of plants is known in the art. See, e.g., United States Patent 6,517,529, incorporated herein by reference.
  • the recombinant expression vectors of the invention may carry additional sequences, such as sequences that regulate replication of the vector in host cells (e.g., origins of replication) and selectable marker genes.
  • the selectable marker gene facilitates selection of host cells into which the vector has been introduced (see e.g., U.S. Patent Nos. 4,399,216, 4,634,665 and 5,179,017, incorporated herein by reference).
  • the selectable marker gene confers resistance to drugs, such as G418, hygromycin or methotrexate, on a host cell into which the vector has been introduced.
  • Preferred selectable marker genes include the dihydrofolate reductase (DHFR) gene (for use in dhfir- host cells with methotrexate selection/amplification), the neo gene (for G418 selection), and the glutamate synthetase gene.
  • DHFR dihydrofolate reductase
  • said vector is a selected from RNA virus vectors, DNA virus vectors, plasmid viral vectors, adenovirus vectors, adenovirus associated virus vectors, herpes virus vectors and retrovirus vectors.
  • the invention provides compositions (e.g., pharmaceutical compositions), methods, kits and reagents, comprising an isolated nucleic acid molecules according or a vectors according to any one of the embodiments herein disclosed for use in the prevention and/or treatment of a SARS-CoV-2 infections, in particular in humans and other mammals.
  • nucleic acid molecules and vectors are formulated in a nanoparticle, for example in lipid nanoparticle, cationic lipid nanoparticle, examples of such formulations can be found in US2020197510 herein incorporated by reference.
  • Nucleic acid molecules encoding anti-SARS-CoV-2 S-protein antibodies and vectors comprising these nucleic acid molecules can be used for transfection or transformation of a suitable mammalian, plant, bacterial or yeast host cell. Transfection or 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, 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 (see, e.g., U.S. Patent Nos. 4,399,216, 4,912,040, 4,740,461, and 4,959,455, incorporated herein by reference).
  • Methods for transforming plant cells are well known in the art, including, e.g., Agrobacterium- mediated transformation, biolistic transformation, direct injection, electroporation and viral transformation.
  • Methods for transforming bacterial and yeast cells are also well known in the art.
  • Mammalian cell lines available as hosts for expression are well known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC).
  • ATCC American Type Culture Collection
  • CHO cells Chinese hamster ovary (CHO) cells, N50 cells, SP2 cells, HEK-293T cells, NH4-3T3 cells, HeLa cells, baby hamster kidney (BHK) cells, African green monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), A549 cells, and a number of other cell lines.
  • Cell lines of particular preference are selected through determining which cell lines have high expression levels.
  • Other cell lines that may be used are insect cell lines, such as Sf9 or Sf21 cells.
  • the antibodies When recombinant expression vectors encoding antibody genes are introduced into mammalian host cells, the antibodies are produced by culturing the host cells for a period of time sufficient to allow for expression of the antibody in the host cells or, more preferably, secretion of the antibody into the culture medium in which the host cells are grown. Antibodies can be recovered from the culture medium using standard protein purification methods.
  • Plant host cells include, e.g., Nicotiana, Arabidopsis, duckweed, corn, wheat, potato, etc.
  • Bacterial host cells include E. coli and Streptomyces species.
  • Yeast host cells include Schizosaccharomyces pombe, Saccharomyces cerevisiae and Pichia pastoris.
  • the glutamine synthetase gene expression system (the GS system) is a common approach for enhancing expression under certain conditions.
  • the GS system is discussed in whole or part in connection with European Patent Nos. 0216 846, 0 256 055, 0 323 997 and 0338 841. It is likely that antibodies expressed by different cell lines or in transgenic animals will have different glycosylation from each other. However, all antibodies encoded by the nucleic acid molecules provided herein, or comprising the amino acid sequences provided herein are part of the instant invention, regardless of the glycosylation of the antibodies.
  • Anti-SARS-CoV-2 S-protein antibodies of the invention also can be produced transgenically through the generation of a mammal or plant that is transgenic for the immunoglobulin heavy and light chain sequences of interest and production of the antibody in a recoverable form therefrom.
  • anti-SARS-CoV-2 S- protein antibodies can be produced in, and recovered from, the milk of goats, cows, or other mammals. See, e.g., U.S. Patent Nos. 5,827,690, 5,756,687, 5,750,172, and 5,741,957, incorporated herein by reference.
  • non- human transgenic animals that comprise human immunoglobulin loci are immunized with SARS-CoV-2 S-protein or an immunogenic portion thereof, as described above.
  • Methods for making antibodies in plants are described, e.g., in U.S. patents 6,046,037 and 5,959,177, incorporated herein by reference.
  • non-human transgenic animals or plants are produced by introducing one or more nucleic acid molecules encoding an anti-SARS-CoV-2 S-protein antibody of the invention into the animal or plant by standard transgenic techniques. See Hogan and United States Patent 6,417,429, supra.
  • the transgenic cells used for making the transgenic animal can be embryonic stem cells or somatic cells or a fertilized egg.
  • the transgenic non- human organisms can be chimeric, nonchimeric heterozygotes, and nonchimeric homozygotes. See, e.g., Hofian et al.
  • the transgenic non-human animals have a targeted disruption and replacement by a targeting construct that encodes a heavy chain and/or a light chain of interest.
  • the transgenic animals comprise and express nucleic acid molecules encoding heavy and light chains that specifically bind to SARS-CoV-2 S-protein, and preferably to (i) the SI domain of SARS-CoV-2 S-protein; (ii) the S2 domain of SARS-CoV-2 S-protein; or (iii) both (i) and (ii).
  • the transgenic animals comprise and express nucleic acid molecules encoding heavy and light chains that specifically bind to human SARS-CoV-2 S-protein.
  • the transgenic animals comprise nucleic acid molecules encoding a modified antibody such as a single-chain antibody, a chimeric antibody or a humanized antibody.
  • the anti-SARS-CoV- 2 S-protein antibodies may be made in any transgenic animal.
  • the nonhuman animals are mice, rats, sheep, pigs, goats, cattle or horses.
  • the non-human transgenic animal expresses said encoded polypeptides in blood, milk, urine, saliva, tears, mucus and other bodily fluids.
  • Another aspect of the invention provides a method for converting the class or subclass of an anti-SARS-CoV-2 S-protein antibody to another class or subclass.
  • a nucleic acid molecule encoding a VL or VH that does not include sequences encoding CL or CH is isolated using methods well-known in the art.
  • the nucleic acid molecule then is operatively linked to a nucleotide sequence encoding a CL or CH from a desired immunoglobulin class or subclass. This can be achieved using a vector or nucleic acid molecule that comprises a CL or CH chain, as described above.
  • an anti- SARS- CoV-2 S-protein antibody that was originally IgM can be class switched to an IgG.
  • Another method for producing an antibody of the invention comprising a desired isotype comprises the steps of isolating a nucleic acid encoding a heavy chain of an anti- SARS-CoV-2 S-protein antibody and a nucleic acid encoding a light chain of an anti- SARS- CoV-2 S-protein antibody, isolating the sequence encoding the VH region, ligating the VH sequence to a sequence encoding a heavy chain constant domain of the desired isotype, expressing the light chain gene and the heavy chain construct in a cell, and collecting the anti-SARS-CoV-2 S-protein antibody with the desired isotype.
  • a fusion antibody or immunoadhesin may be made that comprises all or a portion of an anti-SARS-CoV-2 S-protein antibody of the invention linked to another polypeptide.
  • only the variable domains of the anti-SARS-CoV-2 S- protein antibody are linked to the polypeptide.
  • the VH domain of an anti-SARS-CoV-2 S-protein antibody is linked to a first polypeptide, while the VL domain of an anti-SARS-CoV-2 S-protein antibody is linked to a second polypeptide that associates with the first polypeptide in a manner such that the VH and VL domains can interact with one another to form an antigen binding site.
  • the VH domain is separated from the VL domain by a linker such that the VH and VL domains can interact with one another (see below under Single Chain Antibodies).
  • the VH-linker- VL antibody is then linked to the polypeptide of interest.
  • the fusion antibody is useful for directing a polypeptide to a SARS-CoV-2 S-protein -expressing cell or tissue.
  • the polypeptide may be a therapeutic agent, such as a toxin, chemokine or other regulatory protein, or may be a diagnostic agent, such as an enzyme that may be easily visualized, such as horseradish peroxidase.
  • fusion antibodies can be created in which two (or more) single-chain antibodies are linked to one another.
  • VH- and VL- encoding DNA fragments are operatively linked to another fragment encoding a flexible linker, e.g., encoding the amino acid sequence (GIy4 -Ser)3, such that the VH and VL sequences can be expressed as a contiguous single-chain protein, with the VL and VH domains joined by the flexible linker.
  • a flexible linker e.g., encoding the amino acid sequence (GIy4 -Ser)3
  • the single chain antibody may be monovalent, if only a single VH and VL are used, bivalent, if two VH and VL are used, or polyvalent, if more than two VH and VL are used.
  • Bispecific or polyvalent antibodies may be generated that bind specifically to SARS-CoV-2 S-protein and to another molecule.
  • Bispecific antibodies or antigen-binding fragments can be produced by a variety of methods including fusion of hybridomas or linking of Fab' fragments. See, e.g., Songsivilai & Lachmann, Clin. Exp. Immunol.
  • bispecific antibodies may be formed as “diabodies” or “Janusins”. In some embodiments, the bispecific antibody binds to two different epitopes of SARS-CoV-2 S-protein.
  • the bispecific antibody has a first heavy chain and a first light chain from monoclonal antibody MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) and an additional antibody heavy chain and light chain.
  • the additional light chain and heavy chain also are from one of the aboveidentified monoclonal antibodies, but are different from the first heavy and light chains.
  • the modified antibodies described above are prepared using one or more of the variable domains or CDR regions from a human anti-SARS-CoV-2 S-protein monoclonal antibody provided herein.
  • An anti-SARS-CoV-2 S-protein antibody or antigen-binding portion of the invention can be derivatized or linked to another molecule (e.g., another peptide or protein).
  • another molecule e.g., another peptide or protein.
  • the antibodies or portion thereof are derivatized such that the SARS-CoV-2 S-protein binding is not affected adversely by the derivatization or labelling.
  • the antibodies and antibody portions of the invention are intended to include both intact and modified forms of the human anti-SARS-CoV-2 S-protein antibodies described herein.
  • an antibody or antibody portion of the invention can be functionally linked (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another antibody (e.g., a bispecific antibody or a diabody), a detection agent, a cytotoxic agent, a pharmaceutical agent, and/or a protein or peptide that can mediate association of the antibody or antibody portion with another molecule (such as a streptavidin core region or a polyhistidine tag).
  • another antibody e.g., a bispecific antibody or a diabody
  • a detection agent e.g., a cytotoxic agent, a pharmaceutical agent, and/or a protein or peptide that can mediate association of the antibody or antibody portion with another molecule (such as a streptavidin core region or a polyhistidine tag).
  • a cytotoxic agent e.g., a cytotoxic agent
  • a pharmaceutical agent e.g., a protein or peptid
  • Suitable crosslinkers include those that are heterobifunctional, having two distinctly reactive groups separated by an appropriate spacer (e.g., m-maleimidobenzoyl-N- hydroxysuccinimide ester) or homobifunctional ⁇ e.g., disuccinimidyl suberate).
  • an appropriate spacer e.g., m-maleimidobenzoyl-N- hydroxysuccinimide ester
  • homobifunctional ⁇ e.g., disuccinimidyl suberate are available from Pierce Chemical Company, Rockford, II.
  • Another kind of derivatized antibody is a labelled antibody.
  • Useful detection agents with which an antibody or antigen-binding portion of the invention may be derivatized include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, phycoerythrin, 5-dimethylamine-l-napthalenesulfonyl chloride, lanthanide phosphors and the like.
  • An antibody can also be labelled with enzymes that are useful for detection, such as horseradish peroxidase, [beta]-galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like.
  • an antibody When an antibody is labelled with a detectable enzyme, it is detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present, the addition of hydrogen peroxide and diaminobenzidine leads to a coloured reaction product, which is detectable.
  • An antibody can also be labelled with biotin, and detected through indirect measurement of avidin or streptavidin binding.
  • An antibody can also be labelled with a predetermined polypeptide epitope recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
  • An anti-SARS-CoV-2 S-protein antibody can also be labelled with a radiolabelled amino acid.
  • the radiolabel can be used for both diagnostic and therapeutic purposes. For instance, the radiolabel can be used to detect SARS-CoV-2 S-protein-expressing tumours by x-ray or other diagnostic techniques. Further, the radiolabel can be used therapeutically as a toxin for cancerous cells or tumours.
  • the anti-SARS-CoV-2 S-protein antibody can be labelled with a paramagnetic, radioactive or florigenic ion that is detectable upon imaging.
  • the paramagnetic ion is chromium (III), manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III), ytterbium (III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) or erbium (III).
  • the radioactive ion is iodine 123, technetium 99, indium 111, rhenium 188, rhenium 186, copper 67, iodine 131, yttrium90, iodine 125, astatine 211, and gallium 67.
  • the anti-SARS-CoV-2 S-protein antibody is labelled with an X-ray imaging agent such as lanthanum (III), gold (III) lead (II) and bismuth (III).
  • the invention relates to compositions comprising the human anti-SARS-CoV-2 S-protein antibody of the invention and one or more pharmaceutical acceptable excipients and/or carriers.
  • the composition may comprise antibodies or a binding portion thereof of any of the preceding embodiments.
  • the subject of treatment is a human.
  • the subject is a veterinary subject.
  • an antagonist anti-SARS-CoV-2 S-protein antibody that binds to the SI domain and one that binds to the S2 domain or antigen-binding portions of either or both are both administered to a subject, either together or separately.
  • the antibodies are in a composition comprising a pharmaceutically acceptable carrier.
  • one or more of the antagonist SARS-CoV-2 S-protein antibodies of the invention are administered in combination with one or more additional antagonistic antibodies that bind different epitopes on the S-protein, that bind the S-protein from different isolates of SARS- CoV-2 and/or that bind different stages of SARS-CoV-2 (i.e., early, middle or late stage virus).
  • pharmaceutically acceptable carrier means any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible.
  • pharmaceutically acceptable carriers are water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition.
  • additional examples of pharmaceutically acceptable substances are wetting agents or minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the antibody.
  • compositions of this invention may be in a variety of forms, for example, liquid, semi-solid and solid dosage forms, such as liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, liposomes and suppositories.
  • liquid solutions e.g., injectable and infusible solutions
  • dispersions or suspensions tablets, pills, powders, liposomes and suppositories.
  • the preferred form depends on the intended mode of administration and therapeutic application. Typical preferred compositions are in the form of injectable or infusible solutions, such as compositions similar to those used for passive immunization of humans.
  • the preferred mode of administration is parenteral (e.g., intravenous, subcutaneous, intraperitoneal, intramuscular).
  • the antibody is administered by intravenous infusion or injection.
  • the antibody is administered by intramuscular or subcutaneous injection.
  • compositions are typically sterile and stable under the conditions of manufacture and storage.
  • the composition can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable to high drug concentration.
  • Sterile injectable solutions can be prepared by incorporating the anti-SARS-CoV-2 S-protein antibody in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze-drying that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • the proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin.
  • the antibodies of the present invention can be administered by a variety of methods known in the art, although for many therapeutic applications, the preferred route/mode of administration is subcutaneous, intramuscular, or intravenous infusion. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the desired results. Other modes of administration include intraperitoneal, intrabronchial, transmucosal, intraspinal, intrasynovial, intraaortic, intranasal, ocular, otic, topical and buccal.
  • the active compound of the antibody compositions may be prepared with a carrier that will protect the antibody against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art. See, e.g., Sustained and Controlled Release Drug Delivery Systems (J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978).
  • the invention also provides compositions suitable for administration by inhalation, which comprise the anti-SARS-CoV-2 S-protein antibodies described herein.
  • the anti-SARS- CoV-2 S-protein antibodies may be conveniently delivered to a subject in the form of an aerosol spray presentation from pressurized packs or from a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • the dosage unit may be determined by providing a valve to deliver a metered amount.
  • Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
  • compositions, suitable for administration through the oral mucosa which comprise the anti-SARS-CoV-2 S-protein antibody described herein.
  • Oral transmucosal delivery refers to the delivery of a delivery vehicle across a mucous membrane in the oral cavity, pharyngeal cavity, or esophagus, and may be contrasted, for example, with traditional oral delivery, in which absorption of a drug occurs in the intestine.
  • oral transmucosal delivery routes of administration in which the anti-SARS-CoV- 2 S-protein antibodies are absorbed through the buccal, sublingual, gingival, pharyngeal, and/or esophageal mucosa are all encompassed within "oral transmucosal delivery," as that term is used herein.
  • the anti-SARS- CoV-2 S-protein antibody may be formulated, for example, into chewing gums (see U.S. Pat No. 5,711,961) or buccal patches (see e.g. U.S. Patent No. 5,298,256).
  • the invention also provides compositions suitable for administration through the vaginal mucosa, which comprise the anti-SARS-CoV-2 S-protein antibodies described herein.
  • the anti-SARS- CoV-2 S-protein antibodies of the invention may be formulated into a vaginal suppository, foam, cream, tablet, capsule, ointment, or gel.
  • the compositions comprising the anti-SARS-CoV-2 S-protein antibodies are formulated with permeants appropriate to the transmucosal barrier to be permeated.
  • penetrants are generally known in the art, and include, for example, for trans mucosal administration bile salts and fusidic acid derivatives.
  • an anti-SARS-CoV-2 S-protein antibody of the invention can be orally administered, for example, with an inert diluent or an assailable edible carrier.
  • the compound (and other ingredients, if desired) can also be enclosed in a hard- or soft-shell gelatine capsule, compressed into tablets, or incorporated directly into the subject's diet.
  • the anti-SARS-CoV-2 S-protein antibodies can be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like.
  • an inhibitory anti-SARS-CoV-2 S-protein antibody of the invention is co-formulated with and/or co-administered with one or more additional therapeutic agents, particularly anti-viral agents.
  • These therapeutic agents include, without limitation, antibodies that bind other targets, photosensitizers, androgen, oestrogen, nonsteroidal anti-inflammatory agents, antihypertensive agents, analgesic agents, antidepressants, antibiotics, anticancer agents, anaesthetics, antiemetics, anti-infectants, contraceptives, antidiabetic agents, steroids, anti-allergy agents, chemotherapeutic agents, anti-migraine agents, agents for smoking cessation, anti-viral agents, immunosuppressants, thrombolytic agent, cholesterol-lowering agents and anti-obesity agents.
  • Therapeutic agents also include peptide analogues that inhibit SARS-CoV-2 S-protein activity, antibodies or other molecules that prevent SARS-CoV-2 entry into a cell, including but not limited to preventing S-protein binding to a receptor such as the ACE2 receptor, and agents that inhibit SARS-CoV-2 S-protein expression.
  • the additional agents that inhibit SARS-CoV-2 S-protein expression comprise an antisense nucleic acid capable of hybridizing to a SARS-CoV-2 S-protein mRNA, such as a hairpin RNA or siRNA, locked nucleic acids (LNA) or ribozymes. Sequence-specific nucleic acids capable of inhibiting gene function by RNA interference are well-known in the art.
  • the therapeutic agent(s) that is co-formulated with and/or co-administered with an inhibitory anti-SARS-CoV-2 S- protein antibody of the invention is an antimicrobial agent.
  • Antimicrobial agents include antibiotics (e.g. antibacterial), antiviral agents, antifungal agents, and anti -protozoan agents.
  • Non-limiting examples of antimicrobial agents are sulfonamides, trimethoprimsulfamethoxazole, quinolones, penicillins, and cephalosporins.
  • the compositions of the invention may include a "therapeutically effective amount” or a “prophylactically effective amount” of an antibody or antigen-binding portion of the invention.
  • a “therapeutically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result.
  • a therapeutically effective amount of the antibody or antibody portion may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the antibody or antibody portion to elicit a desired response in the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of the antibody or antibody portion are outweighed by the therapeutically beneficial effects.
  • a “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount may be less than the therapeutically effective amount.
  • the dosage proposed for the monoclonal antibodies against Covidl9 is calculated in order to achieve a neutralizing titer in the serum of 1/100.
  • the 100 - 400 mgs dosages will allow to move from intravenous to intramuscular injection. This route of administration could be a key advantage in emergency scenarios as it will allow to administer the antibodies herein disclosed, such for example MAD0004J08 in non-hospital care settings increasing the number of people that can quickly benefit from its foreseen therapeutic effect.
  • Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus can be administered, several divided doses can be administered over time or the dose can be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.
  • Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the pharmaceutical composition comprising equal or less than 400 mg for dosage unit of the human monoclonal antibody or antigen-binding portion thereof, more preferably less than 400, 350, 300, 250, 200, 150, 100, 50, 25, 10 mg for dosage unit.
  • the pharmaceutical composition comprising such dosage unit is preferably for parental administration, for example for intravenous, subcutaneous, intraperitoneal or intramuscular administration.
  • the pharmaceutical composition is in the liquid form in a concentration between 20 and 200 mg/ml, more preferably between 40 and 80 mg/ml.
  • An exemplary, non-limiting range for a therapeutically or prophylactically- effective amount of an antibody or antibody portion of the invention is 0.025 to 50 mg/kg, more preferably 0.1 to 5 mg/kg, more preferably 0.1-5, 0.1 to 4 or 0.25 to 3 mg/kg.
  • the invention provides human monoclonal antibody or an antigen-binding portion according to any one of the embodiments herein disclosed, for use in a method for prophylactic or therapeutic treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular COVID-19, wherein said method comprising the step of administering to a patient between 0.025 to 50 mg/kg, more preferably 0.1 to 5 mg/kg, more preferably 0.1-5, 0.1 to 4 or 0.25 to 3 mg/kg once a day, for example for at least one, two, three, four, five, six, seven, eight, nine, ten, eleven days.
  • Such patient is a mammal, preferably a human.
  • a formulation contains 5 mg/ml of antibody in a buffer of 20mM sodium citrate, pH 5.5, 140mM NaCl, and 0.2 mg/ml polysorbate 80. It is to be noted that dosage values may vary with the type and severity of the condition to be alleviated. It is to be further understood that for any particular subject, specific dosage regimens should be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions, and that dosage ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed composition.
  • kits comprising an anti-SARS-CoV-2 S-protein, or antigen-binding portion, of the invention or a composition comprising such an antibody or antigen-binding fragment.
  • a kit may include, in addition to the antibody or composition, diagnostic or therapeutic agents.
  • a kit can also include instructions for use in a diagnostic or therapeutic method, as well as packaging material such as, but not limited to, ice, dry ice, styrofoam, foam, plastic, cellophane, shrink wrap, bubble wrap, cardboard and starch peanuts.
  • the kit includes the antibody or a composition comprising it and a diagnostic agent that can be used in a method described below.
  • the kit includes the antibody or a composition comprising it and one or more therapeutic agents that can be used in a method described below.
  • the antibodies or binding portion thereof or composition comprising such antibodies according to any one of the embodiments herein disclosed are for use in the prevention or the treatment of patients infected with Coronavirus, in particular infected with SARS-CoV-2, for example infected with SARS-CoV-2 wild type, Alpha, Beta, Gamma or Delta.
  • the use of such antibodies and compositions of SARS-CoV-2-specific mAbs include, but are not limited to passive immunization in persons at risk of contracting the infection (e.g. professionally exposed personnel, people living in endemic areas) and therapy of acute cases, either hospitalized or not.
  • the invention also relates to compositions for inhibiting viral infection, and in particular Coronavirus infection, more in particular SARS-CoV-2 infection in a mammal comprising an amount of an antibody of the invention in combination with an amount of an antiviral agent, wherein the amounts of the anti-SARS-CoV-2 S- protein antibody and of antiviral agent are together effective in inhibiting viral replication, viral infection of new cells or viral loads.
  • the antibodies according to the invention may use also as diagnostic tools for rapid detection of SARS-CoV-2 infection, in particular for any of the variants selected from Wuhan, Alpha, Beta, Gamma and Delta.
  • the invention provides diagnostic methods.
  • the anti-SARS-CoV-2 S-protein antibodies can be used to detect SARS-CoV-2 S-protein in a biological sample in vitro or in vivo.
  • the invention provides a method for diagnosing the presence or location of SARS-CoV-2 viruses in a subject in need thereof.
  • the anti-SARS-CoV-2 S-protein antibodies can be used in a conventional immunoassay, including, without limitation, an ELISA, an RIA, flow cytometry, tissue immunohistochemistry, Western blot (immunoblot) or immunoprecipitation.
  • the anti- SARS-CoV-2 S-protein antibodies of the invention can be used to detect SARS-CoV-2 S- protein from humans.
  • the invention provides a method for detecting SARS-CoV-2 S-protein in a biological sample comprising contacting the biological sample with an anti-SARS-CoV- 2 S-protein antibody of the invention and detecting the bound antibody.
  • the anti-SARS-CoV-2 S-protein antibody is directly labelled with a detectable label.
  • the anti-SARS-CoV-2 S-protein antibody (the first antibody) is unlabelled and a second antibody or other molecule that can bind the anti-SARS-CoV-2 S- protein antibody is labelled.
  • a second antibody is chosen that is able to specifically bind the particular species and class of the first antibody.
  • the anti-SARS-CoV-2 S-protein antibody is a human IgG
  • the secondary antibody could be an anti-human-IgG.
  • Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially, e.g., from Pierce Chemical Co.
  • Example of biological samples to use in the diagnostic methods herein disclosed are urine, stool, blood, saliva, biopsies, cerebrospinal fluid, nasopharyngeal and oropharyngeal wash, sputum, endotracheal aspirate, bronchoalveolar lavage or other biological samples obtainable from a human subject.
  • Suitable labels for the antibody or secondary antibody have been disclosed supra, and include various enzymes, prosthetic groups, fluorescent materials, luminescent materials and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, [beta]-galactosidase, or acetylcholinesterase
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin
  • an example of a luminescent material includes luminol.
  • SARS-CoV-2 S-protein can be assayed in a biological sample by a competition immunoassay utilizing SARS-CoV-2 S-protein standards labelled with a detectable substance and an unlabelled anti-SARS-CoV-2 S-protein antibody.
  • a competition immunoassay utilizing SARS-CoV-2 S-protein standards labelled with a detectable substance and an unlabelled anti-SARS-CoV-2 S-protein antibody.
  • the biological sample, the labelled SARS-CoV-2 S-protein standards and the anti-SARS-CoV-2 S-protein antibody are combined and the amount of labelled SARS-CoV-2 S-protein standard bound to the unlabelled antibody is determined.
  • the amount of SARS-CoV-2 S-protein in the biological sample is inversely proportional to the amount of labelled SARS-CoV-2 S-protein standard bound to the anti-SARS-CoV-2 S-protein antibody.
  • the anti-SARS-CoV-2 S-protein antibodies can be used to detect SARS-CoV-2 S-protein in cultured cells or as a diagnostic assay in samples from a subject.
  • the diagnostic methods according to any embodiments herein disclosed may be followed by a further step of the administration in the positive subject of an anti-SARS-CoV-2 drugs, for example according to any of the Therapeutic Methods herein disclosed.
  • the invention provides a method for neutralizing SARS- CoV-2 by administering an anti-SARS-CoV-2 S-protein antibody to a patient in need thereof.
  • an anti-SARS-CoV-2 S-protein antibody is a human antibody.
  • the antibody, or antigen-binding portion thereof binds to the SI domain of SARS-CoV-2 S-protein.
  • the patient is a human patient.
  • the patient may be a mammal infected with SARS-CoV-2.
  • the invention provides methods of treating, aiding in the treatment, preventing or aiding in the prevention of, SARS-CoV-2 infection and conditions or disorders resulting from such infection, in a subject by administering to the subject a therapeutically-effective or prophylactically effective amount of an anti-SARS-CoV-2 S-protein antibody of the invention.
  • Antibodies and antigen-binding fragments thereof which are antagonists of SARS-CoV-2 S-protein can be used as therapeutics for SARS-CoV-2 infection.
  • the antibody may be administered locally or systemically.
  • compositions comprising anti-SARS-CoV-2 S- protein antibodies may be administered to the subject, for example, orally, nasally, vaginally, buccally, rectally, via the eye, or via the pulmonary route, in a variety of pharmaceutically acceptable dosing forms, which will be familiar to those skilled in the art.
  • the anti-SARS-CoV-2 S-protein antibodies may be administered via the nasal route using a nasal insufflator device.
  • the anti-SARS-CoV-2 S-protein antibodies can also be administered to the eye in a gel formulation.
  • a formulation containing the anti- SARS-CoV-2 S-protein antibodies may be conveniently contained in a two- compartment unit dose container, one compartment containing a freeze-dried anti-SARS- CoV-2 S-protein antibody preparation and the other compartment containing normal saline.
  • the serum concentration of the antibody may be measured by any method known in the art.
  • the antibodies of the present invention are administered to the subject in combination with other therapeutic agents.
  • the additional therapeutic agents may be treating the symptoms of the SARS-CoV-2 infection on their own, and may optionally synergize with the effects of the antibodies.
  • the additional agent that is administered may be selected by one skilled in the art for treating the infection.
  • Coadministration of the antibody with an additional therapeutic agent encompasses administering a composition comprising the anti-SARS-CoV-2 S-protein antibody and the additional therapeutic agent as well as administering two or more separate compositions, one comprising the anti-SARS-CoV-2 S-protein antibody and the other(s) comprising the additional therapeutic agent(s).
  • co-administration or combination therapy generally means that the antibody and additional therapeutic agents are administered at the same time as one another, it also encompasses instances in which the antibody and additional therapeutic agents are administered at different times. For instance, the antibody may be administered once every three days, while the additional therapeutic agent is administered once daily. Alternatively, the antibody may be administered prior to or subsequent to treatment with the additional therapeutic agent, for example after a patient has failed therapy with the additional agent. Similarly, administration of the anti-SARS- CoV-2 S-protein antibody may be administered prior to or subsequent to other therapy.
  • the antibody and one or more additional therapeutic agents may be administered once, twice or at least the period of time until the condition is treated, palliated or cured.
  • the combination therapy is administered multiple times.
  • the combination therapy may be administered from three times daily to once every six months.
  • the administering may be on a schedule such as three times daily, twice daily, once daily, once every two days, once every three days, once weekly, once every two weeks, once every month, once every two months, once every three months and once every six months, or may be administered continuously via a minipump.
  • the combination therapy may be administered via an oral, mucosal, buccal, intranasal, inhalable, intravenous, subcutaneous, intramuscular, or parenteral.
  • the invention provides a method for treating, preventing or alleviating the symptoms of a SARS-CoV-2 mediated disorder in a subject in need thereof, comprising the step of administering to said subject an antibody or antigenbinding portion according to any one of the preceding embodiments, further comprising at least one additional therapeutic agent selected from the group consisting of: (a) one or more antibodies from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15): and
  • the invention provides a kit for treating, preventing or alleviating the symptoms of a SARS-CoV-2 mediated disorder in a subject in need thereof, comprising a) one or more antibodies from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); and
  • a further object of the invention is the use of the human monoclonal antibody or antigenbinding portion herein disclosed in the manufacturing of a medicament for treating, preventing or alleviating the symptoms of a SARS-CoV-2 mediated disorder in a subject in need thereof.
  • the human monoclonal antibody or antigen-binding portion thereof herein disclosed may also be used advantageously as a diagnostic reagent in an in vitro method for detecting in a biological sample previously obtained from a patient (such as for example a serum, plasma, blood sample or any other suitable biological material, obtained from the patient, preferably a human being) anti-Coronavirus antibodies, in particular SARS-Cov-2 antibodies.
  • a biological sample previously obtained from a patient
  • a patient such as for example a serum, plasma, blood sample or any other suitable biological material, obtained from the patient, preferably a human being
  • anti-Coronavirus antibodies in particular SARS-Cov-2 antibodies.
  • a diagnostic kit comprising the human monoclonal antibody or antigenbinding portion thereof herein disclosed of the invention, as a specific reagent, also falls within the scope of the invention, said kit being in particular designed for the detection and/or quantification, in a biological sample previously obtained from a patient, of anti-coronavirus antibodies.
  • the human monoclonal antibody or antigen-binding portion thereof herein disclosed may also be used in a vaccine composition.
  • the human monoclonal antibody or antigen-binding portion thereof herein disclosed may also be used advantageously for the design of a vaccine against coronavirus.
  • Rappuoli, Rino et al. “Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. ” The Journal of experimental medicine vol. 213,4 (2016): 469-81. doi:10.1084/jem.20151960”
  • human mAb may be used to identify protective antigens/epitopes. Structural characterization of the Ab-antigen complex may be used to instruct antigen design.
  • a method or the use of the human monoclonal antibody or antigen-binding portion thereof herein disclosed for the design of a vaccine against a coronavirus, in particular against the SARS-Cov-2 virus is within the scope of the invention.
  • the human monoclonal antibody or antigen-binding portion thereof herein disclosed may be used for the preparation of mimotopes, such as for example anti-idiotype antibodies, peptides, S-protein truncated or artificial forms or others, endowed with the ability of evoking the antibodies herein disclosed.
  • the anti-idiotype antibodies are preferred.
  • the anti-idiotype antibodies are antibodies specifically directed against the idiotype of the neutralizing antibodies used for the manufacture thereof, and thus are able to mimic the key epitopes that they recognize.
  • the manufacture of anti-idiotype antibodies is carried out by known methodologies that do not need further detailed explanations here.
  • mimotopes, preferably anti-idiotype antibodies, directed against an antibody of the invention fall within the scope of the invention.
  • the human monoclonal antibody or antigen-binding portion thereof herein disclosed may be used for the manufacture of antiidiotype antibodies according to the known methods.
  • Anti-idiotype antibodies are antibodies specifically directed towards the idiotype of the broad-range neutralizing antibodies used to prepare them, and as such are able to mimic the key epitopes they recognize. Therefore, antiidiotype antibodies directed against a monoclonal antibody of the invention are also included in the scope of the invention.
  • the antibody 02M04 possessed the highest neutralization potency among the four antibodies tested, showing a 100% inhibitory concentration (ICioo) of 8.8, 5.9, 3.1, 2.7, 6.5 ng/mL against the Wuhan, alpha, beta, gamma and delta variants respectively followed in potency by the antibodies 02H05, 01023 and 01E15 ( Figure 1A-F).
  • ICioo inhibitory concentration
  • 02M04, 02H05, 01023 and 01E15 antibodies competed with S309, therefore recognizing a similar epitope region on the spike protein, our antibodies showed an ICioo over 40-fold higher compared S309 ( Figure 1, Table 1).
  • the equilibrium dissociation constant (KD) of 02M04, 02H05, 01023 and 01E15 ranged from 0.47 - 4.23 E' 10 M ( Figure 2), 0.82 - 2.64 E' 10 M ( Figure 3), 0.71 - 1.93 E' 10 M ( Figure 4), and 1.62 - 5.92 E' 10 M ( Figure 5) respectively.
  • Table 3 lists the full sequences of the heavy and light chains of these latter antibodies.
  • Table 2 shows the immunoglobulin heavy and light variable (IGHV;IGLV) and junction (IGHJ;IGLJ) gene usage, length of the complementary determining region 3 (CDR3) of the heavy (H-CDR3) and light (L-CDR3) chains and the heavy and light chain V-gene mutation frequencies.
  • IGHV immunoglobulin heavy and light variable
  • IGHJ junction
  • L-CDR3 light chain V-gene mutation frequencies.
  • CDR3 complementary determining region 3
  • 02M04 shows unique heavy and light chain V-J gene rearrangement and the highest level of heavy chain V-gene mutations compared to the other characterized antibodies.
  • 02H05, 01023 and 01E15 share the same IGHV-J gene rearrangement (IGHV2-5;! GHJ4-1) and two out of three antibodies accommodate the same lambda chain which shows the IGLV2-14 and IGLJ2-1 genes with identical L-CDR3 length.
  • both 02M04 and 01023 accommodate the IGKV1-5 gene flanked by the IGKJ1 and IGKJ3 genes respectively.
  • variable domain of Light chain of MAD 1009023 OR ABBREVIATED 01023)
  • ARHRIRELFDY >SEQ ID NO:58 CDR 1 of variable domain of Light chain of MAD1006E15 (OR ABBREVIATED 01E15) SSDVGGYNY
  • variable domain of Light chain of MAD1006E15 OR ABBREVIATED 01E15

Abstract

The present disclosure provides human monoclonal antibodies that have potent neutralizing activity against SARS-CoV-2. The present disclosure also provides prevention methods, treatment methods, compositions, pharmaceutical compositions, and vaccine compositions that comprise or utilize the human monoclonal antibodies provided herein.

Description

ANTIBODIES TO CORONAVIRUS
Field of the invention
Human monoclonal antibodies are provided by the present invention that have a potent neutralizing activity against SARS-CoV-2. According to the present invention human monoclonal antibodies recognizing SARS-CoV-2 have been isolated from memory B cells of people previously exposed to SARS-CoV-2 infection and subsequently vaccinated with the COVID-19 BNT162b2 mRNA vaccine. The invention relates to human monoclonal antibodies recognizing SARS-CoV-2 for their use in therapy, prophylaxis, and diagnosis of SARS-CoV-2 dependent diseases.
Background of the Invention
Human monoclonal antibodies (mAbs) are an industrially mature technology with more than 50 products already approved in the field of cancer, inflammation, and autoimmunity.. So far mAbs have rarely been used in the field of infectious diseases, mostly because the large quantities needed for therapy made them not cost effective. However, in recent years, the technological progress in isolating and screening memory B cells allowed identification of highly potent neutralizing mAbs and further improvement of their potency. This possibility resulted in a decreased quantity of antibodies necessary for therapy thus making non- intravenous delivery of potent neutralizing mAbs possible.
In the case of SARS-CoV-2, where so far there are no effective therapeutic or prophylactic interventions, mAbs have the possibility to become one of the first drugs that can be used for immediate therapy of any patient testing positive for the virus, and even to provide immediate protection from infection in high-risk populations. Preliminary evidences show that plasma from infected subjects improves the outcome of patients with severe disease, therefore it is possible that a mAb-based therapy and/or prophylaxis be highly effective. Furthermore, vaccination strategies inducing neutralizing antibodies have already shown to protect non-human primates from infection. These results further stress the importance of mAbs as a measure to target SARS-CoV-2 infection and to contain its circulation.
Among the many therapeutic options available, mAbs offer a series of advantages. First, they are the ones that can be developed in the shortest period of time. In fact, the extensive clinical experience with the safety of more than 50 commercial mAbs approved to treat cancer, inflammation and autoimmunity provides high confidence on their safety, support the possibility of having an accelerated regulatory pathway. In addition, the long industrial experience in developing and manufacturing mAbs decreases the risks usually associated with technical development of investigational products. Finally, the incredible technical progress in the field allows to shorten the conventional timelines and go from discovery to proof of concept trials in 5-6 months. Several candidates are presently under development in the field of HIV, pandemic influenza, RSV and many other infectious diseases. Perhaps the most striking demonstration of the power of mAbs for emerging infections came from the Ebola experience. In this case rapidly developed potent mAbs were among the first drugs to be tested in the Ebola outbreak and showed remarkable efficacy in preventing mortality. Given the striking efficacy of this intervention, potent mAbs became the first, and, so far, the only drug to be recommended for Ebola by the World Health Organization (WHO). Given the pivotal role of the SARS-CoV-2 transmembrane spike glycoprotein (S-protein) for viral pathogenesis, it is considered as the main target to elicit potent neutralizing antibodies and the focus for the development of therapeutic and prophylactic tools against this virus. Indeed, SARS-CoV-2 entry into host cells is mediated by the interaction between S-protein and the human angiotensin converting enzyme 2 (ACE2). The S-protein is a trimeric class I viral fusion protein which exists as a metastable pre-fusion conformation and as a stable post-fusion conformation. Each S-protein monomer is composed of two distinct regions, the SI and S2 subunits. Structural rearrangement occurs when the receptor binding domain (RBD) present in the SI subunit binds to the host cell membrane. This interaction destabilizes the pre-fusion state of the S-protein triggering the transition into the post-fusion conformation which in turn results in the entry of the virus particle into the host cell. Singlecell RNA-seq analyses evaluating the expression levels of ACE2 in different human organs has shown that SARS-CoV-2, through S-protein binding, can invade human cells in different major physiological systems including the respiratory, cardiovascular, digestive and urinary systems, enhancing the possibility of spreading and infection. Therefore, it is important to produce neutralizing mAbs or antigen-binding portion thereof that are effective to block the entry process of the virus. Accordingly, there remains an urgent need for potent, broad spectrum antibody therapeutics for use in treatment, prophylaxis, and diagnosis of Coronavirus, in particular SARS-CoV-2, dependent diseases. In particular, there remains an urgent need for monoclonal antibodies able to neutralize also the SARS-CoV-2 variants such as alpha, beta, gamma and delta variants.
Summary of the Invention
The inventors surprisingly identified from donors vaccinated with the BNT162b2 mRNA vaccine, human mAbs that have a potent neutralization activity against SARS-CoV-2. In particular, the new isolated antibodies show a potent neutralization activity not only with the Wuhan variant, but also with all the emerging variants such as the Alpha, Beta, Gamma and Delta variants.
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein, wherein said antibody or antigenbinding portion thereof showing 100% inhibitory concentration (ICioo) of less than 25 ng/ml, preferably of less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS- CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma, preferably said in vitro neutralization assay is the CPE-MN assay.
In a further aspect, the invention provides a human monoclonal antibody or antigen-binding portion thereof according to claim 1, having an equilibrium dissociation constant (KD) of less than 6 pM against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Gamma, Delta and Kappa as measured by surface plasmon resonance (SPR).
In a further aspect, the invention provides a human monoclonal antibody or antigen-binding portion thereof comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein said VH and VL comprise the following complementarity-determining regions (CDRs):
-CDR1 of VH having SEQ ID NO: 1,
-CDR2 of VH having SEQ ID NO:2,
-CDR3 of VH having SEQ ID NO:3,
-CDR1 of VL having SEQ ID NO:4,
-CDR2 of VL having the sequence QAS (Gln-Ala-Ser) and
-CDR3 of VL having SEQ ID NO:6; or
-CDR1 of VH having SEQ ID NO: 19,
Figure imgf000004_0001
Figure imgf000005_0001
-CDR1 of VL having SEQ ID NO:22,
-CDR2 of VL having the sequence DVT (Asp-Val-Thr) and
-CDR3 of VL having SEQ ID NO:24; or
-CDR1 of VH having SEQ ID NO:37,
-CDR2 of VH having SEQ ID NO:38,
-CDR3 of VH having SEQ ID NO:39,
-CDR1 of VL having SEQ ID NO:40,
-CDR2 of VL having the sequence KAS (Lys-Ala-Ser) and
-CDR3 of VL having SEQ ID NO:42. or
-CDR1 of VH having SEQ ID NO:55,
-CDR2 of VH having SEQ ID NO: 56,
-CDR3 of VH having SEQ ID NO: 57,
-CDR1 of VL having SEQ ID NO:58,
-CDR2 of VL having the sequence EVS (Glu-Val-Ser) and
-CDR3 of VL having SEQ ID NO:60
In a further aspect, the invention provides a human monoclonal antibody or antigen-binding portion thereof, comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein said VH having SEQ ID NO:7 and said VL having SEQ ID NO:8; or wherein said VH having SEQ ID NO:25 and said VL having SEQ ID NO:26; or wherein said VH having SEQ ID NO:43 and said VL having SEQ ID NO:44 or wherein said VH having SEQ ID NO:61 and said VL having SEQ ID NO:62.
In a further aspect, the invention provides a human monoclonal antibody or antigen-binding portion thereof, wherein said VL and said VH is at least 90% identical in amino acid sequence, preferably at least 95%, more preferably at least 99% of
VH having SEQ ID NO:7 and said VL having SEQ ID NO:8; or
VH having SEQ ID NO:25 and said VL having SEQ ID NO:26; or
VH having SEQ ID NO:43 and said VL having SEQ ID NO:44 or VH having SEQ ID NO:61 and said VL having SEQ ID NO:62 , in particular showing 100% inhibitory concentration (ICioo) of less than 25 ng/ml, preferably of less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS-CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma, wherein said in vitro neutralization assay is measured for example using the CPE-MN assay and/or having an equilibrium dissociation constant (KD) of less than 6 pM against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Gamma, Delta and Kappa as measured by surface plasmon resonance (SPR).
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to a severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein wherein said antibody or antigen-binding portion thereof has one or more of the following characteristics: (a) neutralizing one or more of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and Delta with an IC100 of less than 25 ng/ml; (b) having an equilibrium dissociation constant (KD) against the Spike (S) protein of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and/or Delta of less than 6 E" 10M; and/or (c) comprises three heavy chain complementarity determining regions (CDRs) (CDR-H1, CDR-H2, and CDR-H3) contained within a heavy chain variable region (VH) comprising an amino acid sequence having at least about 90% sequence identity to a VH of a monoclonal antibody selected from the group consisting of: MAD1005M04, MAD1005H05, MAD1009023 and MAD1006E15; and three light chain CDRs (CDR-L1, CDR-L2, and CDR-L3) contained within a light chain variable region (VL) comprising an amino acid sequence having at least about 90% sequence identity to a VL of a monoclonal antibody selected from the group consisting of: MAD1005M04, MAD1005H05, MAD 1009023 AND MAD1006E15.
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the light chain variable domain (VL) and heavy chain variable domain (VH) of a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the CDRs of a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the VL and VH domains that are at least 85%, 90%, 95%, 97%, 98% or 99% identical in amino acid sequence to the VL and VH domains, respectively, of a monoclonal antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In certain aspects, the invention provides human monoclonal antibodies or antigen-binding portion thereof that compete for the SARS-CoV-2 S-protein with any of the antibodies herein disclosed.
In certain aspects, the invention provides human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed, for use in a prophylactic or therapeutic treatment of a viral infection or conditions or disorders resulting from such infection.
In certain aspects, the invention provides human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed, for use in a prophylactic or therapeutic treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19).
In certain aspects, the invention provides a method of preventing or treating the SARS-CoV- 2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19), comprising administering a human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed, to a subject in need thereof.
The invention further provides human monoclonal antibody or an antigen-binding portion according to any embodiments herein disclosed for use in the diagnosis, prophylaxis and/or treatment of a subject having, or at risk of developing, a virus infection, in particular a coronavirus infection, more in particular SARS-CoV-2 infection, more in particular an infection of the SARS-CoV-2 variant Alpha, Beta, Delta or Gamma.
Furthermore, the invention pertains to the use of the human binding molecules and/or the nucleic acid molecules of the invention in the diagnosis/detection of such viral infections.
In certain aspects, the invention provides a pharmaceutical composition comprising at least one or more human monoclonal antibodies or antigen-binding portions thereof according to any one of the embodiments herein disclosed and a pharmaceutically acceptable carrier and its use in the prevention and/or treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19).
In certain aspects, the invention provides an isolated cell line that produces the antibody or antigen-binding portion thereof according to any one of the embodiments herein disclosed.
In certain aspects, the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes the antibody or antigen-binding portion thereof according to any one of the embodiments herein disclosed.
In certain aspects, the invention provides a vector comprising the nucleic acid molecule encoding the antibody or antigen-binding portion thereof embodiments according to any one of the embodiments herein disclosed, wherein the vector optionally comprises an expression control sequence operably linked to the nucleic acid molecule.
In certain aspects, the invention provides a non-human transgenic animal or transgenic plant comprising the nucleic acid according to any one of the preceding embodiments, wherein the non- human transgenic animal or transgenic plant expresses said nucleic acid. In certain embodiments, said non-human transgenic animal is a mammal.
In certain aspects, the invention provides the use of the human monoclonal antibody or an antigen-binding portion thereof according to any one of the embodiments herein disclosed in the diagnosis of the SARS-CoV-2 infection.
In certain aspects, the invention provides an in vitro method for revealing the presence of the SARS-CoV-2 in a sample comprising the following steps: i) Contacting the antibody or an antigen-binding portion thereof according to any one of the embodiments herein disclosed; ii) Detecting the binding of said antibody or an antigen-binding portion thereof to the S-protein of the SARS-CoV-2.
In certain aspects, the invention provides an in vitro method for the diagnosis of the SARS- CoV-2 infection in a subject comprising the following steps: i) Contacting the antibody or an antigen-binding portion thereof according to any one of the embodiments herein disclosed with a biological sample of said subject; ii) Detecting the binding of said antibody or an antigen-binding portion thereof to the S-protein of the SARS-CoV-2. The invention contemplates combinations of any of the foregoing aspects and embodiments of the invention.
In certain aspects, the invention provides a method for the prevention or treatment a viral infection or conditions or disorders resulting from such infection in a subject, comprising administering a therapeutically effective amount of one or more of any of the antibodies or an antigen-binding portion thereof herein disclosed to said subj ect in need thereof. In particular for the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular Coronavirus disease 2019 (COVID-19).
Brief Description of the Drawings
Figure 1. Neutralization activity against SARS-CoV-2 and emerging variants. (A-D) Graphs show the ability of mAbs 02M04 (A), 2H05 (B), 01023 (C), 01E15 (D) and S309 (E) to neutralize SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the CPE-MN assay. All experiments were performed in technical duplicates. (F) The table summarizes the IC100 obtained for all tested antibodies.
Figure 2. Binding affinity of 02M04 antibody to SARS-CoV-2 spike proteins. (A-E) Graphs show the ability of mAbs 02M04 to bind the spike protein of the SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the surface plasmon resonance (SPR) assay. (F) The table summarizes the Kd obtained. Figure 3. Binding affinity of 02H05 antibody to SARS-CoV-2 spike proteins. (A-E) Graphs show the ability of mAbs 02H05 to bind the spike protein of the SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the surface plasmon resonance (SPR) assay. (F) The table summarizes the Kd obtained. Figure 4. Binding affinity of 01023 antibody to SARS-CoV-2 spike proteins. (A-E) Graphs show the ability of mAbs 01023 to bind the spike protein of the SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the surface plasmon resonance (SPR) assay. (F) The table summarizes the Kd obtained. Figure 5. Binding affinity of 01E15 antibody to SARS-CoV-2 spike proteins. (A-E) Graphs show the ability of mAbs 01E15 to bind the spike protein of the SARS-CoV-2 Wuhan, B. l.1.7 (alpha), B.1.351 (beta), B.1.1.248 (gamma) and B.1.617.2 (delta) viruses using the surface plasmon resonance (SPR) assay. (F) The table summarizes the Kd obtained.
Figure 6. Neutralization activity against SARS-CoV-2 variants.
Detailed description of the invention
Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The singular terms "a," "an," and "the" include plural referents unless context clearly indicates otherwise. Similarly, the word "or" is intended to include "and" unless the context clearly indicates otherwise. The term "plurality" refers to two or more. The term “at least one” refers to one or more.
Unless otherwise defined herein, scientific and technical terms used in connection with the present invention shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. Generally, nomenclature used in connection with, and techniques of, cell and tissue culture, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein are those well-known and commonly used in the art. The methods and techniques of the present invention are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. See, e.g., Sambrook et al. Molecular Cloning: A Laboratory Manual, second ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) and Ausubel et al, Current Protocols in Molecular Biology, Greene Publishing Associates (1992), and Harlow and Lane Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1990), incorporated herein by reference.
The following terms, unless otherwise indicated, shall be understood to have the following meanings:
The term "polypeptide" encompasses native or artificial proteins, protein fragments and polypeptide analogues of a protein sequence. A polypeptide may be monomeric or polymeric. The term "isolated protein", "isolated polypeptide" or "isolated antibody" is a protein, polypeptide or antibody that by virtue of its origin or source of derivation (1) is not associated with naturally associated components that accompany it in its native state, (2) is free of other proteins from the same species, (3) is expressed by a cell from a different species, or (4) does not occur in nature. Thus, a polypeptide that is chemically synthesized or synthesized in a cellular system different from the cell from which it naturally originates will be "isolated" from its naturally associated components. A protein may also be rendered substantially free of naturally-associated components by isolation, using protein purification techniques well known in the art. Examples of isolated antibodies include an anti- SARS- CoV-2 S-protein antibody that has been affinity purified using SARS-CoV-2 S-protein or a portion thereof, an anti- SARS-CoV-2 S-protein antibody that has been synthesized by a hybridoma or other cell line in vitro, and a human anti- SARS-CoV-2 S-protein antibody derived from a transgenic animal. A protein or polypeptide is "substantially pure", "substantially homogeneous", or "substantially purified" when at least about 60 to 75% of a sample exhibits a single polypeptide. The polypeptide or protein may be monomeric or multimeric. A substantially pure polypeptide or protein will typically comprise about 50%, 60%, 70%, 80% or 90% W/W of a protein sample, more usually about 95%, and preferably will be over 99% pure. Protein purity or homogeneity may be indicated by a number of means well known in the art, such as polyacrylamide gel electrophoresis of a protein sample, followed by visualizing a single polypeptide band upon staining the gel with a stain well known in the art. For certain purposes, higher resolution may be provided by using HPLC or other means well known in the art for purification. The term "polypeptide fragment" as used herein refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion, but where the remaining amino acid sequence is identical to the corresponding positions in the naturally occurring sequence. In some embodiments, fragments are at least 5, 6, 8 or 10 amino acids long. In other embodiments, the fragments are at least 14, at least 20, at least 50, or at least 70, 80, 90, 100, 150 or 200 amino acids long. The term "polypeptide analogue" as used herein refers to a polypeptide that comprises a segment that has substantial identity to a portion of an amino acid sequence and that has at least one of the following properties: (1) specific binding to SARS-CoV-2 S-protein under suitable binding conditions, (2) ability to inhibit SARS-CoV-2 S-protein. Typically, polypeptide analogues comprise a conservative amino acid substitution (or insertion or deletion) with respect to the native sequence. Analogues typically are at least 20 or 25 amino acids long, preferably at least 50, 60, 70, 80, 90, 100, 150 or 200 amino acids long or longer, and can often be as long as a full- length polypeptide. Some embodiments of the invention include polypeptide fragments or polypeptide analogue antibodies with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 substitutions from the germline amino acid sequence. In certain embodiments, amino acid substitutions to an anti- SARS-CoV-2 S-protein antibody or antigen-binding portion thereof are those which: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity to form protein complexes, and (4) confer or modify other physicochemical or functional properties of such analogues, but still retain specific binding to SARS-CoV-2 S-protein. Analogues can include various muteins of a sequence other than the normally occurring peptide sequence. For example, single or multiple amino acid substitutions, preferably conservative amino acid substitutions, may be made in the normally occurring sequence, preferably in the portion of the polypeptide outside the domain(s) forming intermolecular contacts. A conservative amino acid substitution should not substantially change the structural characteristics of the parent sequence; e.g., a replacement amino acid should not alter the anti-parallel [beta]-sheet that makes up the immunoglobulin binding domain that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence. In general, glycine and proline would not be used in an anti-parallel [beta]-sheet. Examples of art-recognized polypeptide secondary and tertiary structures are described in Proteins, Structures and Molecular Principles (Creighton, Ed., W. H. Freeman and Company, New York (1984)); Introduction to Protein Structure (C. Branden and J. Tooze, eds., Garland Publishing, New York, N.Y. (1991)); and Thornton et ai, Nature 354: 105 (1991), incorporated herein by reference.
The term “SARS-CoV-2” is for Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2), the type of coronavirus that causes coronavirus disease 2019 (COVID-19), where an "antibody" is referred to herein with respect to the invention, it is normally understood that an antigen-binding portion thereof may also be used. An antigen-binding portion competes with the intact antibody for specific binding. See generally, Fundamental Immunology, Ch. 7 (Paul, W., ed., second ed. Raven Press, N.Y. (1989)) (incorporated by reference in its entirety for all purposes). Antigen-binding portions may be produced by recombinant DNA techniques or by enzymatic or chemical cleavage of intact antibodies. In some embodiments, antigen-binding portions include Fab, Fab', F(ab')2, Fd, Fv, dAb, and complementarity determining region (CDR) fragments, single-chain antibodies (scFv), chimeric antibodies, diabodies, nanobodies and any polypeptides that contain at least a portion of an antibody that is sufficient to confer specific antigen binding to the polypeptide. From N-terminus to C-terminus, both the mature light and heavy chain variable domains comprise the regions FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. The assignment of amino acids to each domain herein is in accordance with the definitions of IMGT convention described in Lefranc et al. (2003), Developmental & Comparative Immunology 27.1 (2003): 55-77.
As used herein, an antibody that is referred to by number is the same as a monoclonal antibody that is obtained from the human peripheral blood mononuclear cells (PBMCs) isolated from the donor of the same number. For example, monoclonal antibody MAD1005M04 (or abbreviated as 02M04) is the same antibody as one obtained from PBMCs isolated from subject identified by the code, or a subclone thereof.
As used herein, a Fd fragment means an antibody fragment that consists of the VH and CH 1 domains; an Fv fragment consists of the VL and VH domains of a single arm of an antibody; and a dAb fragment (Ward et al, Nature 341 :544-546 (1989)) consists of a VH domain.
In some embodiments, the antibody is a single-chain antibody (scFv) in which a VL and VH domains are paired to form a monovalent molecule via a synthetic linker that enables them to be made as a single protein chain. (Bird et al, Science 242:423-426 (1988) and Huston et al, Proc. Natl Acad. ScL USA 85:5879-5883 (1988)). In some embodiments, the antibodies are diabodies, i.e., are bivalent antibodies in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites. (See e.g., Holliger P. et al, Proc. Natl. Acad. ScL USA 90:6444-6448 (1993), and Poljak R. J. et al, Structure 2: 1121- 1123 (1994)). In such embodiments, the CDR(s) may be incorporated as part of a larger polypeptide chain, may be covalently linked to another polypeptide chain, or may be incorporated noncovalently. In embodiments having one or more binding sites, the binding sites may be identical to one another or may be different.
As used herein, the term "human antibody" means any antibody in which the variable and constant domain sequences are human sequences or any of the CDRs of the variable domain sequences are human sequences. The term encompasses antibodies with sequences derived from human genes, but which have been changed, e.g. to decrease possible immunogenicity, increase affinity, eliminate cysteine that might cause undesirable folding, etc. The term encompasses such antibodies produced recombinant in non-human cells, which might impart glycosylation not typical of human cells. The term "chimeric antibody" as used herein means an antibody that comprises regions from two or more different antibodies.
The term "epitope" includes any protein determinant capable of specific binding to an immunoglobulin or T-cell receptor or otherwise interacting with a molecule. Epitopes or antigenic determinants generally consist of chemically active surface groupings of molecules such as amino acids or carbohydrate or sugar side chains and generally have specific three- dimensional structural characteristics, as well as specific charge characteristics. An epitope may be "linear" or "conformational." In a linear epitope, all of the points of interaction between the protein and the interacting molecule (such as an antibody) occur linearly along the primary amino acid sequence of the protein. In a conformational epitope, the points of interaction occur across amino acid residues on the protein that are separated from one another.
A "neutralizing antibody", an antibody with "neutralizing activity", as used herein means an antibody that neutralizes a biological effect that its target (e.g., a pathogen or an infectious particle) may have. A "neutralizing antibody", an antibody with "neutralizing activity", as used herein is for example an antibody or antigen-binding portion thereof showing a 100% inhibitory concentration (ICioo) of at least less than 25 ng/ml, preferably less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS-CoV-2 virus. ICioo is measured preferably using the CPE-MN assay as disclosed for example in Andreano et al. Cell 184, 1821- 1835.el816 (2021).
An antibody is said to specifically bind an antigen when the dissociation constant is for example < 1 mM, preferably < 100 nM and most preferably < 10 nM. The dissociation constant may be measured by any of the methods available in the state of the art as for example using enzyme-linked immunosorbent assay (ELISAs), radioimmunoassay (RIAs), flow cytometry, surface plasmon resonance, such as BIACORE(TM).
The term "polynucleotide" as referred to herein means a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxyribonucleotides or a modified form of either type of nucleotide. The term includes single and double stranded forms.
The term "isolated polynucleotide" as used herein means a polynucleotide of genomic, cDNA, or synthetic origin or some combination thereof, which by virtue of its origin the "isolated polynucleotide" (1) is not associated with all or a portion of a polynucleotides with which the "isolated polynucleotide" is found in nature, (2) is operably linked to a polynucleotide to which it is not linked in nature, or (3) does not occur in nature as part of a larger sequence.
The term "naturally occurring nucleotides" as used herein includes deoxyribonucleotides and ribonucleotides. The term "modified nucleotides" as used herein includes nucleotides with modified or substituted sugar groups and the like. The term "oligonucleotide linkages" referred to herein includes oligonucleotides linkages such as phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phoshoraniladate, phosphoroamidate, and the like. See e.g., LaPlanche et al., Nucl. Acids Res. 14:9081 (1986); Stec et al, J. Am. Chem. Soc. 106:6077 (1984); Stein et al., Nucl. Acids Res. 16:3209 (1988); Zon et al., Anti-Cancer Drug Design 6:539 (1991); Zon et al.. Oligonucleotides and Analogues: A Practical Approach, pp. 87-108 (F. Eckstein, Ed., Oxford University Press, Oxford England (1991)); U.S. Patent No. 5,151,510; Uhlmann and Peyman, Chemical Reviews 90:543 (1990), the disclosures of which are hereby incorporated by reference. An oligonucleotide can include a label for detection, if desired. "Operably linked" sequences include both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest. The term "expression control sequence" as used herein means polynucleotide sequences that are necessary to affect the expression and processing of coding sequences to which they are ligated. Expression control sequences include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance protein secretion. The nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include promoter, ribosomal binding site, and transcription termination sequence; in eukaryotes, generally, such control sequences include promoters and transcription termination sequence. The term "control sequences" is intended to include, at a minimum, all components whose presence is essential for expression and processing, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. The term "vector", as used herein, means a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. In some embodiments, the vector is a plasmid, i.e., a circular double stranded piece of DNA into which additional DNA segments may be ligated. In some embodiments, the vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. In some embodiments, the vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). In other embodiments, the vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply, "expression vectors").
The term "recombinant host cell" (or simply "host cell"), as used herein, means a cell into which a recombinant expression vector has been introduced. It should be understood that "recombinant host cell" and "host cell" mean not only the particular subject cell but also the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term "host cell" as used herein.
The term "percent sequence identity" in the context of nucleotide or aminoacidic sequences means the residues in two sequences that are the same when aligned for maximum correspondence. The length of sequence identity comparison may be over a stretch of at least about nine nucleotides, usually at least about 18 nucleotides, more usually at least about 24 nucleotides, typically at least about 28 nucleotides, more typically at least about 32 nucleotides, and preferably at least about 36, 48 or more nucleotides. There are a number of different algorithms known in the art which can be used to measure nucleotide sequence identity. For instance, polynucleotide sequences can be compared using FASTA, Gap or Bestfit, which are programs available, provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences (Pearson, Methods Enzymol. 183:63-98 (1990); Pearson, Methods Mol. Biol. 132: 185-219 (2000); Pearson, Methods Enzymol. 266:227-258 (1996); Pearson, J Mol. Biol 276:71-84 (1998); incorporated herein by reference). The term "substantial similarity" or "substantial sequence similarity," when referring to a nucleic acid or fragment thereof, or aminoacidic means that when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 85%, preferably at least about 90%, and more preferably at least about 95%, 96%, 97%, 98% or 99% of the nucleotide bases, as measured by any well-known algorithm of sequence identity, such as FASTA, BLAST or Gap, as discussed above. As applied to polypeptides, the term "substantial identity" means that two peptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights as supplied with the programs, share at least 70%, 75% or 80% sequence identity, preferably at least 90% or 95% sequence identity, and more preferably at least 97%, 98% or 99% sequence identity. In certain embodiments, residue positions that are not identical differ by conservative amino acid substitutions. A "conservative amino acid substitution" is one in which an amino acid residue is substituted by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or hydrophobicity). In general, a conservative amino acid substitution will not substantially change the functional properties of a protein. In cases where two or more amino acid sequences differ from each other by conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well- known to those of skill in the art. See, e.g., Pearson, Methods Mol. Biol. 243 :307-31 (1994). Examples of groups of amino acids that have side chains with similar chemical properties include 1) aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine; 2) aliphatic- hydroxyl side chains: serine and threonine; 3) amide-containing side chains: asparagine and glutamine; 4) aromatic side chains: phenylalanine, tyrosine, and tryptophan; 5) basic side chains: lysine, arginine, and histidine; 6) acidic side chains: aspartic acid and glutamic acid; and 7) sulphur-containing side chains: cysteine and methionine. Conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, glutamate-aspartate, and asparagine-glutamine. Alternatively, a conservative replacement is any change having a positive value in the PAM250 log-likelihood matrix disclosed in Gonnet et al, Science 256: 1443-45 (1992), incorporated herein by reference. A "moderately conservative" replacement is any change having a nonnegative value in the PAM250 log-likelihood matrix. Sequence identity for polypeptides is typically measured using sequence analysis software. Protein analysis software matches sequences using measures of similarity assigned to various substitutions, deletions and other modifications, including conservative amino acid substitutions. For instance, GCG contains programs such as "Gap" and "Bestfit" which can be used with default parameters as specified by the programs to determine sequence homology or sequence identity between closely related polypeptides, such as homologous polypeptides from different species of organisms or between a wild type protein and a mutein thereof.
As used herein, the terms "label" or "labelled" refers to incorporation of another molecule in the antibody. In one embodiment, the label is a detectable marker, e.g., incorporation of a radiolabelled amino acid or attachment to a polypeptide of biotinyl moieties that can be detected by marked avidin (e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods). In another embodiment, the label or marker can be therapeutic, e.g., a drug conjugate or toxin. Various methods of labelling polypeptides and glycoproteins are known in the art and may be used.
As used herein, the terms "variant of SARS-CoV-2" refers to viruses with one or more mutations that differentiate it from other variants of the SARS-CoV-2 viruses. Examples of SARS-CoV-2 variant are Wuhan virus, B.l.1.7 (alpha, isolated in the United Kingdom), B.1.351 (beta, isolated in South Africa), B.1.1.248 (gamma, isolated in Brazil) and B.1.617.2 (delta, isolated in India).
Human Anti-SARS-CoV-2 S-protein Antibodies and Characterization Thereof
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein characterized in that is capable of neutralizing one or more of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and Delta with an ICioo of less than 25 ng/ml, preferably the ICioo is measured by CPE-MN assay.
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein characterized in that having an equilibrium dissociation constant (KD) against the Spike (S) protein of the SARS-CoV-2 variants Wuhan, Alpha, Beta, Gamma and Delta of less than 6 E'10M, preferably of less than 4, 3, 2, 1 E'10M, the KD is measured for example by surface plasmon resonance assay.
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein characterized in that is capable of neutralizing the SARS-CoV-2 variant Alpha with an ICioo of less than 6.0 ng/ml and/or the SARS-CoV-2 variant Beta with an ICioo of less than 4.0 ng/ml and/or the SARS-CoV-2 variant Gamma with an ICioo of less than 3.0 ng/ml and/or the SARS-CoV-2 variant Delta with an ICioo of less than 7.0 ng/ml, preferably the ICioo is measured by CPE-MN assay, more preferably said human monoclonal antibody or antigen-binding portion thereof having a VL and VH with at least 90% identical in amino acid sequence, preferably at least 95%, more preferably at least 99% with the VH and VL of the antibody MAD1005M04.
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof having an equilibrium dissociation constant (KD) of less than 6 pM6 E'10M, preferably of less than 4, 3, 2, 1 E'10M, against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma as measured by surface plasmon resonance (SPR). In preferred embodiments, the amino acidic sequence of the VH and VL of said human monoclonal antibody or antigen-binding portion thereof is at least 90% identical in amino acid sequence, preferably at least 95%, more preferably at least 99% of the VH an VL of the sequence of the antibody selected from MAD1005M04 or MAD1005H05 or MAD 1009023 or MAD1006E15.
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising: (a) a heavy chain variable domain amino acid sequence that comprises the amino acid sequence of the heavy chain variable domain of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); (b) a light chain variable domain amino acid sequence that comprises the amino acid sequence of the light chain variable domain of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); (c) a heavy chain variable domain of (a) and a light chain variable domain of (b); or (d) heavy chain and light chain variable domain amino acid sequences comprising the heavy chain and light chain variable domain amino acid sequences, respectively, from the same antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15).
In certain aspects, the invention provides a monoclonal antibody or an antigen-binding portion thereof that specifically binds human SARS-CoV-2 S-protein, comprising: (a) a heavy chain variable domain amino acid sequence that comprises the heavy chain CDR1 , CDR2 and CDR3 amino acid sequences of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); (b) a light chain variable domain amino acid sequence that comprises the light chain CDR1 , CDR2 and CDR3 amino acid sequences of an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15): (c) a heavy chain variable domain of (a) and a light chain variable domain of (b); or (d) the heavy chain variable domain and light chain variable domain of (c), comprising heavy chain and light chain CDR amino acid sequences from the same antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15).
In certain aspects, the invention provides a monoclonal antibody or an antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein, wherein the antibody comprises FR1, FR2, FR3 and FR4 amino acid sequences from an antibody selected from: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In certain aspects, the invention provides a monoclonal antibody that specifically binds SARS-CoV-2 S-protein, wherein said antibody comprises a heavy chain of an antibody selected from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) . In certain aspects, the invention provides a monoclonal antibody that specifically binds SARS-CoV-2 S-protein, wherein said antibody comprises a light chain of an antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) . In certain aspects, the invention provides a monoclonal antibody that specifically binds SARS-CoV-2 S-protein, wherein said antibody comprises a heavy chain and a light chain of the same antibody which is selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising VL and VH domains that are at least 85%, 90%, 95%, 97%, 98% or 99% identical in amino acid sequence to the VL and VH domains, respectively, of a monoclonal antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In certain aspects, the invention provides a human monoclonal antibody or antigen-binding portion thereof that specifically binds SARS-CoV-2 S-protein comprising the light chain and the heavy chain that are at least 85%, 90%, 95%, 97%, 98% or 99% identical in amino acid sequence to the light chain and the heavy chain, respectively, of a monoclonal antibody selected from the group consisting of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
One type of amino acid substitution that may be made is to change one or more cysteines in the antibody, which may be chemically reactive, to another residue, such as, without limitation, alanine or serine. In one embodiment, there is a substitution of a non-canonical cysteine. The substitution can be made in a CDR or framework region of a variable domain or in the constant domain of an antibody. In some embodiments, the cysteine is canonical. Another type of amino acid substitution that may be made is to change any potential proteolytic sites in the antibody. Such sites may occur in a CDR or framework region of a variable domain or in the constant domain of an antibody. Substitution of cysteine residues and removal of proteolytic sites may decrease the risk of any heterogeneity in the antibody product and thus increase its homogeneity. Another type of amino acid substitution is to eliminate asparagine-glycine pairs, which form potential deamidation sites, by altering one or both of the residues. In some embodiments, the C-terminal lysine of the heavy chain of the anti SARS-CoV-2 S-protein antibody of the invention is cleaved. In various embodiments of the invention, the heavy and light chains of the anti-SARS-CoV-2 S-protein antibodies may optionally include a signal sequence.
The class and subclass of anti-SARS-CoV-2 S-protein antibodies may be determined by any method known in the art. In general, the class and subclass of an antibody may be determined using antibodies that are specific for a particular class and subclass of antibody. Such antibodies are commercially available. The class and subclass can be determined by ELISA, or Western blot (immunoblot) as well as other techniques. Alternatively, the class and subclass may be determined by sequencing all or a portion of the constant domains of the heavy and/or light chains of the antibodies, comparing their amino acid sequences to the known amino acid sequences of various class and subclasses of immunoglobulins, and determining the class and subclass of the antibodies.
In some embodiments, the human anti-SARS-CoV-2 S-protein antibody is an IgG, an IgM, an IgE, an IgA, or an IgD molecule. In one embodiment, the human anti-SARS-CoV-2 S- protein antibody is an IgG and is an IgGl, IgG2, IgG3, IgG4 subclass. In still another embodiment, the human antibody subclass is IgGl.
Binding Affinity of Anti-SARS-CoV-2 S-protein Antibodies to SARS-CoV-2 S-protein.
In some embodiments of the invention, the anti-SARS-CoV-2 S-protein antibodies bind to SARS-CoV-2 S-protein with high affinity. In some embodiments, the anti-SARS-CoV-2 S- protein antibodies bind with high affinity to the SI domain of SARS-CoV-2 S-protein. In some embodiments, the anti-SARS-CoV-2 S-protein antibodies bind to the S2 domain of SARS-CoV-2 S-protein. In another embodiment, the anti-SARS-CoV-2 S-protein antibody binds to SARS-CoV S-protein. The binding affinity and dissociation rate of an anti-SARS- CoV-2 S-protein antibody to SARS-CoV-2 S-protein can be determined by methods known in the art. The binding affinity can be measured by ELISAs, RIAs, flow cytometry, surface plasmon resonance, such as BIACORE(TM). The dissociate rate can be measured by surface plasmon resonance. Preferably, the binding affinity and dissociation rate is measured by surface plasmon resonance. More preferably, the binding affinity and dissociation rate are measured using BIACORE(TM). One can determine whether an antibody has substantially the same KD as an anti-SARS-CoV-2 S-protein antibody by using methods known in the art. Example V exemplifies a method for determining affinity constants of anti-SARS-CoV- 2 S-protein monoclonal antibodies.
Identification of SARS-CoV-2 S-protein Epitopes Recognized by Anti-SARS-CoV-2 S- protein Antibodies.
The invention provides a human anti-SARS-CoV-2 S-protein monoclonal antibody that binds to SARS-CoV-2 S-protein and competes or cross-competes with and/or binds the same epitope as an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) . If two antibodies reciprocally compete with each other for binding to SARS-CoV-2 S-protein, they are said to crosscompete.
One can determine whether an antibody binds to the same epitope or cross competes for binding with an anti-SARS-CoV-2 S-protein antibody by using methods known in the art. In one embodiment, one allows the anti-SARS-CoV-2 S-protein antibody of the invention to bind to SARS-CoV-2 S-protein under saturating conditions and then measures the ability of the test antibody to bind to SARS-CoV-2 S-protein. If the test antibody is able to bind to SARS-CoV-2 S-protein at the same time as the anti-SARS-CoV-2 S-protein antibody, then the test antibody binds to a different epitope as the anti-SARS-CoV-2 S-protein antibody. However, if the test antibody is not able to bind to SARS-CoV-2 S-protein at the same time, then the test antibody binds to the same epitope, an overlapping epitope, or an epitope that is in close proximity to the epitope bound by the human anti-SARS-CoV-2 S-protein antibody, or the binding of the human anti-SARS-CoV-2 S-protein antibody may induce a conformational change in the SARS-CoV-2 S-protein that prevents or reduces binding of the test antibody. This experiment can be performed using ELISA, RIA, BIACORE(TM), flow cytometry or other methods known in the art.
To test whether an anti-SARS-CoV-2 S-protein antibody cross-competes with another anti- SARS-CoV-2 S-protein antibody, one may use the competition method described above in two directions i.e. determining if the reference antibody blocks the test antibody and vice versa. In one embodiment, the experiment is performed using ELISA. Methods of determining KD are discussed further below.
In another embodiment, the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases SARS-CoV-2 S-protein binding to a receptor, in particular, to angiotensin-converting enzyme 2 (ACE2). In another embodiment, the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases SARS-CoV-2 S- protein-mediated viral entry into cells. In another embodiment, the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases fusion of viral and cell membranes. In another embodiment, the invention provides an anti-SARS-CoV-2 S- protein antibody that decreases viral load. In another embodiment, the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases in severity for any period of time symptoms or conditions resulting from SARS-CoV-2 infection. In certain embodiments, the invention provides an anti-SARS-CoV-2 S-protein antibody that inhibits, blocks, or decreases in severity for a day, a week, a month, 6 months, a year, or for the remainder of the subjects’ life symptoms or conditions resulting from SARS-CoV-2 infection by 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%. In certain embodiments, the invention provides an anti-SARS-CoV-2 S-protein antibody that may perform any combination of the preceding embodiments.
In certain embodiments, the mAb constant region of the antibodies is modified for half-life extension and reduced risk of Antibody-Dependent Enhancement (ADE) of disease. For example, to enhance the therapeutic activity of mAbs two different and alternative sets of mutations into their constant domains (M252Y/S254T/T256E according to Dall’Acqua et al., 2006; M428L/N434S as reported by Zalevsky et al., 2010) may be applied.
In certain embodiments, in order to reduce the risk of Antibody-Dependent Enhancement (ADE) of disease, mutations that abrogate binding to Fc receptors will be introduced in the Fc part of the IgGl molecule as previously described (L234A/L235A as in Hezareh et al., 2001; Beltramello et al., 2010; P329G LALA as in Schlothauer et al., 2016). All of these modifications may be carried out by means of site-directed mutagenesis, for example using the Agilent Quick-Change II Site-Directed Mutagenesis Kit, according to the manufacturer’s recommendations.
In certain embodiments, the antibody comprises the variable regions of an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) and a mutant IgGl constant region backbone, which contains one or more of the following groups of mutations: L234A/L235A (as in Hezareh et al., 2001; Beltramello et al., 2010), P329G (as in Schlothauer et al., 2016); M428L/N434S (as in Zalevsky et al., 2010). Preferably the antibody comprises the variable regions of an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) and a mutant IgGl constant region backbone, which contains all three groups of such mutations.
Nucleic Acids, Vectors, Host Cells, and Recombinant Methods of Making Antibodies Nucleic Acids
The present invention also encompasses nucleic acid molecules encoding anti- SARS-CoV- 2 S-protein antibodies or antigen-binding portions thereof. In some embodiments, different nucleic acid molecules encode a heavy chain and a light chain of an anti-SARS-CoV-2 S- protein immunoglobulin. In other embodiments, the same nucleic acid molecule encodes a heavy chain and a light chain of an anti-SARS-CoV-2 S-protein immunoglobulin. In one embodiment, the nucleic acid encodes a SARS-CoV-2 S-protein antibody, or antigenbinding portion thereof, of the invention. In some embodiments, the nucleic acid molecule comprises a nucleotide sequence that encodes a VL amino acid sequence comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 conservative amino acid substitutions and/or 1, 2, or 3 non- conservative substitutions compared to germline. Substitutions may be in the CDR regions, the framework regions, or in the constant domain. In some embodiments, the nucleic acid molecule encodes a VL amino acid sequence comprising one or more variants compared to germline sequence that are identical to the variations found in the VL of one of the antibodies selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In some embodiments, the nucleic acid molecule encodes at least three amino acid substitutions compared to the germline sequence found in the VL of one of the antibodies selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
In some embodiments, the nucleic acid molecule comprises a nucleotide sequence that encodes the VL amino acid sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or a variant or portion thereof. In some embodiments, the nucleic acid encodes an amino acid sequence comprising the light chain CDRs of one of said above-listed antibodies. In some embodiments, said portion is a contiguous portion comprising CDR1-CDR3. In some embodiments, the nucleic acid encodes the amino acid sequence of the light chain CDRs of said antibody. In some embodiments, said portion encodes a contiguous region from CDR1-CDR3 of the light chain of an anti-SARS-CoV-2 S-protein antibody.
In some embodiments, the nucleic acid molecule encodes a VL amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to a VL amino acid sequence of a VL region of any one of antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) . Nucleic acid molecules of the invention include nucleic acids that hybridize under highly stringent conditions, such as those described above, to a nucleotide sequence encoding the amino acid sequence of a VL region.
In another embodiment, the nucleic acid encodes a full-length light chain of an antibody selected MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or a light chain comprising a mutation, such as one disclosed herein.
In still another embodiment, the nucleic acid molecule encodes the variable domain of the heavy chain (VH) that comprises a human VH1, VH3 or VH4 family gene sequence or a sequence derived therefrom. In some embodiments, the nucleic acid molecule encodes one or more amino acid mutations compared to the germline sequence that are identical to amino acid mutations found in the VH of one of monoclonal antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15).
In some embodiments, the nucleic acid molecule comprises a nucleotide sequence that encodes at least a portion of the VH amino acid sequence of a monoclonal antibody selected from monoclonal antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) all three CDR regions, a contiguous portion including CDR1 -CDR3, or the entire VH region, with or without a signal sequence. In some embodiments, the nucleic acid molecule comprises a nucleotide sequence that encodes the amino acid sequence of one of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or said sequence lacking the signal sequence. In some preferred embodiments, the nucleic acid molecule comprises at least a portion of the nucleotide sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or said sequence lacking the signal sequence. In some embodiments, said portion encodes the VH region (with or without a signal sequence), a CDR3 region, all three CDR regions, or a contiguous region including CDR1-CDR3.
In some embodiments, the nucleic acid molecule encodes a VH amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the VH amino acid sequences of any one of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) .
Nucleic acid molecules of the invention include nucleic acids that hybridize under highly stringent conditions, such as those described above, to a nucleotide sequence encoding the amino acid sequence ofMAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or that encodes a VH region thereof.
In another embodiment, the nucleic acid encodes a full-length heavy chain of an antibody selected from MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or a heavy chain having the amino acid sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) with or without a signal sequence, or a heavy chain comprising a mutation, such as one of the variants discussed herein. Further, the nucleic acid may comprise the nucleotide sequence of MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) with or without a signal sequence, or a nucleic acid molecule encoding a heavy chain comprising a mutation, such as one of the variants discussed herein.
A nucleic acid molecule encoding the heavy or light chain of an anti-SARS-CoV-2 S-protein antibody or portions thereof can be isolated from any source that produces such antibody. In various embodiments, the nucleic acid molecules are isolated from a B cell isolated from an animal immunized with SARS-CoV-2 S-protein or from an immortalized cell derived from such a B cell that expresses or encodes an anti-SARS-CoV-2 S-protein antibody. Methods of isolating mRNA encoding an antibody are well known in the art. See, e.g., Sambrook et al. The mRNA may be used to produce cDNA for use in the polymerase chain reaction (PCR) or cDNA cloning of antibody genes. In one embodiment, the nucleic acid molecule is isolated from a hybridoma that has as one of its fusion partners a human immunoglobulin- producing cell from a non-human transgenic animal. In an even more preferred embodiment, the human immunoglobulin producing cell is isolated from a XENOMOUSE animal. In another embodiment, the human immunoglobulin-producing cell is from a non-human, nonmouse transgenic animal, as described above. In another embodiment, the nucleic acid is isolated from a non-human, non-transgenic animal. The nucleic acid molecules isolated from a non-human, non-transgenic animal may be used, e.g., for humanized antibodies. In some embodiments, a nucleic acid encoding a heavy chain of an anti-SARS-CoV-2 S-protein antibody of the invention can comprise a nucleotide sequence encoding a VH domain of the invention joined in-frame to a nucleotide sequence encoding a heavy chain constant domain from any source. Similarly, a nucleic acid molecule encoding a light chain of an anti-SARS- CoV-2 S-protein antibody of the invention can comprise a nucleotide sequence encoding a VL domain of the invention joined in-frame to a nucleotide sequence encoding a light chain constant domain from any source. In a further aspect of the invention, nucleic acid molecules encoding the variable domain of the heavy (VH) and/or light (VL) chains are "converted" to full-length antibody genes. In one embodiment, nucleic acid molecules encoding the VH or VL domains are converted to full-length antibody genes by insertion into an expression vector already encoding heavy chain constant (CH) or light chain constant (CL) domains, respectively, such that the VH segment is operatively linked to the CH segment(s) within the vector, and/or the VL segment is operatively linked to the CL segment within the vector. In another embodiment, nucleic acid molecules encoding the VH and/or VL domains are converted into full-length antibody genes by linking, e.g., ligating, a nucleic acid molecule encoding a VH and/or VL domains to a nucleic acid molecule encoding a CH and/or CL domain using standard molecular biological techniques. Nucleotide sequences of human heavy and light chain immunoglobulin constant domain genes are known in the art. See, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed., NIH Publ. No. 91- 3242, 1991. Nucleic acid molecules encoding the full-length heavy and/or light chains may then be expressed from a cell into which they have been introduced and the anti-SARS-CoV- 2 S-protein antibody isolated.
The nucleic acid molecules may be used to recombinantly express large quantities of anti- SARS-CoV-2 S-protein antibodies. The nucleic acid molecules also may be used to produce chimeric antibodies, bispecific antibodies, single chain antibodies, immunoadhesins, diabodies, mutated antibodies and antibody derivatives, as described further below. If the nucleic acid molecules are derived from a non-human, non-transgenic animal, the nucleic acid molecules may be used for antibody humanization, also as described below.
In another embodiment, a nucleic acid molecule of the invention is used as a probe or PCR primer for a specific antibody sequence. For instance, the nucleic acid can be used as a probe in diagnostic methods or as a PCR primer to amplify regions of DNA that could be used, inter alia, to isolate additional nucleic acid molecules encoding variable domains of anti- SARS-CoV-2 S-protein antibodies. In some embodiments, the nucleic acid molecules are oligonucleotides. In some embodiments, the oligonucleotides are from highly variable domains of the heavy and light chains of the antibody of interest. In some embodiments, the oligonucleotides encode all or a part of one or more of the CDRs of antibodies MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) or variants thereof as described herein. The nucleic acid molecules herein disclosed may be DNA or RNA molecules.
Vectors
The invention provides vectors comprising nucleic acid molecules that encode the heavy chain of an anti-SARS-CoV-2 S-protein antibody of the invention or an antigen-binding portion thereof. The invention also provides vectors comprising nucleic acid molecules that encode the light chain of such antibodies or antigen-binding portion thereof. The invention further provides vectors comprising nucleic acid molecules encoding fusion proteins, modified antibodies, antibody fragments, and probes thereof. In some embodiments, the anti- SARS-CoV-2 S-protein antibodies or antigen-binding portions of the invention are expressed by inserting DNAs encoding partial or full-length light and heavy chains, obtained as described above, into expression vectors such that the genes are operatively linked to necessary expression control sequences such as transcriptional and translational control sequences. Expression vectors include plasmids, retroviruses, adenoviruses, adeno- associated viruses (AAV), plant viruses such as cauliflower mosaic virus, tobacco mosaic virus, cosmids, YACs, EBV derived episomes, and the like. The antibody gene is ligated into a vector such that transcriptional and translational control sequences within the vector serve their intended function of regulating the transcription and translation of the antibody gene. The expression vector and expression control sequences are chosen to be compatible with the expression host cell used. The antibody light chain gene and the antibody heavy chain gene can be inserted into separate vectors. In one embodiment, both genes are inserted into the same expression vector. The antibody genes are inserted into the expression vector by standard methods (e.g., ligation of complementary restriction sites on the antibody gene fragment and vector, or blunt end ligation if no restriction sites are present). A convenient vector is one that encodes a functionally complete human CH or CL immunoglobulin sequence, with appropriate restriction sites engineered so that any VH or VL sequence can easily be inserted and expressed, as described above. In such vectors, splicing usually occurs between the splice donor site in the inserted J region and the splice acceptor site preceding the human C domain, and also at the splice regions that occur within the human CH exons. Polyadenylation and transcription termination occur at native chromosomal sites downstream of the coding regions.
The recombinant expression vector also can encode a signal peptide that facilitates secretion of the antibody chain from a host cell. The antibody chain gene may be cloned into the vector such that the signal peptide is linked in-frame to the amino terminus of the immunoglobulin chain. The signal peptide can be an immunoglobulin signal peptide or a heterologous signal peptide (i.e. a signal peptide from a non -immunoglobulin protein). In addition to the antibody chain genes, the recombinant expression vectors of the invention carry regulatory sequences that control the expression of the antibody chain genes in a host cell. It will be appreciated by those skilled in the art that the design of the expression vector, including the selection of regulatory sequences may depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. Preferred regulatory sequences for mammalian host cell expression include viral elements that direct high levels of protein expression in mammalian cells, such as promoters and/or enhancers derived from retroviral LTRs, cytomegalovirus (CMV) (such as the CMV promoter/enhancer), Simian Virus 40 (SV40) (such as the SV40 promoter/enhancer), adenovirus, (e.g. the adenovirus major late promoter (AdMLP)), polyoma and strong mammalian promoters such as native immunoglobulin and actin promoters. For further description of viral regulatory elements, and sequences thereof, see e.g., U.S. Patent No. 5,168,062, U.S. Patent No. 4,510,245 and U.S. Patent No. 4,968,615. Methods for expressing antibodies in plants, including a description of promoters and vectors, as well as transformation of plants is known in the art. See, e.g., United States Patent 6,517,529, incorporated herein by reference. Methods of expressing polypeptides in bacterial cells or fungal cells, e.g., yeast cells, are also well known in the art. In addition to the antibody chain genes and regulatory sequences, the recombinant expression vectors of the invention may carry additional sequences, such as sequences that regulate replication of the vector in host cells (e.g., origins of replication) and selectable marker genes. The selectable marker gene facilitates selection of host cells into which the vector has been introduced (see e.g., U.S. Patent Nos. 4,399,216, 4,634,665 and 5,179,017, incorporated herein by reference). For example, typically the selectable marker gene confers resistance to drugs, such as G418, hygromycin or methotrexate, on a host cell into which the vector has been introduced. Preferred selectable marker genes include the dihydrofolate reductase (DHFR) gene (for use in dhfir- host cells with methotrexate selection/amplification), the neo gene (for G418 selection), and the glutamate synthetase gene.
In some embodiments said vector is a selected from RNA virus vectors, DNA virus vectors, plasmid viral vectors, adenovirus vectors, adenovirus associated virus vectors, herpes virus vectors and retrovirus vectors.
In some aspects, the invention provides compositions (e.g., pharmaceutical compositions), methods, kits and reagents, comprising an isolated nucleic acid molecules according or a vectors according to any one of the embodiments herein disclosed for use in the prevention and/or treatment of a SARS-CoV-2 infections, in particular in humans and other mammals. In some embodiments such nucleic acid molecules and vectors are formulated in a nanoparticle, for example in lipid nanoparticle, cationic lipid nanoparticle, examples of such formulations can be found in US2020197510 herein incorporated by reference.
Non-Hybridoma Host Cells and Methods of Recombinantly Producing Protein
Nucleic acid molecules encoding anti-SARS-CoV-2 S-protein antibodies and vectors comprising these nucleic acid molecules can be used for transfection or transformation of a suitable mammalian, plant, bacterial or yeast host cell. Transfection or 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, and direct microinjection of the DNA into nuclei. In addition, nucleic acid molecules may be introduced into mammalian cells by viral vectors. Methods of transforming cells are well known in the art (see, e.g., U.S. Patent Nos. 4,399,216, 4,912,040, 4,740,461, and 4,959,455, incorporated herein by reference). Methods for transforming plant cells are well known in the art, including, e.g., Agrobacterium- mediated transformation, biolistic transformation, direct injection, electroporation and viral transformation. Methods for transforming bacterial and yeast cells are also well known in the art. Mammalian cell lines available as hosts for expression are well known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC). These include, inter alia, Chinese hamster ovary (CHO) cells, N50 cells, SP2 cells, HEK-293T cells, NH4-3T3 cells, HeLa cells, baby hamster kidney (BHK) cells, African green monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), A549 cells, and a number of other cell lines. Cell lines of particular preference are selected through determining which cell lines have high expression levels. Other cell lines that may be used are insect cell lines, such as Sf9 or Sf21 cells. When recombinant expression vectors encoding antibody genes are introduced into mammalian host cells, the antibodies are produced by culturing the host cells for a period of time sufficient to allow for expression of the antibody in the host cells or, more preferably, secretion of the antibody into the culture medium in which the host cells are grown. Antibodies can be recovered from the culture medium using standard protein purification methods. Plant host cells include, e.g., Nicotiana, Arabidopsis, duckweed, corn, wheat, potato, etc. Bacterial host cells include E. coli and Streptomyces species. Yeast host cells include Schizosaccharomyces pombe, Saccharomyces cerevisiae and Pichia pastoris. Further, expression of antibodies of the invention from production cell lines can be enhanced using a number of known techniques. For example, the glutamine synthetase gene expression system (the GS system) is a common approach for enhancing expression under certain conditions. The GS system is discussed in whole or part in connection with European Patent Nos. 0216 846, 0 256 055, 0 323 997 and 0338 841. It is likely that antibodies expressed by different cell lines or in transgenic animals will have different glycosylation from each other. However, all antibodies encoded by the nucleic acid molecules provided herein, or comprising the amino acid sequences provided herein are part of the instant invention, regardless of the glycosylation of the antibodies. Transgenic Animals and Plants
Anti-SARS-CoV-2 S-protein antibodies of the invention also can be produced transgenically through the generation of a mammal or plant that is transgenic for the immunoglobulin heavy and light chain sequences of interest and production of the antibody in a recoverable form therefrom. In connection with the transgenic production in mammals, anti-SARS-CoV-2 S- protein antibodies can be produced in, and recovered from, the milk of goats, cows, or other mammals. See, e.g., U.S. Patent Nos. 5,827,690, 5,756,687, 5,750,172, and 5,741,957, incorporated herein by reference. In some embodiments, non- human transgenic animals that comprise human immunoglobulin loci are immunized with SARS-CoV-2 S-protein or an immunogenic portion thereof, as described above. Methods for making antibodies in plants are described, e.g., in U.S. patents 6,046,037 and 5,959,177, incorporated herein by reference.
In some embodiments, non-human transgenic animals or plants are produced by introducing one or more nucleic acid molecules encoding an anti-SARS-CoV-2 S-protein antibody of the invention into the animal or plant by standard transgenic techniques. See Hogan and United States Patent 6,417,429, supra. The transgenic cells used for making the transgenic animal can be embryonic stem cells or somatic cells or a fertilized egg. The transgenic non- human organisms can be chimeric, nonchimeric heterozygotes, and nonchimeric homozygotes. See, e.g., Hofian et al. Manipulating the Mouse Embryo: A Laboratory Manual second ed., Cold Spring Harbor Press (1999); Jackson et al, Mouse Genetics and Transgenics: A Practical Approach, Oxford University Press (2000); and Pinkert, Transgenic Animal Technology: A Laboratory Handbook, Academic Press (1999), all incorporated herein by reference. In some embodiments, the transgenic non-human animals have a targeted disruption and replacement by a targeting construct that encodes a heavy chain and/or a light chain of interest. In one embodiment, the transgenic animals comprise and express nucleic acid molecules encoding heavy and light chains that specifically bind to SARS-CoV-2 S-protein, and preferably to (i) the SI domain of SARS-CoV-2 S-protein; (ii) the S2 domain of SARS-CoV-2 S-protein; or (iii) both (i) and (ii). In one embodiment, the transgenic animals comprise and express nucleic acid molecules encoding heavy and light chains that specifically bind to human SARS-CoV-2 S-protein. In some embodiments, the transgenic animals comprise nucleic acid molecules encoding a modified antibody such as a single-chain antibody, a chimeric antibody or a humanized antibody. The anti-SARS-CoV- 2 S-protein antibodies may be made in any transgenic animal. In one embodiment, the nonhuman animals are mice, rats, sheep, pigs, goats, cattle or horses. The non-human transgenic animal expresses said encoded polypeptides in blood, milk, urine, saliva, tears, mucus and other bodily fluids.
Class switching
Another aspect of the invention provides a method for converting the class or subclass of an anti-SARS-CoV-2 S-protein antibody to another class or subclass. In some embodiments, a nucleic acid molecule encoding a VL or VH that does not include sequences encoding CL or CH is isolated using methods well-known in the art. The nucleic acid molecule then is operatively linked to a nucleotide sequence encoding a CL or CH from a desired immunoglobulin class or subclass. This can be achieved using a vector or nucleic acid molecule that comprises a CL or CH chain, as described above. For example, an anti- SARS- CoV-2 S-protein antibody that was originally IgM can be class switched to an IgG. Further, the class switching may be used to convert one IgG subclass to another, e.g., from IgGl to IgG2. Another method for producing an antibody of the invention comprising a desired isotype comprises the steps of isolating a nucleic acid encoding a heavy chain of an anti- SARS-CoV-2 S-protein antibody and a nucleic acid encoding a light chain of an anti- SARS- CoV-2 S-protein antibody, isolating the sequence encoding the VH region, ligating the VH sequence to a sequence encoding a heavy chain constant domain of the desired isotype, expressing the light chain gene and the heavy chain construct in a cell, and collecting the anti-SARS-CoV-2 S-protein antibody with the desired isotype.
Modified Antibodies In another embodiment, a fusion antibody or immunoadhesin may be made that comprises all or a portion of an anti-SARS-CoV-2 S-protein antibody of the invention linked to another polypeptide. In one embodiment, only the variable domains of the anti-SARS-CoV-2 S- protein antibody are linked to the polypeptide. In still another embodiment, the VH domain of an anti-SARS-CoV-2 S-protein antibody is linked to a first polypeptide, while the VL domain of an anti-SARS-CoV-2 S-protein antibody is linked to a second polypeptide that associates with the first polypeptide in a manner such that the VH and VL domains can interact with one another to form an antigen binding site. In still another embodiment, the VH domain is separated from the VL domain by a linker such that the VH and VL domains can interact with one another (see below under Single Chain Antibodies). The VH-linker- VL antibody is then linked to the polypeptide of interest. The fusion antibody is useful for directing a polypeptide to a SARS-CoV-2 S-protein -expressing cell or tissue. The polypeptide may be a therapeutic agent, such as a toxin, chemokine or other regulatory protein, or may be a diagnostic agent, such as an enzyme that may be easily visualized, such as horseradish peroxidase. In addition, fusion antibodies can be created in which two (or more) single-chain antibodies are linked to one another. This is useful if one wants to create a divalent or polyvalent antibody on a single polypeptide chain, or if one wants to create a bispecific antibody or nanobody. To create a single chain antibody, (scFv) the VH- and VL- encoding DNA fragments are operatively linked to another fragment encoding a flexible linker, e.g., encoding the amino acid sequence (GIy4 -Ser)3, such that the VH and VL sequences can be expressed as a contiguous single-chain protein, with the VL and VH domains joined by the flexible linker. See, e.g., Bird et al, Science 242:423-426 (1988); Huston et al, Proc. Natl. Acad. ScL USA 85:5879-5883 (1988); McCafferty et al., Nature 348:552-554 (1990). The single chain antibody may be monovalent, if only a single VH and VL are used, bivalent, if two VH and VL are used, or polyvalent, if more than two VH and VL are used. Bispecific or polyvalent antibodies may be generated that bind specifically to SARS-CoV-2 S-protein and to another molecule. Bispecific antibodies or antigen-binding fragments can be produced by a variety of methods including fusion of hybridomas or linking of Fab' fragments. See, e.g., Songsivilai & Lachmann, Clin. Exp. Immunol. 79: 315-321 (1990), Kostelny et al, J. Immunol. 148: 1547-1553 (1992). In addition, bispecific antibodies may be formed as "diabodies" or "Janusins". In some embodiments, the bispecific antibody binds to two different epitopes of SARS-CoV-2 S-protein. In some embodiments, the bispecific antibody has a first heavy chain and a first light chain from monoclonal antibody MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15) and an additional antibody heavy chain and light chain. In some embodiments, the additional light chain and heavy chain also are from one of the aboveidentified monoclonal antibodies, but are different from the first heavy and light chains. In some embodiments, the modified antibodies described above are prepared using one or more of the variable domains or CDR regions from a human anti-SARS-CoV-2 S-protein monoclonal antibody provided herein.
Derivatized and Labelled Antibodies
An anti-SARS-CoV-2 S-protein antibody or antigen-binding portion of the invention can be derivatized or linked to another molecule (e.g., another peptide or protein). In general, the antibodies or portion thereof are derivatized such that the SARS-CoV-2 S-protein binding is not affected adversely by the derivatization or labelling. Accordingly, the antibodies and antibody portions of the invention are intended to include both intact and modified forms of the human anti-SARS-CoV-2 S-protein antibodies described herein. For example, an antibody or antibody portion of the invention can be functionally linked (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another antibody (e.g., a bispecific antibody or a diabody), a detection agent, a cytotoxic agent, a pharmaceutical agent, and/or a protein or peptide that can mediate association of the antibody or antibody portion with another molecule (such as a streptavidin core region or a polyhistidine tag). One type of derivatized antibody is produced by crosslinking two or more antibodies (of the same type or of different types, e.g., to create bispecific antibodies). Suitable crosslinkers include those that are heterobifunctional, having two distinctly reactive groups separated by an appropriate spacer (e.g., m-maleimidobenzoyl-N- hydroxysuccinimide ester) or homobifunctional {e.g., disuccinimidyl suberate). Such linkers are available from Pierce Chemical Company, Rockford, II. [0179], Another kind of derivatized antibody is a labelled antibody. Useful detection agents with which an antibody or antigen-binding portion of the invention may be derivatized include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, phycoerythrin, 5-dimethylamine-l-napthalenesulfonyl chloride, lanthanide phosphors and the like. An antibody can also be labelled with enzymes that are useful for detection, such as horseradish peroxidase, [beta]-galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like. When an antibody is labelled with a detectable enzyme, it is detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present, the addition of hydrogen peroxide and diaminobenzidine leads to a coloured reaction product, which is detectable. An antibody can also be labelled with biotin, and detected through indirect measurement of avidin or streptavidin binding. An antibody can also be labelled with a predetermined polypeptide epitope recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance. An anti-SARS-CoV-2 S-protein antibody can also be labelled with a radiolabelled amino acid. The radiolabel can be used for both diagnostic and therapeutic purposes. For instance, the radiolabel can be used to detect SARS-CoV-2 S-protein-expressing tumours by x-ray or other diagnostic techniques. Further, the radiolabel can be used therapeutically as a toxin for cancerous cells or tumours. In some embodiments, the anti-SARS-CoV-2 S-protein antibody can be labelled with a paramagnetic, radioactive or florigenic ion that is detectable upon imaging. In some embodiments, the paramagnetic ion is chromium (III), manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III), ytterbium (III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) or erbium (III). In other embodiments, the radioactive ion is iodine 123, technetium 99, indium 111, rhenium 188, rhenium 186, copper 67, iodine 131, yttrium90, iodine 125, astatine 211, and gallium 67. In other embodiments, the anti-SARS-CoV-2 S-protein antibody is labelled with an X-ray imaging agent such as lanthanum (III), gold (III) lead (II) and bismuth (III).
Compositions and Kits
The invention relates to compositions comprising the human anti-SARS-CoV-2 S-protein antibody of the invention and one or more pharmaceutical acceptable excipients and/or carriers.
In certain embodiments, the composition may comprise antibodies or a binding portion thereof of any of the preceding embodiments. In some embodiments, the subject of treatment is a human. In other embodiments, the subject is a veterinary subject. In some embodiments, an antagonist anti-SARS-CoV-2 S-protein antibody that binds to the SI domain and one that binds to the S2 domain or antigen-binding portions of either or both, are both administered to a subject, either together or separately. In certain embodiments the antibodies are in a composition comprising a pharmaceutically acceptable carrier. In another embodiment, one or more of the antagonist SARS-CoV-2 S-protein antibodies of the invention are administered in combination with one or more additional antagonistic antibodies that bind different epitopes on the S-protein, that bind the S-protein from different isolates of SARS- CoV-2 and/or that bind different stages of SARS-CoV-2 (i.e., early, middle or late stage virus). As used herein, "pharmaceutically acceptable carrier" means any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. Some examples of pharmaceutically acceptable carriers are water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition. Additional examples of pharmaceutically acceptable substances are wetting agents or minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the antibody. The compositions of this invention may be in a variety of forms, for example, liquid, semi-solid and solid dosage forms, such as liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, liposomes and suppositories. The preferred form depends on the intended mode of administration and therapeutic application. Typical preferred compositions are in the form of injectable or infusible solutions, such as compositions similar to those used for passive immunization of humans. The preferred mode of administration is parenteral (e.g., intravenous, subcutaneous, intraperitoneal, intramuscular). In one embodiment, the antibody is administered by intravenous infusion or injection. In still another embodiment, the antibody is administered by intramuscular or subcutaneous injection. Therapeutic compositions are typically sterile and stable under the conditions of manufacture and storage. The composition can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable to high drug concentration. Sterile injectable solutions can be prepared by incorporating the anti-SARS-CoV-2 S-protein antibody in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin. The antibodies of the present invention can be administered by a variety of methods known in the art, although for many therapeutic applications, the preferred route/mode of administration is subcutaneous, intramuscular, or intravenous infusion. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the desired results. Other modes of administration include intraperitoneal, intrabronchial, transmucosal, intraspinal, intrasynovial, intraaortic, intranasal, ocular, otic, topical and buccal. In certain embodiments, the active compound of the antibody compositions may be prepared with a carrier that will protect the antibody against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art. See, e.g., Sustained and Controlled Release Drug Delivery Systems (J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978). The invention also provides compositions suitable for administration by inhalation, which comprise the anti-SARS-CoV-2 S-protein antibodies described herein. The anti-SARS- CoV-2 S-protein antibodies may be conveniently delivered to a subject in the form of an aerosol spray presentation from pressurized packs or from a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. Dellamary et al. (2004) J Control Release. ;95(3): 489-500 describes formulations for the pulmonary delivery of antibodies. The invention also provides compositions, suitable for administration through the oral mucosa, which comprise the anti-SARS-CoV-2 S-protein antibody described herein. Oral transmucosal delivery refers to the delivery of a delivery vehicle across a mucous membrane in the oral cavity, pharyngeal cavity, or esophagus, and may be contrasted, for example, with traditional oral delivery, in which absorption of a drug occurs in the intestine. Accordingly, routes of administration in which the anti-SARS-CoV- 2 S-protein antibodies are absorbed through the buccal, sublingual, gingival, pharyngeal, and/or esophageal mucosa are all encompassed within "oral transmucosal delivery," as that term is used herein. For administration through the transmucosal mucosa, the anti-SARS- CoV-2 S-protein antibody may be formulated, for example, into chewing gums (see U.S. Pat No. 5,711,961) or buccal patches (see e.g. U.S. Patent No. 5,298,256). The invention also provides compositions suitable for administration through the vaginal mucosa, which comprise the anti-SARS-CoV-2 S-protein antibodies described herein. The anti-SARS- CoV-2 S-protein antibodies of the invention may be formulated into a vaginal suppository, foam, cream, tablet, capsule, ointment, or gel. In certain embodiments, the compositions comprising the anti-SARS-CoV-2 S-protein antibodies are formulated with permeants appropriate to the transmucosal barrier to be permeated. Such penetrants are generally known in the art, and include, for example, for trans mucosal administration bile salts and fusidic acid derivatives. In certain embodiments, an anti-SARS-CoV-2 S-protein antibody of the invention can be orally administered, for example, with an inert diluent or an assailable edible carrier. The compound (and other ingredients, if desired) can also be enclosed in a hard- or soft-shell gelatine capsule, compressed into tablets, or incorporated directly into the subject's diet. For oral therapeutic administration, the anti-SARS-CoV-2 S-protein antibodies can be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. To administer a compound of the invention by other than parenteral administration, it may be necessary to coat the compound with, or co-administer the compound with, a material to prevent its inactivation. Additional active compounds also can be incorporated into the compositions. In certain embodiments, an inhibitory anti-SARS-CoV-2 S-protein antibody of the invention is co-formulated with and/or co-administered with one or more additional therapeutic agents, particularly anti-viral agents. These therapeutic agents include, without limitation, antibodies that bind other targets, photosensitizers, androgen, oestrogen, nonsteroidal anti-inflammatory agents, antihypertensive agents, analgesic agents, antidepressants, antibiotics, anticancer agents, anaesthetics, antiemetics, anti-infectants, contraceptives, antidiabetic agents, steroids, anti-allergy agents, chemotherapeutic agents, anti-migraine agents, agents for smoking cessation, anti-viral agents, immunosuppressants, thrombolytic agent, cholesterol-lowering agents and anti-obesity agents. Therapeutic agents also include peptide analogues that inhibit SARS-CoV-2 S-protein activity, antibodies or other molecules that prevent SARS-CoV-2 entry into a cell, including but not limited to preventing S-protein binding to a receptor such as the ACE2 receptor, and agents that inhibit SARS-CoV-2 S-protein expression. In one embodiment, the additional agents that inhibit SARS-CoV-2 S-protein expression comprise an antisense nucleic acid capable of hybridizing to a SARS-CoV-2 S-protein mRNA, such as a hairpin RNA or siRNA, locked nucleic acids (LNA) or ribozymes. Sequence-specific nucleic acids capable of inhibiting gene function by RNA interference are well-known in the art. Such combination therapies may require lower dosages of the inhibitory anti-SARS-CoV-2 S-protein antibody as well as the co-administered agents, thus avoiding possible toxicities or complications associated with the various monotherapies. In certain specific embodiments, the therapeutic agent(s) that is co-formulated with and/or co-administered with an inhibitory anti-SARS-CoV-2 S- protein antibody of the invention is an antimicrobial agent. Antimicrobial agents include antibiotics (e.g. antibacterial), antiviral agents, antifungal agents, and anti -protozoan agents. Non-limiting examples of antimicrobial agents are sulfonamides, trimethoprimsulfamethoxazole, quinolones, penicillins, and cephalosporins. The compositions of the invention may include a "therapeutically effective amount" or a "prophylactically effective amount" of an antibody or antigen-binding portion of the invention. A "therapeutically effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result. A therapeutically effective amount of the antibody or antibody portion may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the antibody or antibody portion to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the antibody or antibody portion are outweighed by the therapeutically beneficial effects. A "prophylactically effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount may be less than the therapeutically effective amount. For example, the dosage proposed for the monoclonal antibodies against Covidl9 (mAbCol9) is calculated in order to achieve a neutralizing titer in the serum of 1/100. Since most Covid-19 convalescent people have a neutralizing titer ranging from 1/20 to 1/320, it is assumed that a titer exceeding 1/100 will provide sufficient neutralizing potency to eliminate the virus from the blood and the lungs. Considering for example the MAD0004J08 neutralization potency of 3 ng/mL (i.e. 3 pg/L or 3 pg/Kg) we can assume that we can achieve a neutralization titer of 1/100 with 0.3 mg/kg. Therefore, 21 mgs for a person of 70 kg would be sufficient to achieve a titer of 1/100. A proposed dose of 100 mg exceeds the titer of 1/100 by 5fold, while a proposed titer of 400 mg exceeds the titer of 1/100 by 20 fold. Advantageously, the 100 - 400 mgs dosages will allow to move from intravenous to intramuscular injection. This route of administration could be a key advantage in emergency scenarios as it will allow to administer the antibodies herein disclosed, such for example MAD0004J08 in non-hospital care settings increasing the number of people that can quickly benefit from its foreseen therapeutic effect.
Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus can be administered, several divided doses can be administered over time or the dose can be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on (a) the unique characteristics of the anti-SARS-CoV-2 S-protein antibody or portion thereof and the particular therapeutic or prophylactic effect to be achieved, and (b) the limitations inherent in the art of compounding such an antibody for the treatment of sensitivity in individuals.
In one preferred embodiment, the pharmaceutical composition comprising equal or less than 400 mg for dosage unit of the human monoclonal antibody or antigen-binding portion thereof, more preferably less than 400, 350, 300, 250, 200, 150, 100, 50, 25, 10 mg for dosage unit.
The pharmaceutical composition comprising such dosage unit is preferably for parental administration, for example for intravenous, subcutaneous, intraperitoneal or intramuscular administration. In one preferred embodiment, the pharmaceutical composition is in the liquid form in a concentration between 20 and 200 mg/ml, more preferably between 40 and 80 mg/ml. An exemplary, non-limiting range for a therapeutically or prophylactically- effective amount of an antibody or antibody portion of the invention is 0.025 to 50 mg/kg, more preferably 0.1 to 5 mg/kg, more preferably 0.1-5, 0.1 to 4 or 0.25 to 3 mg/kg. In one embodiment, the invention provides human monoclonal antibody or an antigen-binding portion according to any one of the embodiments herein disclosed, for use in a method for prophylactic or therapeutic treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular COVID-19, wherein said method comprising the step of administering to a patient between 0.025 to 50 mg/kg, more preferably 0.1 to 5 mg/kg, more preferably 0.1-5, 0.1 to 4 or 0.25 to 3 mg/kg once a day, for example for at least one, two, three, four, five, six, seven, eight, nine, ten, eleven days. Such patient is a mammal, preferably a human.
In some embodiments, a formulation contains 5 mg/ml of antibody in a buffer of 20mM sodium citrate, pH 5.5, 140mM NaCl, and 0.2 mg/ml polysorbate 80. It is to be noted that dosage values may vary with the type and severity of the condition to be alleviated. It is to be further understood that for any particular subject, specific dosage regimens should be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions, and that dosage ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed composition. Another aspect of the present invention provides kits comprising an anti-SARS-CoV-2 S-protein, or antigen-binding portion, of the invention or a composition comprising such an antibody or antigen-binding fragment. A kit may include, in addition to the antibody or composition, diagnostic or therapeutic agents. A kit can also include instructions for use in a diagnostic or therapeutic method, as well as packaging material such as, but not limited to, ice, dry ice, styrofoam, foam, plastic, cellophane, shrink wrap, bubble wrap, cardboard and starch peanuts. In one embodiment, the kit includes the antibody or a composition comprising it and a diagnostic agent that can be used in a method described below. In still another embodiment, the kit includes the antibody or a composition comprising it and one or more therapeutic agents that can be used in a method described below.
In one embodiment, the antibodies or binding portion thereof or composition comprising such antibodies according to any one of the embodiments herein disclosed are for use in the prevention or the treatment of patients infected with Coronavirus, in particular infected with SARS-CoV-2, for example infected with SARS-CoV-2 wild type, Alpha, Beta, Gamma or Delta. The use of such antibodies and compositions of SARS-CoV-2-specific mAbs include, but are not limited to passive immunization in persons at risk of contracting the infection (e.g. professionally exposed personnel, people living in endemic areas) and therapy of acute cases, either hospitalized or not. The invention also relates to compositions for inhibiting viral infection, and in particular Coronavirus infection, more in particular SARS-CoV-2 infection in a mammal comprising an amount of an antibody of the invention in combination with an amount of an antiviral agent, wherein the amounts of the anti-SARS-CoV-2 S- protein antibody and of antiviral agent are together effective in inhibiting viral replication, viral infection of new cells or viral loads.
Diagnostic Methods of Use
The antibodies according to the invention may use also as diagnostic tools for rapid detection of SARS-CoV-2 infection, in particular for any of the variants selected from Wuhan, Alpha, Beta, Gamma and Delta. In another aspect, the invention provides diagnostic methods. The anti-SARS-CoV-2 S-protein antibodies can be used to detect SARS-CoV-2 S-protein in a biological sample in vitro or in vivo. In one embodiment, the invention provides a method for diagnosing the presence or location of SARS-CoV-2 viruses in a subject in need thereof. The anti-SARS-CoV-2 S-protein antibodies can be used in a conventional immunoassay, including, without limitation, an ELISA, an RIA, flow cytometry, tissue immunohistochemistry, Western blot (immunoblot) or immunoprecipitation. The anti- SARS-CoV-2 S-protein antibodies of the invention can be used to detect SARS-CoV-2 S- protein from humans. The invention provides a method for detecting SARS-CoV-2 S-protein in a biological sample comprising contacting the biological sample with an anti-SARS-CoV- 2 S-protein antibody of the invention and detecting the bound antibody. In one embodiment, the anti-SARS-CoV-2 S-protein antibody is directly labelled with a detectable label. In another embodiment, the anti-SARS-CoV-2 S-protein antibody (the first antibody) is unlabelled and a second antibody or other molecule that can bind the anti-SARS-CoV-2 S- protein antibody is labelled. As is well known to one of skill in the art, a second antibody is chosen that is able to specifically bind the particular species and class of the first antibody. For example, if the anti-SARS-CoV-2 S-protein antibody is a human IgG, then the secondary antibody could be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially, e.g., from Pierce Chemical Co. Example of biological samples to use in the diagnostic methods herein disclosed are urine, stool, blood, saliva, biopsies, cerebrospinal fluid, nasopharyngeal and oropharyngeal wash, sputum, endotracheal aspirate, bronchoalveolar lavage or other biological samples obtainable from a human subject.
Suitable labels for the antibody or secondary antibody have been disclosed supra, and include various enzymes, prosthetic groups, fluorescent materials, luminescent materials and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, [beta]-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol. In other embodiments, SARS-CoV-2 S-protein can be assayed in a biological sample by a competition immunoassay utilizing SARS-CoV-2 S-protein standards labelled with a detectable substance and an unlabelled anti-SARS-CoV-2 S-protein antibody. In this assay, the biological sample, the labelled SARS-CoV-2 S-protein standards and the anti-SARS-CoV-2 S-protein antibody are combined and the amount of labelled SARS-CoV-2 S-protein standard bound to the unlabelled antibody is determined. The amount of SARS-CoV-2 S-protein in the biological sample is inversely proportional to the amount of labelled SARS-CoV-2 S-protein standard bound to the anti-SARS-CoV-2 S-protein antibody. One can use the immunoassays disclosed above for a number of purposes. For example, the anti-SARS-CoV-2 S-protein antibodies can be used to detect SARS-CoV-2 S-protein in cultured cells or as a diagnostic assay in samples from a subject. The diagnostic methods according to any embodiments herein disclosed may be followed by a further step of the administration in the positive subject of an anti-SARS-CoV-2 drugs, for example according to any of the Therapeutic Methods herein disclosed. Therapeutic Methods of Use
In another embodiment, the invention provides a method for neutralizing SARS- CoV-2 by administering an anti-SARS-CoV-2 S-protein antibody to a patient in need thereof. Any of the types of antibodies described herein may be used therapeutically. In various embodiments, the anti-SARS-CoV-2 S-protein antibody is a human antibody. In some embodiments, the antibody, or antigen-binding portion thereof, binds to the SI domain of SARS-CoV-2 S-protein. In some embodiments, the patient is a human patient. Alternatively, the patient may be a mammal infected with SARS-CoV-2. In one embodiment, the invention provides methods of treating, aiding in the treatment, preventing or aiding in the prevention of, SARS-CoV-2 infection and conditions or disorders resulting from such infection, in a subject by administering to the subject a therapeutically-effective or prophylactically effective amount of an anti-SARS-CoV-2 S-protein antibody of the invention. Antibodies and antigen-binding fragments thereof which are antagonists of SARS-CoV-2 S-protein can be used as therapeutics for SARS-CoV-2 infection. The antibody may be administered locally or systemically. The therapeutic compositions comprising anti-SARS-CoV-2 S- protein antibodies may be administered to the subject, for example, orally, nasally, vaginally, buccally, rectally, via the eye, or via the pulmonary route, in a variety of pharmaceutically acceptable dosing forms, which will be familiar to those skilled in the art. For example, the anti-SARS-CoV-2 S-protein antibodies may be administered via the nasal route using a nasal insufflator device. The anti-SARS-CoV-2 S-protein antibodies can also be administered to the eye in a gel formulation. For example, before administration, a formulation containing the anti- SARS-CoV-2 S-protein antibodies may be conveniently contained in a two- compartment unit dose container, one compartment containing a freeze-dried anti-SARS- CoV-2 S-protein antibody preparation and the other compartment containing normal saline. The serum concentration of the antibody may be measured by any method known in the art. In another embodiment, the antibodies of the present invention are administered to the subject in combination with other therapeutic agents. In one embodiment, the additional therapeutic agents may be treating the symptoms of the SARS-CoV-2 infection on their own, and may optionally synergize with the effects of the antibodies. The additional agent that is administered may be selected by one skilled in the art for treating the infection. Coadministration of the antibody with an additional therapeutic agent (combination therapy) encompasses administering a composition comprising the anti-SARS-CoV-2 S-protein antibody and the additional therapeutic agent as well as administering two or more separate compositions, one comprising the anti-SARS-CoV-2 S-protein antibody and the other(s) comprising the additional therapeutic agent(s). Further, although co-administration or combination therapy generally means that the antibody and additional therapeutic agents are administered at the same time as one another, it also encompasses instances in which the antibody and additional therapeutic agents are administered at different times. For instance, the antibody may be administered once every three days, while the additional therapeutic agent is administered once daily. Alternatively, the antibody may be administered prior to or subsequent to treatment with the additional therapeutic agent, for example after a patient has failed therapy with the additional agent. Similarly, administration of the anti-SARS- CoV-2 S-protein antibody may be administered prior to or subsequent to other therapy.
The antibody and one or more additional therapeutic agents (the combination therapy) may be administered once, twice or at least the period of time until the condition is treated, palliated or cured. Preferably, the combination therapy is administered multiple times. The combination therapy may be administered from three times daily to once every six months. The administering may be on a schedule such as three times daily, twice daily, once daily, once every two days, once every three days, once weekly, once every two weeks, once every month, once every two months, once every three months and once every six months, or may be administered continuously via a minipump. The combination therapy may be administered via an oral, mucosal, buccal, intranasal, inhalable, intravenous, subcutaneous, intramuscular, or parenteral. In certain aspects, the invention provides a method for treating, preventing or alleviating the symptoms of a SARS-CoV-2 mediated disorder in a subject in need thereof, comprising the step of administering to said subject an antibody or antigenbinding portion according to any one of the preceding embodiments, further comprising at least one additional therapeutic agent selected from the group consisting of: (a) one or more antibodies from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15): and
(b) one or more antibodies that specifically bind SARS-CoV-2 S-protein of a plurality of SARS-CoV-2 strains; and/or
(c) one or more neutralizing antibodies that do not bind SARS-CoV-2 S-protein; and/or (d) one or more agents that bind SARS-CoV-2 S-protein receptor; and/or
(e) one or more anti-viral agents.
In certain aspects, the invention provides a kit for treating, preventing or alleviating the symptoms of a SARS-CoV-2 mediated disorder in a subject in need thereof, comprising a) one or more antibodies from the group consisting of: MAD1005M04 (OR ABBREVIATED 02M04), MAD1005H05 (OR ABBREVIATED 02H05), MAD 1009023 (OR ABBREVIATED 01023) AND MAD1006E15 (OR ABBREVIATED 01E15); and
(b) one or more antibodies that specifically bind SARS-CoV-2 S-protein of a plurality of SARS-CoV-2 strains; and/or
(c) one or more neutralizing antibodies that do not bind SARS-CoV-2 S-protein; and/or
(d) one or more agents that bind SARS-CoV-2 S-protein receptor; and/or
(e) one or more anti-viral agents.
A further object of the invention is the use of the human monoclonal antibody or antigenbinding portion herein disclosed in the manufacturing of a medicament for treating, preventing or alleviating the symptoms of a SARS-CoV-2 mediated disorder in a subject in need thereof.
The human monoclonal antibody or antigen-binding portion thereof herein disclosed may also be used advantageously as a diagnostic reagent in an in vitro method for detecting in a biological sample previously obtained from a patient (such as for example a serum, plasma, blood sample or any other suitable biological material, obtained from the patient, preferably a human being) anti-Coronavirus antibodies, in particular SARS-Cov-2 antibodies. These antibodies may be found in the biological sample obtained from the patient for instance as a result of a previous exposure to the virus, or because a monoclonal antibody of the invention had been previously administered to the patient for therapeutic or prophylactic or research purposes. Thus, a diagnostic kit comprising the human monoclonal antibody or antigenbinding portion thereof herein disclosed of the invention, as a specific reagent, also falls within the scope of the invention, said kit being in particular designed for the detection and/or quantification, in a biological sample previously obtained from a patient, of anti-coronavirus antibodies.
The human monoclonal antibody or antigen-binding portion thereof herein disclosed may also be used in a vaccine composition. The human monoclonal antibody or antigen-binding portion thereof herein disclosed may also be used advantageously for the design of a vaccine against coronavirus. As disclosed in Rappuoli, Rino et al. “Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. ” The Journal of experimental medicine vol. 213,4 (2016): 469-81. doi:10.1084/jem.20151960”, human mAb may be used to identify protective antigens/epitopes. Structural characterization of the Ab-antigen complex may be used to instruct antigen design. Thus, also a method or the use of the human monoclonal antibody or antigen-binding portion thereof herein disclosed for the design of a vaccine against a coronavirus, in particular against the SARS-Cov-2 virus is within the scope of the invention.
The human monoclonal antibody or antigen-binding portion thereof herein disclosed may be used for the preparation of mimotopes, such as for example anti-idiotype antibodies, peptides, S-protein truncated or artificial forms or others, endowed with the ability of evoking the antibodies herein disclosed. Among these, the anti-idiotype antibodies are preferred. The anti-idiotype antibodies are antibodies specifically directed against the idiotype of the neutralizing antibodies used for the manufacture thereof, and thus are able to mimic the key epitopes that they recognize. The manufacture of anti-idiotype antibodies is carried out by known methodologies that do not need further detailed explanations here. Thus, also mimotopes, preferably anti-idiotype antibodies, directed against an antibody of the invention fall within the scope of the invention. The human monoclonal antibody or antigen-binding portion thereof herein disclosed may be used for the manufacture of antiidiotype antibodies according to the known methods. Anti-idiotype antibodies are antibodies specifically directed towards the idiotype of the broad-range neutralizing antibodies used to prepare them, and as such are able to mimic the key epitopes they recognize. Therefore, antiidiotype antibodies directed against a monoclonal antibody of the invention are also included in the scope of the invention.
The following experimental section is provided solely by way of illustration and not limitation and does not intend to restrict the scope of the invention as defined in the appended claims. The claims are an integral part of the description. EXAMPLES AND EXPERIMENTAL DATA
BACKGROUND:
In a previous study the inventors enrolled 10 donors vaccinated with the BNT162b2 mRNA vaccine, 5 of them were healthy people naive to SARS-CoV-2 infection at vaccination (seronegative) and other 5 had recovered from SARS-CoV-2 infection before vaccination (seropositive)1. From these donors we collected human peripheral blood mononuclear cells (PBMCs) which were used to perform single cell sorting of spike (S) protein specific class- switched memory B cells (MBCs). From all donors a total of 5,884 S protein specific-MBCs were isolated and when tested by ELISA to confirm their binding specificity to the S protein, over 3,200 antibodies resulted to be positive. All antibodies were then tested in a cytopathic effect-based neutralization assay (CPE-MN) to identify SARS-CoV-2 neutralizing antibodies (nAbs). A total of 411 were identified showing different level of neutralization potency and breadth of coverage against the SARS-CoV-2 Wuhan virus and all variants of concern. Out of all identified nAbs, four antibodies, named 02M04, 02H05, 01023 and 01E15, showed unique potency and breadth of activity against the ancestral SARS-CoV-2 Wuhan virus and all four VoCs (alpha, beta, gamma and delta). Herein we report the specific characteristic of these newly discovered antibodies.
Example 1: Cross-neutralization of all current SARS-CoV-2 variants of concern
To further characterize neutralization breadth and potency of human monoclonal antibodies (mAbs) isolated from people vaccinated with the COVID-19 BNT162b2 mRNA vaccine, we tested in our CPE-MN assay the four most promising antibodies identified in our previous study1. The CPE-MN assay was performed as previously described2. These antibodies were named MAD1005M04 (or abbreviated 02M04), MAD1005H05 (or abbreviated 02H05), MAD1009023 (or abbreviated 01023) and MAD1006E15 (or abbreviated 01E15) and showed to compete with the known mAb S309, which binds outside the spike protein receptor binding motif1,3. All mAbs were tested for neutralization against the SARS-CoV-2 Wuhan virus and VoCs B.1.1.7 (isolated in the United Kingdom)4, B.1.351 (isolated in South Africa)5, B.1.1.248 (isolated in Brazil)6, and B.1.617.2 (isolated in India)7. These variants of concern (VoCs) have been re-named by the World Health Organization (WHO) as Alpha, Beta, Gamma, and Delta variants, respectively8. The CPE-MN assay demonstrated that all tested mAbs were able to neutralize the Wuhan virus and all VoCs (Figure 1). The antibody 02M04 possessed the highest neutralization potency among the four antibodies tested, showing a 100% inhibitory concentration (ICioo) of 8.8, 5.9, 3.1, 2.7, 6.5 ng/mL against the Wuhan, alpha, beta, gamma and delta variants respectively followed in potency by the antibodies 02H05, 01023 and 01E15 (Figure 1A-F). In addition, despite we previously observed that 02M04, 02H05, 01023 and 01E15 antibodies competed with S309, therefore recognizing a similar epitope region on the spike protein, our antibodies showed an ICioo over 40-fold higher compared S309 (Figure 1, Table 1).
Table 1. Neutralization activity against SARS-CoV-2 variants of concern [ | | | | |
Figure imgf000051_0001
Example 2: Affinity evaluation against SARS-CoV-2 spike proteins
Following the neutralization activity, we aimed to assess the affinity of 02M04, 02H05, 01023 and 01E15 to different SARS-CoV-2 spike proteins. In our laboratory we have so far produced the alpha, gamma, kappa9 and delta variants against which the four mAbs were tested. Affinity was evaluated by surface plasmon resonance assay as described in our previous work2. All antibodies tested showed picomolar affinity to the different S proteins tested. The equilibrium dissociation constant (KD) of 02M04, 02H05, 01023 and 01E15 ranged from 0.47 - 4.23 E'10M (Figure 2), 0.82 - 2.64 E'10M (Figure 3), 0.71 - 1.93 E'10M (Figure 4), and 1.62 - 5.92 E'10M (Figure 5) respectively.
Example 3: Genetic characterization of SARS-CoV-2 neutralizing antibodies
The genes encoding for the heavy and light chains of 02M04, 02H05, 01023 and 01E15 were characterized. Table 3 lists the full sequences of the heavy and light chains of these latter antibodies. Table 2 shows the immunoglobulin heavy and light variable (IGHV;IGLV) and junction (IGHJ;IGLJ) gene usage, length of the complementary determining region 3 (CDR3) of the heavy (H-CDR3) and light (L-CDR3) chains and the heavy and light chain V-gene mutation frequencies. Overall, we observed higher level of V-gene mutations in the heavy chains compared to the light chains. In addition, 02M04 shows unique heavy and light chain V-J gene rearrangement and the highest level of heavy chain V-gene mutations compared to the other characterized antibodies. Conversely, 02H05, 01023 and 01E15 share the same IGHV-J gene rearrangement (IGHV2-5;! GHJ4-1) and two out of three antibodies accommodate the same lambda chain which shows the IGLV2-14 and IGLJ2-1 genes with identical L-CDR3 length. Interestingly, despite using different IGHV genes, both 02M04 and 01023 accommodate the IGKV1-5 gene flanked by the IGKJ1 and IGKJ3 genes respectively.
Table 2. Genetic features of SARS-CoV-2 neutralizing antibodies
Figure imgf000052_0001
Table 3. Some sequences of the variable domains of the SARS-CoV-2 neutralizing antibodies herein disclosed (corresponding SEQ ID Number are in the sequence listing in the description)
Figure imgf000053_0001
Example 4: Neutralization activity against SARS-CoV-2 MAD0004J08 escape mutant
To evaluate the possibility to combine 02M04, 02H05, 01023 and 01E15 with MAD0004J08 for passive prophylaxis and therapy of COVID-19, we performed our CPE-
MN assay against the SARS-CoV-2 MAD0004J08 escape mutant (J08-EM). This virus was obtained following co-incubation of MAD0004J08 with the SARS-CoV-2 Wuhan virus for multiple passages in vitro. The same approach was used to evaluate in vitro the ability of SARS-CoV-2 to escape from a highly neutralizing COVID-19 convalescent plasma (REF.
Figure imgf000054_0001
01023 showed to be able to neutralize SARS-CoV-2 J08-EM with extreme potency with and ICioo of 9.8, 15.6 and 19.7 ng/mL respectively (Figure 6). Only 01E15 showed almost 100-fold decrease in neutralization potency against SARS-CoV-2 J08-EM compared to its activity against the SARS-CoV-2 Wuhan virus (Figure ID and F; Figure 6). Our data suggest that 02M04, 02H05 and 01023, which already showed an extremely high neutralization potency against SARS-CoV-2 VoCs, are able to resist against mutations on the S protein that evade MAD0004J08 highlighting the possibility of a cocktail development with this latter antibody currently tested in a phase 2-3 clinical trial for the treatment of COVID-19.
REFERENCES
1. Andreano, E., et al. Hybrid immunity improves B cells and antibodies against SARS-CoV-2 variants. Nature (2021).
2. Andreano, E., et al. Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Cell 184, 1821-1835. el816 (2021).
3. Pinto, D., et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290-295 (2020).
4. Public Health England. Investigation of novel SARS-CoV-2 variant Technical briefing. (2021).
5. Tegally, H., et al. Emergence and rapid spread of a new severe acute respiratory syndrome- related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv, 2020.2012.2021.20248640 (2020).
6. Faria, N.R., et al. Genomics and epidemiology of the P.l SARS-CoV-2 lineage in Manaus, Brazil. Science (New York, N.Y.) 372, 815-821 (2021).
7. Cherian, S., et al. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms 9, 1542 (2021).
8. Parums, V. Editorial: Revised World Health Organization (WHO) Terminology for Variants of Concern and Variants of Interest of SARS-CoV-2. Medical science monitor : international medical journal of experimental and clinical research 27, e933622 (2021).
9. Edara, V.-V., et al. Infection and vaccine-induced neutralizing antibody responses to the SARS-CoV-2 B.l.617.1 variant. bioRxiv, 2021.2005.2009.443299 (2021).
Declaration according to Art. 170bis
In compliance with Art. 170bis of the Italian code of industrial property, the applicant of the present patent application declares that:
-For the biological material, containing microorganisms or genetically modified organisms, object or used in the aforementioned patent application, the obligations deriving from national or Community regulations, and in particular, from the provisions referred to in paragraph 6 of the Legislative Decree of 12 April 2001 n.206 and 8 July 2003 n. 224, concerning these modifications, have been respected;
-The donors of the human blood samples used in the present patent application gave their informed written consent. The study was approved by local ethics committees.
Sequence listing in the description
Sequence of the antibody herein identified as MAD1005M04 (or abbreviated 02M04)
AMINO ACID SEQUENCES OF MAD1005M04 (OR ABBREVIATED 02M04):
>SEQ ID NO: 1 CDR 1 of variable domain of Heavy chain of MAD1005M04 (OR ABBREVIATED 02M04) GYSFSYYW
>SEQ ID NO:2 CDR 2 of variable domain of Heavy chain of MAD1005M04 (OR ABBREVIATED 02M04) IYPGNSDT
>SEQ ID NO:3 CDR 3 of variable domain of Heavy chain of MAD1005M04 (OR ABBREVIATED 02M04) GRHEWGDPIDY
>SEQ ID NO:4 CDR 1 of variable domain of Light chain of MAD1005M04 (OR ABBREVIATED 02M04) QSISRW
>SEQ ID NO:5 CDR 2 of variable domain of Light chain of MAD1005M04 (OR ABBREVIATED 02M04) this sequence is not included in the sequence listing because is less than 4 amino acid QAS
>SEQ ID NO:6 CDR 3 of variable domain of Light chain of MAD1005M04 (OR ABBREVIATED 02M04) QQSESYPWT
>SEQ ID NO:7 variable domain of Heavy chain of MAD1005M04 (OR ABBREVIATED 02M04)
QVQLVQSGVEVKKPGESLKISCQGSGYSFSYYWIAWVRQVPGKGLELMGIIYPGNSDTKYSPSFQG
QVTISADKSITTAYLQWSSLKASDTAMYYCGRHEWGDPIDYWGQGTLVTVSSASTK
>SEQ ID NO:8 variable domain of Light chain of MAD1005M04 (OR ABBREVIATED 02M04)
AIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWYQQKPGKAPKLLIYQASSLESGVPSRFSGSGSE
TEFTLTISILQPDDLATYYCQQSESYPWTFGQGTKVEIKRTVAA
>SEQ ID NO:9 Heavy chain of MAD1005M04 (OR ABBREVIATED 02M04)
MGWSCIILFLVATATGVHSQVQLVQSGVEVKKPGESLKISCQGSGYSFSYYWIAWVRQVPGKGLEL
MGIIYPGNSDTKYSPSFQGQVTISADKSITTAYLQWSSLKASDTAMYYCGRHEWGDPIDYWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKP
KDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQD
WLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAV
EWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP GK*
>SEQ ID NO: 10 Light chain of MAD1005M04 (OR ABBREVIATED 02M04)
GWSCIILFLVATATGVHSAIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWYQQKPGKAPKLLIYQ
ASSLESGVPSRFSGSGSETEFTLTISILQPDDLATYYCQQSESYPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY
EKHKVYACEVTHQGLS SPVTKSFNRGEC*
NUCLEIC ACID SEQUENCES OF MAD1005M04 (OR ABBREVIATED 02M04):
> SEQ ID NO: 11 MAD1005M04 (OR ABBREVIATED 02M04)_heavy_chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO: 12 MAD1005M04 (OR ABBREVIATED 02M04)_heavy chain Variable domain
CAGGTGCAGCTGGTGCAGTCTGGAGTAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCC
TGTCAGGGTTCTGGATACAGCTTTTCCTACTACTGGATCGCCTGGGTGCGCCAGGTGCCCGGGA
AAGGCCTGGAATTGATGGGGATCATCTATCCTGGTAACTCTGATACCAAATACAGCCCGTCCTT CCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCACTACCGCCTACCTACAATGGAGCAGC CTGAAGGCCTCGGACACCGCCATGTATTACTGTGGGAGACACGAGTGGGGTGACCCGATTGACT ACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAG
> SEQ ID NO:13 MAD1005M04 (OR ABBREVIATED 02M04)_heavy chain Constant domain
ACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGG
CCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCTGTGACGGTCTCGTGGAACTCAGGCGC
CCTGACCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGC
AGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACA
AGCCCAGCAACACCAAGGTGGACAAGAGAGTTGAGCCCAAATCTTGTGACAAAACTCACACAT
GCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC
CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCAC
GAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACA
AAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCAC CAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCC ATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCC
CCATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATC
CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACG
CCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCA
GGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACAC
GCAGAAGAGCCTCTCCCTGTCCCCGGGTAAATGA
> SEQ ID NO: 14 MAD1005M04 (OR ABBREVIATED 02M04)_heavy chain Complete
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCCAGGTGCA
GCTGGTGCAGTCTGGAGTAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTCAGGG
TTCTGGATACAGCTTTTCCTACTACTGGATCGCCTGGGTGCGCCAGGTGCCCGGGAAAGGCCTG
GAATTGATGGGGATCATCTATCCTGGTAACTCTGATACCAAATACAGCCCGTCCTTCCAAGGCC
AGGTCACCATCTCAGCCGACAAGTCCATCACTACCGCCTACCTACAATGGAGCAGCCTGAAGGC
CTCGGACACCGCCATGTATTACTGTGGGAGACACGAGTGGGGTGACCCGATTGACTACTGGGGC
CAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGCCATCGGTCTTCCCCCTGGCACCCTC
CTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAA
CCTGTGACGGTCTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTTCCCGGCTGTCC
TACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCAC
CCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAGAGTTGA
GCCCAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGA
CCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGT
CACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGA
CGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACC
GTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCA
AGGTCTCCAACAAAGCCCTCCCAGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC
CCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGAGGAGATGACCAAGAACCAGGTCA
GCCTGACCTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGG
GCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTC
TATAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTG
ATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCCCCGGGTAAATGA
> SEQ ID NO:15 MAD1005M04 (OR ABBREVIATED 02M04) light chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO: 16 MAD1005M04 (OR ABBREVIATED 02M04)_light_chain Variable Domain
GCCATCCAGATGACCCAGTCTCCATCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCA
CTTGCCGGGCCAGTCAGAGTATTAGTAGGTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAG
CCCCTAAGCTCCTGATCTATCAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGATTCAGCGG
CAGTGGATCTGAGACAGAATTCACTCTCACCATCAGCATCCTGCAGCCTGATGATCTTGCAACT
TATTACTGCCAACAGTCTGAGAGTTATCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCA AACGAACTGTGGCTGCA
> SEQ ID NO: 17 MAD1005M04 (OR ABBREVIATED 02M04)_light_chain ConstantRegion
GTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTC
TGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAAC
GCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCTAC
AGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGC
GAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGTTAG
> SEQ ID NO:18 MAD1005M04 (OR ABBREVIATED 02M04)_light_kappa_complete_seq
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCGCCATCCA
GATGACCCAGTCTCCATCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGG
GCCAGTCAGAGTATTAGTAGGTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAG
CTCCTGATCTATCAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGATTCAGCGGCAGTGGAT
CTGAGACAGAATTCACTCTCACCATCAGCATCCTGCAGCCTGATGATCTTGCAACTTATTACTGC
CAACAGTCTGAGAGTTATCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAACGAACT
GTGGCTGCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTCTGT
TGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCC
CTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCTACAGC
CTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGCGAA GTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGTTAG
AMINO ACID SEQUENCES OF MAD1005H05 (OR ABBREVIATED 02H05): >SEQ ID NO: 19 CDR 1 of variable domain of Heavy chain of MAD1005H05 (OR ABBREVIATED 02H05) GFSFSSSGVG
>SEQ ID NO:20 CDR 2 of variable domain of Heavy chain of MAD1005H05 (OR ABBREVIATED 02H05)
IYWDDDP
>SEQ ID NO:21 CDR 3 of variable domain of Heavy chain of MAD1005H05 (OR ABBREVIATED 02H05)
AHRSLAAPVLYFDY
>SEQ ID NO:22 CDR 1 of variable domain of Light chain of MAD1005H05 (OR ABBREVIATED 02H05) SSDVGGYNY
>SEQ ID NO:23 CDR 2 of variable domain of Light chain of MAD1005H05 (OR ABBREVIATED 02H05) this sequence is not included in the sequence listing because is less than 4 amino acid
DVT
>SEQ ID NO:24 CDR 3 of variable domain of Light chain of MAD1005H05 (OR ABBREVIATED 02H05) SSFTSTNTYVL
>SEQ ID NO:25 variable domain of Heavy chain of MAD1005H05 (OR ABBREVIATED 02H05)
QVTLKESGPTLVKPTQTLTLTCTFSGFSFSSSGVGVGWIRQPPGKALEWLALIYWDDDPRYNPSLKS
RLTITTDTSKNQVVLTITNMDPVDTATYYCAHRSLAAPVLYFDYWGQGTLVTVSSASTK
>SEQ ID NO:26 variable domain of Light chain of MAD1005H05 (OR ABBREVIATED 02H05)
QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLLIYDVTNRPSGVSNRFSGS
KSGNTASLTISGLQAEDEAGYYCSSFTSTNTYVLFGGGTKLTVLGQPKAA
>SEQ ID NO:27 Heavy chain of MAD1005H05 (OR ABBREVIATED 02H05)
MGWSCIILFLVATATGVHSQVTLKESGPTLVKPTQTLTLTCTFSGFSFSSSGVGVGWIRQPPGKALE
WLALIYWDDDPRYNPSLKSRLTITTDTSKNQVVLTITNMDPVDTATYYCAHRSLAAPVLYFDYWG
QGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLF
PPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTV
LHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYP
SDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQK SLSLSPGK*
>SEQ ID NO:28 Light chain of MAD1005H05 (OR ABBREVIATED 02H05)
GWSCIILFLVATATGVHSQSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLLI
YDVTNRPSGVSNRFSGSKSGNTASLTISGLQAEDEAGYYCSSFTSTNTYVLFGGGTKLTVLGQPKAA
PSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC*
NUCLEIC ACID SEQUENCES OF MAD1005H05 (OR ABBREVIATED 02H05):
> SEQ ID NO:29 MAD1005H05 (OR ABBREVIATED 02H05)_heavy_chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO:30 MAD1005H05 (OR ABBREVIATED 02H05)_heavy chain Variable domain
CAGGTCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCT
GCACCTTCTCTGGGTTCTCATTCAGCAGTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCC
AGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATCCGCGCTACAACCCATCT
CTGAAGAGCAGGCTCACCATCACCACGGACACCTCCAAAAACCAGGTGGTCCTTACAATTACTA
ACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGGAGCTTGGCAGCACCTGTACT
ATACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAG
> SEQ ID NO:31 MAD1005H05 (OR ABBREVIATED 02H05)_heavy chain Constant domain
ACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGG
CCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCTGTGACGGTCTCGTGGAACTCAGGCGC
CCTGACCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGC
AGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACA
AGCCCAGCAACACCAAGGTGGACAAGAGAGTTGAGCCCAAATCTTGTGACAAAACTCACACAT
GCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC
CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCAC
GAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACA
AAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCAC
CAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCC
ATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCC
CCATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATC
CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACG
CCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCA GGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACAC GCAGAAGAGCCTCTCCCTGTCCCCGGGTAAATGA
> SEQ ID NO:32 MAD1005H05 (OR ABBREVIATED 02H05)_heavy chain Complete
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCCAGGTCAC
CTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTC
TCTGGGTTCTCATTCAGCAGTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGG
CCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATCCGCGCTACAACCCATCTCTGAAGAG
CAGGCTCACCATCACCACGGACACCTCCAAAAACCAGGTGGTCCTTACAATTACTAACATGGAC
CCTGTGGACACAGCCACATATTACTGTGCACACAGGAGCTTGGCAGCACCTGTACTATACTTTG
ACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGCCATCGGTCTTCCC
CCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCTGCCTGGTCAAGGAC
TACTTCCCCGAACCTGTGACGGTCTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCT
TCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGC
AGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCAACACCAAGGTGGAC
AAGAGAGTTGAGCCCAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAA
CTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCC
GGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCA
ACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACA
ACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGA
GTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCCATCGAGAAAACCATCTCCAAAGC
CAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGAGGAGATGACCAA
GAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGG
GAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGC
TCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCT
CATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCCCC GGGTAAATGA
> SEQ ID NO:33 MAD1005H05 (OR ABBREVIATED 02H05) light chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO:34 MAD1005H05 (OR ABBREVIATED 02H05)_light_chain Variable Domain
CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTG
CACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGC
AAAGCCCCCAAACTCTTGATTTATGATGTCACTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTC
TGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCT
GGTTATTACTGCAGCTCATTCACAAGCACCAACACTTATGTGCTATTCGGCGGAGGGACCAAGC TGACCGTCCTAGGTCAGCCCAAGGCTGCC
> SEQ ID NO:35 MAD1005H05 (OR ABBREVIATED 02H05)_light_chain ConstantRegion
GTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTC
TGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAAC
GCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCTAC
AGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGC
GAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGTTAG
> SEQ ID NO:36 MAD1005H05 (OR ABBREVIATED 02H05)_light_kappa_complete_seq
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCCAGTCTGC
CCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAA
CCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCC
CAAACTCTTGATTTATGATGTCACTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCA
AGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGGTTATTA
CTGCAGCTCATTCACAAGCACCAACACTTATGTGCTATTCGGCGGAGGGACCAAGCTGACCGTC
CTAGGTCAGCCCAAGGCTGCCTCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGG
AACTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAG
GTGGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGAC
AGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTC
TACGCCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGA
GAGTGTTAG
AMINO ACID SEQUENCES OF MAD1009023 (OR ABBREVIATED 01023):
>SEQ ID NO:37 CDR 1 of variable domain of Heavy chain of MAD1009023 (OR ABBREVIATED 01023) GFSLSTPGVA
>SEQ ID NO:38 CDR 2 of variable domain of Heavy chain of MAD1009023 (OR ABBREVIATED 01023) LYWDDDK
>SEQ ID NO:39 CDR 3 of variable domain of Heavy chain of MAD1009023 (OR ABBREVIATED 01023)
AHYRNNGPDTYFFDY
>SEQ ID NO:40 CDR 1 of variable domain of Light chain of MAD1009023 (OR ABBREVIATED 01023)
QSISSW
>SEQ ID NO:41 CDR 2 of variable domain of Light chain of MAD 1009023 (OR ABBREVIATED 01023) this sequence is not included in the sequence listing because is less than 4 amino acid
KAS
>SEQ ID NO:42 CDR 3 of variable domain of Light chain of MAD1009023 (OR ABBREVIATED 01023)
QQYSSYFS
>SEQ ID NO:43 variable domain of Heavy chain of MAD 1009023 (OR ABBREVIATED 01023)
QVTLKESGPALVKPTQTLTLTCTFSGFSLSTPGVAVGWIRQPPGKALEWLALLYWDDDKRYSPSLKS
RLTITADTSKNQVVLTMTNMDPVDTATFYCAHYRNNGPDTYFFDYWGQGTLVTVSSASTK
>SEQ ID NO:44 variable domain of Light chain of MAD 1009023 (OR ABBREVIATED 01023)
AIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQHKPGKAPKLLIYKASTLESGVPSRFSGSGSG
TEFTLTISSLQPDDFASYYCQQYSSYFSFGPGTKVDIKRTVAA
>SEQ ID NO:45 Heavy chain of MAD 1009023 (OR ABBREVIATED 01023)
MGWSCIILFLVATATGVHSQVTLKESGPALVKPTQTLTLTCTFSGFSLSTPGVAVGWIRQPPGKALE
WLALLYWDDDKRYSPSLKSRLTITADTSKNQVVLTMTNMDPVDTATFYCAHYRNNGPDTYFFDY
WGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVF
LFPPKPKDTLMISRTPEVTCWVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRWSVLT
VLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFY
PSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQ KSLSLSPGK*
>SEQ ID NO:46 Light chain of MAD 1009023 (OR ABBREVIATED 01023)
GWSCIILFLVATATGVHSAIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQHKPGKAPKLLIYK
ASTLESGVPSRFSGSGSGTEFTLTISSLQPDDFASYYCQQYSSYFSFGPGTKVDIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYE
KHKVYACEVTHQGLSSPVTKSFNRGEC*
NUCLEIC ACID SEQUENCES OF MAD1009023 (OR ABBREVIATED 01023):
> SEQ ID NO:47 MAD 1009023 (OR ABBREVIATED 01O23)_heavy_chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO:48 MAD 1009023 (OR ABBREVIATED 01O23)_heavy chain Variable domain
CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACGCTGACCT
GCACCTTCTCTGGGTTCTCACTCAGCACTCCTGGAGTGGCTGTGGGCTGGATCCGTCAGCCCCCA
GGAAAGGCCCTGGAGTGGCTTGCACTCCTTTATTGGGATGATGATAAGCGCTACAGCCCATCTC
TGAAGAGCAGGCTCACCATCACCGCGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCA
ACATGGACCCTGTAGACACAGCCACATTTTACTGTGCACACTACCGCAATAATGGCCCGGACAC
CTATTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAG
> SEQ ID NO:49 MAD 1009023 (OR ABBREVIATED 01O23)_heavy chain Constant domain
ACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGG
CCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCTGTGACGGTCTCGTGGAACTCAGGCGC
CCTGACCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGC
AGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACA
AGCCCAGCAACACCAAGGTGGACAAGAGAGTTGAGCCCAAATCTTGTGACAAAACTCACACAT
GCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC
CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCAC
GAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACA
AAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCAC
CAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCC
ATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCC
CCATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATC
CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACG
CCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCA
GGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACAC GCAGAAGAGCCTCTCCCTGTCCCCGGGTAAATGA
> SEQ ID NO:50 MAD 1009023 (OR ABBREVIATED 01O23)_heavy chain Complete ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCCAGGTCAC
CTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTC
TCTGGGTTCTCACTCAGCACTCCTGGAGTGGCTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGG
CCCTGGAGTGGCTTGCACTCCTTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAG
CAGGCTCACCATCACCGCGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGA
CCCTGTAGACACAGCCACATTTTACTGTGCACACTACCGCAATAATGGCCCGGACACCTATTTC
TTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGCCATCGGTCT
TCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCTGCCTGGTCAA
GGACTACTTCCCCGAACCTGTGACGGTCTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCAC
ACCTTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCTC
CAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCAACACCAAGGT
GGACAAGAGAGTTGAGCCCAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACC
TGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATC
TCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAG
TTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAG
TACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCA
AGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCCATCGAGAAAACCATCTCCA
AAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGAGGAGATGA
CCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGA
GTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGA
CGGCTCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTC
TTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGT
CCCCGGGTAAATGA
> SEQ ID NO:51 MAD 1009023 (OR ABBREVIATED 01023) light chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO:52 MAD 1009023 (OR ABBREVIATED 01O23)_light_chain Variable Domain
GCCATCCAGATGACCCAGTCTCCATCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCA
CTTGCCGGGCCAGTCAGAGTATTAGTAGTTGGTTGGCCTGGTATCAGCATAAACCAGGGAAAGC
CCCTAAACTGCTGATCTATAAGGCGTCTACTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGC
AGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAAGTT
ATTACTGCCAACAGTATAGTAGTTATTTCAGTTTCGGCCCTGGGACCAAAGTGGATATCAAACG
AACTGTGGCTGCA
> SEQ ID NO:53 MAD 1009023 (OR ABBREVIATED 01O23)_light_chain ConstantRegion
GTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTC
TGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAAC
GCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCTAC
AGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGC
GAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGTTAG
> SEQ ID NO:54 MAD 1009023 (OR ABBREVIATED 01O23)_light_kappa_complete_seq
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCGCCATCCA
GATGACCCAGTCTCCATCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGG
GCCAGTCAGAGTATTAGTAGTTGGTTGGCCTGGTATCAGCATAAACCAGGGAAAGCCCCTAAAC
TGCTGATCTATAAGGCGTCTACTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATC
TGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAAGTTATTACTGC
CAACAGTATAGTAGTTATTTCAGTTTCGGCCCTGGGACCAAAGTGGATATCAAACGAACTGTGG
CTGCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTCTGTTGTG
TGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCTCC
AATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCTACAGCCTCA
GCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCA
CCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGTTAG
AMINO ACID SEQUENCES OF MAD1006E15 (OR ABBREVIATED 01E15):
>SEQ ID NO:55 CDR 1 of variable domain of Heavy chain of MAD1006E15 (OR ABBREVIATED 01E15)
GFSLTTSGVG
>SEQ ID NO:56 CDR 2 of variable domain of Heavy chain of MAD1006E15 (OR ABBREVIATED 01E15)
IYWDGDD
>SEQ ID NO:57 CDR 3 of variable domain of Heavy chain of MAD1006E15 (OR ABBREVIATED 01E15)
ARHRIRELFDY >SEQ ID NO:58 CDR 1 of variable domain of Light chain of MAD1006E15 (OR ABBREVIATED 01E15) SSDVGGYNY
>SEQ ID NO:59 CDR 2 of variable domain of Light chain of MAD1006E15 (OR ABBREVIATED 01E15) this sequence is not included in the sequence listing because is less than 4 amino acid
EVS
>SEQ ID NO:60 CDR 3 of variable domain of Light chain of MAD1006E15 (OR ABBREVIATED 01E15) NSYTSSSTLVI
>SEQ ID NO:61 variable domain of Heavy chain of MAD1006E15 (OR ABBREVIATED 01E15)
QVTLKESGPTLVKPTQTLTLTCTFSGFSLTTSGVGVGWIRQTPGKALEWLALIYWDGDDRYSPALKS
RLTITKDTSKNQVVLTMTNMDPLDTATYYCARHRIRELFDYWGQGTLVTVSSASTK
>SEQ ID NO:62 variable domain of Light chain of MAD1006E15 (OR ABBREVIATED 01E15)
QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQHHPGKAPKLMIYEVSNRPSGVSNRFSGS
KSGNTASLTISGLQAEDEADYYCNSYTSSSTLVIFGGGTKLTVLGQPKAA
>SEQ ID NO:63 Heavy chain of MAD1006E15 (OR ABBREVIATED 01E15)
MGWSCIILFLVATATGVHSQVTLKESGPTLVKPTQTLTLTCTFSGFSLTTSGVGVGWIRQTPGKALE
WLALIYWDGDDRYSPALKSRLTITKDTSKNQVVLTMTNMDPLDTATYYCARHRIRELFDYWGQGT
LVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPK
PKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQ
DWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIA
VEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL SPGK*
>SEQ ID NO:64 Light chain of MAD1006E15 (OR ABBREVIATED 01E15)
GWSCIILFLVATATGVHSQSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQHHPGKAPKLMI
YEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCNSYTSSSTLVIFGGGTKLTVLGQPKAAP
SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC*
NUCLEIC ACID SEQUENCES OF MAD1006E15 (OR ABBREVIATED 01E15):
> SEQ ID NO:65 MAD1006E15 (OR ABBREVIATED 01E15)_heavy_chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO:66 MAD1006E15 (OR ABBREVIATED 01E15)_heavy chain Variable domain
CAGGTCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCT
GCACCTTCTCTGGGTTCTCACTCACCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGACCCC
AGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGGTGATGACCGCTACAGCCCAGCT
CTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACC
AACATGGACCCTTTGGACACAGCCACATATTACTGTGCACGCCATCGCATCAGGGAGTTATTCG ACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAG
> SEQ ID NO:67 MAD1006E15 (OR ABBREVIATED 01E15)_heavy chain Constant domain
ACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGG
CCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCTGTGACGGTCTCGTGGAACTCAGGCGC
CCTGACCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGC
AGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACA
AGCCCAGCAACACCAAGGTGGACAAGAGAGTTGAGCCCAAATCTTGTGACAAAACTCACACAT
GCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCAC GAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACA
AAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCAC
CAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCC
ATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCC CCATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATC CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACG
CCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCA
GGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACAC GCAGAAGAGCCTCTCCCTGTCCCCGGGTAAATGA
> SEQ ID NO:68 MAD1006E15 (OR ABBREVIATED 01E15)_heavy chain Complete
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCCAGGTCAC CTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTC TCTGGGTTCTCACTCACCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGACCCCAGGAAAGG CCCTGGAGTGGCTTGCACTCATTTATTGGGATGGTGATGACCGCTACAGCCCAGCTCTGAAGAG
CAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGA
CCCTTTGGACACAGCCACATATTACTGTGCACGCCATCGCATCAGGGAGTTATTCGACTACTGG
GGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGCCATCGGTCTTCCCCCTGGCAC
CCTCCTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAACCTGTGACGGTCTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTTCCCGGCT
GTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGCTTGG
GCACCCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAGAG
TTGAGCCCAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAACTCCTGGG
GGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACCCCT
GAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTAC
GTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCAC
GTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAG
TGCAAGGTCTCCAACAAAGCCCTCCCAGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGG
CAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGAGGAGATGACCAAGAACCAG
GTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCA
ATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTT
CCTCTATAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCC
GTGATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCCCCGGGTAAAT
GA
> SEQ ID NO:69 MAD1006E15 (OR ABBREVIATED 01E15) light chain LeaderSequence
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCC
> SEQ ID NO:70 MAD1006E15 (OR ABBREVIATED 01E15)_light_chain Variable Domain
CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTG
CACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACACCACCCAGGC
AAAGCCCCCAAACTCATGATTTATGAGGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCT
CTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGC
TGATTATTATTGCAACTCATATACAAGCAGCAGCACTCTTGTGATATTCGGCGGCGGGACCAAG
CTGACCGTCCTAGGTCAGCCCAAGGCTGCC
> SEQ ID NO:71 MAD1006E15 (OR ABBREVIATED 01E15)_light_chain ConstantRegion
GTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTC
TGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAAC
GCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCTAC
AGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCTGC
GAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGTTAG
> SEQ ID NO:72 MAD1006E15 (OR ABBREVIATED 01E15)_light_kappa_complete_seq
ATGGGATGGTCATGTATCATCCTTTTTCTAGTAGCAACTGCAACCGGTGTACATTCCCAGTCTGC
CCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAA
CCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACACCACCCAGGCAAAGCCCC
CAAACTCATGATTTATGAGGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCA
AGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTA
TTGCAACTCATATACAAGCAGCAGCACTCTTGTGATATTCGGCGGCGGGACCAAGCTGACCGTC
CTAGGTCAGCCCAAGGCTGCCTCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGG
AACTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAG
GTGGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGAC
AGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTC
TACGCCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGA
GAGTGTTAG

Claims

64 CLAIMS
1. A human monoclonal antibody or antigen-binding portion thereof that specifically binds to the human severe acute respiratory syndrome (SARS) Corona Virus 2 (SARS-CoV-2) Spike (S) protein showing 100% inhibitory concentration (ICioo) of less than 25 ng/ml, preferably of less than 10 ng/ml, when tested in an in vitro neutralization assay against the SARS-CoV-2 Wuhan virus and its variant Alpha, Beta, Delta and Gamma, wherein said in vitro neutralization assay is the CPE-MN assay.
2. The human monoclonal antibody or antigen-binding portion thereof according to claim 1, having an equilibrium dissociation constant (KD) of less than 6 pM against the Spike (S) protein of the SARS-CoV-2 Wuhan virus and its variant Alpha, Gamma, Delta and Kappa as measured by surface plasmon resonance (SPR).
3. The human monoclonal antibody or antigen-binding portion thereof according to claim 1 or claim 2 , comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein said VH and VL comprise the following complementarity-determining regions (CDRs): -CDR1 of VH having SEQ ID NO: 1,
-CDR2 of VH having SEQ ID NO:2, -CDR3 of VH having SEQ ID NO:3, -CDR1 of VL having SEQ ID NO:4,
-CDR2 of VL having the sequence QAS (Gln-Ala-Ser) and
-CDR3 of VL having SEQ ID NO:6; or
-CDR1 of VH having SEQ ID NO: 19,
-CDR2 of VH having SEQ ID NO:20, -CDR3 of VH having SEQ ID NO:21, -CDR1 of VL having SEQ ID NO:22,
-CDR2 of VL having the sequence DVT (Asp-Val-Thr) and
-CDR3 of VL having SEQ ID NO:24; or
-CDR1 of VH having SEQ ID NO:37,
-CDR2 of VH having SEQ ID NO:38, 65
-CDR3 of VH having SEQ ID NO:39,
-CDR1 of VL having SEQ ID NO:40,
-CDR2 of VL having the sequence KAS (Lys-Ala-Ser) and
-CDR3 of VL having SEQ ID NO:42; or
-CDR1 of VH having SEQ ID NO:55,
-CDR2 of VH having SEQ ID NO: 56,
-CDR3 of VH having SEQ ID NO: 57,
-CDR1 of VL having SEQ ID NO:58,
-CDR2 of VL having the sequence EVS (Glu-Val-Ser); and
-CDR3 of VL having SEQ ID NO:60
4. The human monoclonal antibody or antigen-binding portion thereof according to any one of claims 1 to 3, comprising a VH and a VL, wherein: said VH comprises SEQ ID NO:7 and said VL comprises SEQ ID NO:8; or said VH comprises SEQ ID NO:25 and said VL comprises SEQ ID NO:26; or said VH comprises SEQ ID NO:43 and said VL comprises SEQ ID NO:44; or said VH comprises SEQ ID NO:61 and said VL comprises SEQ ID NO:62.
5. The human monoclonal antibody or antigen-binding portion thereof according to any one of claims 1 to 4, wherein said VL and said VH is at least 90%, preferably at least 95%, more preferably at least 99% identical in amino acid sequence to the following: said VH having SEQ ID NO: 7 and said VL having SEQ ID NO: 8; or said VH having SEQ ID NO:25 and said VL having SEQ ID NO:26; or said VH having SEQ ID NO:43 and said VL having SEQ ID NO:44; or said VH having SEQ ID NO:61 and said VL having SEQ ID NO:62.
6. The human monoclonal antibody according to any one of claims 1 to 5, wherein the heavy chain of said antibody comprises SEQ ID NO:9 and the light chain of said antibody comprises SEQ ID NOTO; or the heavy chain of said antibody comprises SEQ ID NO:27 and the light chain of said antibody comprises SEQ ID NO:28;or 66 the heavy chain of said antibody comprises SEQ ID NO:45 and the light chain of said antibody comprises SEQ ID NO:46;or the heavy chain of said antibody comprises SEQ ID NO:63 and the light chain of said antibody comprises SEQ ID NO:64.
7. A human monoclonal antibody or antigen-binding portion thereof that competes for binding to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike (S) protein with the antibody or antigen-binding portion thereof of any one of claims 1-6.
8. The human monoclonal antibody or antigen-binding portion thereof according to any one of claims 1 to 7 for use in a prophylactic or therapeutic treatment of a virus infection or conditions or disorders resulting from such infection, in particular for use in the prevention and/or treatment of a coronavirus infection, in particular SARS-CoV-2, more in particular the variant of SARS-CoV-2 Alpha, Beta, Delta or Gamma.
9. The human monoclonal antibody or antigen-binding portion thereof according to any one of claims 1 to 7, for use in a prophylactic or therapeutic treatment of the SARS-CoV-2 infection or conditions or disorders resulting from such infection, in particular said Coronavirus disease 2019 (CO VID- 19).
10. A pharmaceutical composition comprising at least one human monoclonal antibody or antigenbinding portion thereof according to any one of claims 1 to 7 and a pharmaceutically acceptable carrier.
11. The composition according to claim 10 for use in the prevention and/or treatment of a SARS-CoV-2 infection, in particular of a SARS-CoV-2 infection of the Alpha, Beta, Delta or Gamma variant.
12. An isolated nucleic acid molecule comprising a nucleotide sequence that encodes the antibody or antigen-binding portion thereof of any one of claims 1 to 7.
13. A vector comprising the nucleic acid molecule according to claim 12, wherein the vector 67 optionally comprises an expression control sequence operably linked to the nucleic acid molecule, preferably said vector is selected from RNA virus vectors, DNA virus vectors, plasmid viral vectors, adenovirus vectors, adenovirus associated virus vectors, herpes virus vectors, and retrovirus vectors.
14. Use of the human monoclonal antibody or an antigen-binding portion thereof according to any one of claims 1 to 8 in the diagnosis of the SARS-CoV-2 infection.
15. An in vitro method for revealing the presence or for the diagnosis of the SARS-CoV-2 infection in a sample comprising the following steps: i) contacting the antibody or antigen-binding portion thereof according to any one of the claims 1 to 8 with said sample; ii) detecting the binding of said antibody or antigen-binding portion thereof with the S-protein of the SARS-CoV-2.
16. A Sars-Cov-2 vaccine composition comprising the antibody or antigen-binding portion thereof of any one of claims 1 to 7.
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