WO2023173577A1 - 冠状病毒抗体及其用途 - Google Patents

冠状病毒抗体及其用途 Download PDF

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WO2023173577A1
WO2023173577A1 PCT/CN2022/094029 CN2022094029W WO2023173577A1 WO 2023173577 A1 WO2023173577 A1 WO 2023173577A1 CN 2022094029 W CN2022094029 W CN 2022094029W WO 2023173577 A1 WO2023173577 A1 WO 2023173577A1
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antigen
antibody
binding fragment
cov
monoclonal antibody
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PCT/CN2022/094029
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English (en)
French (fr)
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康悦
潘麓蓉
焦阳
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慧壹科技(上海)有限公司
圆壹智慧有限公司
圆壹智慧科技有限公司
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Priority to CN202280001307.6A priority Critical patent/CN117203229A/zh
Publication of WO2023173577A1 publication Critical patent/WO2023173577A1/zh

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    • 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
    • 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

Definitions

  • the present invention relates to the field of antibody technology, and in particular to an antibody or an antigen-binding fragment thereof that specifically binds to the receptor binding region RBD of the coronavirus spike protein, and the use of the antibody or fragment to treat and/or prevent coronavirus infection. the use of.
  • COVID-19 is a global epidemic caused by infection with a new coronavirus, SARS-CoV-2.
  • Clinical features of COVID-19 include fever, dry cough, and fatigue, and the disease may lead to respiratory failure, leading to death. The epidemic spreads rapidly and has caused huge personal health damage and major socioeconomic harm.
  • the new coronavirus (SARS-CoV-2) has four main structural proteins: spike protein (Spike protein, S protein), nucleocapsid protein (Nucleocapsid, N protein), membrane protein (Membrane protein, M protein), and Membrane protein (Envelope protein, E protein).
  • S protein spike protein
  • N protein nucleocapsid protein
  • M protein membrane protein
  • Envelope protein E protein
  • S protein has two subunits: S1 and S2, and the receptor binding domain (RBD) is located on the S1 subunit.
  • the S protein forms a spike on the outer membrane surface of the virus particle in the form of a trimer. Its main function is to recognize host cell surface receptors and mediate fusion with the host cell.
  • the present invention aims to solve the technical problem of the lack of new coronavirus antibodies in clinical practice and provide an antibody against the new coronavirus SARS-CoV-2, which can efficiently and specifically interact with the receptor of the spike protein of the SARS-CoV-2 virus. Combined with the RBD region, it can inhibit the infection of the new coronavirus SARS-CoV-2.
  • an isolated monoclonal antibody or an antigen-binding fragment thereof which binds to the receptor binding region RBD of the SARS-CoV-2 virus spike protein, and the antibody or an antigen-binding fragment thereof comprises: Amino acid sequences of any group of VHCDR1, VHCDR2, VHCDR3 and VLCDR1, VLCDR2, VLCDR3 from Table 1 below.
  • the antibody or its antigen-binding fragment includes: the amino acid sequence of the heavy chain variable region VH and the light chain variable region VL selected from any group of Table 2 below.
  • the antibody or antigen-binding fragment thereof also includes: a heavy chain constant region with an amino acid sequence shown in SEQ ID NO. 9, SEQ ID NO. 162, or SEQ ID NO. 164.
  • the antibody or antigen-binding fragment thereof also includes: a light chain constant region with the amino acid sequence shown in SEQ ID NO. 10 or SEQ ID NO. 163.
  • a bispecific antibody comprising the above-mentioned antibody or antigen-binding fragment thereof, and a second antibody or antigen-binding fragment thereof.
  • Bispecific antibodies have two specific antigen-binding sites and can interact with target cells and functional cells (generally T cells) at the same time, thereby enhancing the killing effect on target cells.
  • composition in another aspect of the present invention, includes the above-mentioned monoclonal antibody or antigen-binding fragment thereof, and a pharmaceutically acceptable carrier or diluent.
  • the pharmaceutical composition further includes a second therapeutic agent, the second therapeutic agent is selected from: a second antibody that binds to the SARS-CoV-2 virus spike protein or an antigen-binding fragment thereof, an anti-inflammatory agent, an anti-malarial agent agents, and antibodies that bind TMPRSS2 or antigen-binding fragments thereof.
  • a second therapeutic agent is selected from: a second antibody that binds to the SARS-CoV-2 virus spike protein or an antigen-binding fragment thereof, an anti-inflammatory agent, an anti-malarial agent agents, and antibodies that bind TMPRSS2 or antigen-binding fragments thereof.
  • nucleic acid encoding the heavy chain or light chain variable region of the above-mentioned monoclonal antibody or antigen-binding fragment thereof.
  • a recombinant expression vector comprising the above nucleic acid is also provided.
  • a host cell comprising a recombinant expression vector is also provided.
  • kits for detecting viruses comprising the above-mentioned monoclonal antibody or antigen-binding fragment thereof.
  • a detection chip comprising the above-mentioned monoclonal antibody or its antigen-binding portion.
  • the viral infection includes coronavirus infection.
  • the antibody of the present invention can treat or prevent a variety of viruses that can escape immunity, such as the new coronavirus SARS-CoV-2, etc., and has broad-spectrum antiviral activity.
  • the use of the above-mentioned monoclonal antibody or antigen-binding fragment thereof in preparing a product for diagnosing viral infection is also provided.
  • the anti-novel coronavirus SARS-CoV-2 antibody of the present invention can efficiently and specifically combine with the receptor binding region RBD of the SARS-CoV-2 spike protein and inhibit the infection of the new coronavirus SARS-CoV-2.
  • RBD receptor binding region of the SARS-CoV-2 spike protein
  • For the new coronavirus The prevention and control of viral pneumonia (COVID-19) epidemic is of great significance.
  • Figure 1 is a diagram showing the results of measuring the binding ability of antibodies to the spike protein receptor binding domain (RBD) of the SARS-CoV-2 virus and each mutant strain through ELISA experiments in Example 2 of the present invention;
  • RBD spike protein receptor binding domain
  • Figure 2 is a cell growth curve after adding antibodies in the cytopathic effect (CPE) reduction experiment of Example 4 of the present invention
  • Figure 3 is a graph showing the cytotoxicity results of the detection antibody in Example 4 of the present invention.
  • coronavirus refers to any virus of the coronavirus family, including but not limited to SARS-CoV-2, MERS-CoV, and SARS-CoV.
  • SARS-CoV-2 refers to a newly emerging coronavirus identified.
  • SARS-CoV-2 is also known as 2019-nCoV. It binds to the human host cell receptor angiotensin-converting enzyme 2 (ACE2) through the viral spike protein. The spike protein also binds to and is cleaved by TMPRSS2, which activates the spike protein for membrane fusion of the virus.
  • ACE2 human host cell receptor angiotensin-converting enzyme 2
  • CoV-S refers to the spike protein of coronaviruses and can refer to specific S proteins such as SARS-CoV-2-S, MERS-CoV S and SARS-CoV S.
  • SARS-CoV-2 spike protein is a 1,273 amino acid type I membrane glycoprotein that assembles into trimers that make up the spikes or membrane particles on the surface of enveloped coronavirus particles.
  • S protein has two important functions of the N-terminal (S1) part and the C-terminal (S2) part: host receptor binding and membrane fusion.
  • S1 N-terminal
  • S2 C-terminal
  • S2 C-terminal
  • CoV-S binds to its cognate receptor through the receptor binding domain (RBD) present in the S1 subunit.
  • RBD receptor binding domain
  • CoV-S encompasses protein variants of the CoV spike protein isolated from different CoV isolates as well as recombinant CoV spike proteins or fragments thereof.
  • coronavirus infection refers to infection with a coronavirus, such as SARSCoV-2, MERS-CoV, or SARS-CoV, including coronavirus respiratory infections, usually in the lower respiratory tract.
  • Symptoms can include high fever, dry cough, shortness of breath, pneumonia, gastrointestinal symptoms (such as diarrhea), organ failure (kidney failure and renal dysfunction), septic shock, and death in severe cases.
  • virus includes any virus whose infection in a subject can be treated or prevented by administration of an anti-CoV-S antibody or antigen-binding fragment thereof (e.g., where the infectivity of the virus is at least partially dependent on CoV-S) .
  • a "virus” is any virus that expresses a spike protein (eg, CoV-S).
  • the term "virus” also includes CoV-S-dependent respiratory viruses that infect the respiratory tissue of a subject (e.g., upper and/or lower respiratory tract, trachea, bronchioles, lungs) and that can be induced by administration of anti-CoV-S antibodies or viruses treated or prevented by antigen-binding fragments thereof.
  • viruses include coronaviruses, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), SARS-CoV (severe acute respiratory syndrome coronavirus), and MERS-CoV (Middle East respiratory syndrome coronavirus). syndrome (MERS coronavirus).
  • Coronaviruses may include the genera alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus.
  • the antibodies or antigen-binding fragments provided by the invention can bind to and/or neutralize alpha coronavirus, beta coronavirus, gamma coronavirus, and/or delta coronavirus. coronavirus and/or delta coronavirus.
  • binding and/or neutralization may be specific for a particular coronavirus genus or for a particular subpopulation of a genus.
  • "Viral infection” refers to the invasion and reproduction of viruses in a subject's body.
  • Coronaviruses are spherical, with a diameter of approximately 125nm. The most distinctive feature of coronaviruses are the rod-like spikes that protrude from the surface of the virion. These spikes are the defining feature of the virion and give it the appearance of a corona, which prompted its name coronavirus. Within the envelope of the virion is the nucleocapsid. Coronaviruses have helical symmetry of the nucleocapsid, which is unusual for positive-sense RNA viruses but more common for negative-sense RNA viruses. SARS-CoV-2, MERS-CoV and SARS-CoV belong to the coronavirus family.
  • Initial attachment of virions to host cells is initiated by the interaction between the S protein and its receptor.
  • the location of the receptor binding domain (RBD) within the S1 region of the coronavirus S protein varies depending on the virus, with some viruses having the RBD at the C-terminus of S1.
  • the S protein/receptor interaction is a major determinant of host species infection by coronaviruses and also controls virus tissue tropism. Many coronaviruses use peptidases as their cellular receptors. After receptor binding, the virus must next gain access to the host cell cytoplasm. This is usually accomplished by acid-dependent protein cleavage of the S protein by cathepsin, TMPRRS2, or another protease, followed by fusion of the viral and cell membranes.
  • the term "antibody” should be interpreted to encompass any specific binding factor having a binding domain with the desired specificity.
  • the term encompasses homologous antibody fragments, derivatives, and functional equivalents and homologs of the antibody, as well as any polypeptide containing an antigen-binding domain, whether natural or synthetically produced.
  • antibodies are immunoglobulin subtypes (such as IgG, IgE, IgM, IgD and IgA) and subclasses thereof; also fragments containing an antigen-binding domain such as Fab, scFv, Fv, dAb or Fd, or Diabodies.
  • chimeric molecules or equivalents comprising an antigen-binding domain fused to another polypeptide.
  • the monoclonal antibodies of the present invention can be monovalent or single-chain antibodies, diabodies, chimeric antibodies, and derivatives, functional equivalents and homologues of the above antibodies, and also include antibody fragments and antigen-binding domains. Any peptide.
  • Antibodies can be modified in many ways, and recombinant DNA techniques can be used to produce other antibodies or chimeric molecules that retain the specificity of the original antibody. This technique may involve introducing DNA encoding the immunoglobulin variable regions or complementarity determining regions (CDRs) of an antibody into the constant region or constant plus framework regions of a different immunoglobulin.
  • CDRs complementarity determining regions
  • the monoclonal antibody of the present invention is a framework region.
  • the framework region can be replaced by other sequences without affecting the three-dimensional structure required for binding.
  • the molecular basis of antibody specificity mainly comes from its highly variable regions CDR1, CDR2 and CDR3. These regions are key to binding to antigens. parts.
  • the sequence of the CDR should be retained as much as possible. However, some amino acid changes may be required to optimize the binding properties. Those skilled in the art can use standard practices to achieve this goal.
  • antigen-binding portion or “antigen-binding fragment” or the like of an antibody or antigen-binding protein include any naturally occurring, enzymatically obtainable, synthetic or genetically engineered polypeptide that specifically binds to an antigen to form a complex or Glycoproteins.
  • Non-limiting examples of antigen-binding fragments include: (i) Fab fragments; (ii) F(ab')2 fragments; (iii) Fd fragments; (iv) Fv fragments; (v) single-chain Fv (scFv) molecules; (vi) a dAb fragment; and (vii) a minimal recognition unit consisting of amino acid residues that mimic the hypervariable region of the antibody (e.g., an isolated complementarity determining region (CDR), such as a CDR3 peptide) or a constrained FR3-CDR3- FR4 peptide.
  • CDR complementarity determining region
  • the antigen-binding fragments include three or more CDRs of the Table 3 antibodies (eg, VHCDR1, VHCDR2, and VHCDR3; or VLCDR1, VLCDR2, and VLCDR3).
  • the antigen-binding fragment of the antibody will comprise at least one variable domain.
  • Variable domains can be of any size or amino acid composition, variable regions can be dimers and contain VH-VH, VH-VL or VL-VL dimers.
  • the antigen-binding fragment of an antibody may contain a monomeric VH or VL domain.
  • an antibody or antigen-binding fragment of the invention modified in some way retains the ability to specifically bind to CoV-S, e.g., retains at least 10% of its CoV-S binding activity when expressed on a molar basis. % (when compared to the parent antibody).
  • an antibody or antigen-binding fragment of the invention retains at least 20%, 50%, 70%, 80%, 90%, 95% or 100% or more of CoV-S binding affinity compared to the parent antibody.
  • An antibody or antigen-binding fragment of the invention may also contain conservative or non-conservative amino acid substitutions that do not substantially alter its biological activity (referred to as "conservative variants" or “functionally conserved variants" of the antibody).
  • Variant of a polypeptide is intended to include those described herein (e.g., SEQ ID NO: 22, 50, 114, 134, 162, 170, 178, 186, 194, 186, 206 , 210, or 214) at least about 70-99.9% (e.g., 70%, 72%, 74%, 75%, 76%, 79%, 80%, 81%, 82%, 83%) of the reference amino acid sequence , 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5 %, 99.9%) polypeptides with identical or similar amino acid sequences; when compared by the BLAST algorithm, wherein the parameters of the algorithm are chosen to give the maximum match between corresponding sequences over the entire length of the corresponding reference sequence (e.g., Expected threshold: 10; font size: 3; maximum number of
  • Conservatively modified variant anti-CoV-S antibodies and antigen-binding fragments thereof are also part of the invention.
  • Constantly modified variants or “conservative substitutions” are those in which an amino acid in a polypeptide is replaced by another amino acid with similar properties (e.g., charge, side chain size, hydrophobicity/hydrophilicity, backbone conformation and rigidity, etc.) One or more variants. Such changes can often be made without significantly destroying the biological activity of the antibody or fragment.
  • Those skilled in the art recognize that, generally, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter the biological activity. Additionally, substitutions of structurally or functionally similar amino acids are unlikely to significantly disrupt biological activity.
  • Functionally conserved variants of anti-CoV-S antibodies and antigen-binding fragments thereof are also part of the invention. Any variant of an anti-CoV-S antibody and its antigen-binding fragment may be a "functionally conserved variant.” In some cases, such functionally conserved variants may also be characterized as conservatively modified variants. "Functionally conserved variant” as used herein refers to an anti-CoV-S antibody or its antigen in which one or more amino acid residues have been changed without significantly altering one or more functional properties of the antibody or fragment. Binding fragment variants. In embodiments of the invention, the functionally conserved variant anti-CoV-S antibody or antigen-binding fragment thereof of the invention includes a variant amino acid sequence and exhibits one or more of the following functional properties:
  • coronaviruses e.g., SARS-CoV-2, SARS-CoV and/or MERS-CoV
  • ACE2 and/or TMPRSS2 e.g., Calu-3 cells
  • mice expressing human TMPRSS2 and/or ACE2 protein from coronavirus infection e.g., SARS-CoV-2, SARS-CoV or MERS-CoV
  • coronavirus infection e.g., SARS-CoV-2, SARS-CoV or MERS-CoV
  • mice expressing human TMPRSS2 and/or ACE2 protein from coronavirus infection e.g., SARS-CoV-2, SARS-CoV or MERS-CoV
  • coronavirus infection e.g., SARS-CoV-2, SARS-CoV or MERS-CoV
  • the amino acid sequence of an exemplary anti-SARS-CoV-2 spike protein (SARS-CoV-2-S) antibody is shown in the following exemplary sequence list, which exemplifies the variable heavy and light chains of some of the antibodies of the present invention.
  • the amino acid sequences of the heavy chain and light chain variable regions of the 70 antibodies of the present invention are detailed in the sequence list below.
  • preferred antibodies include: AINNL0002, AINNL0004, AINNL0010, AINNL0011, AINNL0014, AINNL0017, AINNL0031, AINNL0051, AINNL0053, AINNL0054, AINNL0057, AINNL0060, AINNL0061, AINNL0066, AINNL0068.
  • the Ainnocence macromolecule virtual screening computing platform TM of the present invention is independently developed based on data-driven and deep network.
  • Molecular artificial intelligence model Among them, the antibody affinity maturation module can be used for antibody-antigen affinity modification. In the design of broadly neutralizing antibody molecules against SARS-CoV-2, the specific calculation process is as follows:
  • virus variant sequence For each virus variant sequence, use the antibody template sequence and virus sequence as input, use the Ainnocence macromolecule virtual screening computing platform to perform antibody affinity improvement modifications based on single point mutations and multiple point mutations, and perform the modified antibody sequences. Record, define the preferred antibody library for this virus mutant strain.
  • step 3 For all 64 virus mutant strains (and wild type), perform step 3) respectively.
  • top 70 sequences i.e., the top 70 with the highest broad-spectrum neutralization probability
  • amino acid sequence numbers of the heavy chain and light chain variable regions of the 70 antibodies of the present invention are shown in Table 3 below, in which the CDR amino acid sequences are numbered according to the Kabat nomenclature system.
  • ELISA reaction Dilute the antibody to 1 ⁇ g/ml with the above-mentioned elution buffer containing 0.1% BSA. Add 100 ⁇ l of the diluted antibody to each well, mix evenly, and react at room temperature for 2 hours. Discard and wash three times with 300 ⁇ l of the elution buffer and pat dry. Add 100 ⁇ l of working concentration of Jackson: Goat Anti-Human IgG (H+L)/HRP secondary antibody to each well, mix evenly, and incubate at room temperature for 1 hour. Discard and wash three times with 300 ⁇ l elution buffer and pat dry.
  • TMB chromogenic solutions A and B at a ratio of 1:1, add 200 ⁇ l to each well, and incubate in the dark at room temperature for 20 minutes. Add 50 ⁇ l of 2M sulfuric acid stop solution to each well, and immediately measure the OD value at a wavelength of 450 nm.
  • the antibodies of the present invention bind to RBD proteins of various strains at different concentrations. From the measured OD450 values, it can be seen that multiple antibodies of the present invention bind to the receptors of the SARS-CoV-2 spike protein.
  • the binding region (RBD) has strong binding ability and reaches a supersaturated state (OD value greater than 2.0). Some antibodies can also bind well to low concentrations of SARS-CoV-2 virus RBD protein (0.03 ⁇ g/ml), with an OD of The value is between 0.1-2.0.
  • Negative and positive controls are listed at the bottom of Table 4.
  • Pseudoviruses are composed of a lipid envelope expressing specific glycoproteins (such as those from the novel coronavirus) and a replaced viral core. Often the viral core is genetically modified so that it cannot express its own surface proteins. Pseudoviruses are able to infect susceptible cells of different species with higher titers and resistance to serum complement, but they only replicate for 1 round in infected host cells. Fake viruses are safer than their corresponding real viruses and are easier to operate for virus neutralization experiments.
  • the pseudovirus-based neutralization test platform can safely conduct serological research and quickly Assessment and screening of neutralizing antibodies or serum neutralizing activity. This experiment uses a pseudovirus platform to test antibody neutralization ability.
  • SARS-CoV-2 (2019-nCoV) Spike pseudovirus After transfecting 293T cells with HIV-1 (human immunodeficiency virus type I) as the basic vector, it is packaged into SARS-CoV-2 (2019-nCoV) Spike pseudovirus , expressing SARS-CoV-2 (2019-nCoV) Spike protein on its surface and carrying a luciferase reporter gene, it can be used to infect cells overexpressing ACE2, and luciferase is expressed within the cells.
  • This fake virus has no ability to replicate autonomously and has the characteristics of high security and strong operability.
  • the SARS-CoV-2 Spike pseudovirus is incubated with the antibody to be tested and then infected into 293T-ACE2 cells.
  • the chemiluminescence method is used to detect the relative light intensity value RLU of luciferase.
  • the pseudovirus inhibition rate of the antibody to be tested is calculated based on the RLU reading. Evaluate the neutralizing effect of the antibody to be tested.
  • Inhibition rate (%) 1 - (average RLU of the antibody to be tested - average RLU of the negative control) / (average RLU of the positive control - RLU value of the negative control)
  • IC50 values were calculated using the Reed-Muench method.
  • the results of the pseudovirus neutralization experiment are shown in Table 6 below.
  • the data listed in the table are the inhibition rates at various antibody concentrations and the IC50 under effective inhibition conditions.
  • AINNL0001-AINNL0050 are the neutralization results of the delta variant pseudovirus.
  • AINNL0051-AINNL0070 are the neutralization results of omicron mutant pseudoviruses.
  • the inhibition rate is likely to be negative when there is no neutralizing signal or when the value is too low. When the inhibition rate is less than 50% at the highest concentration, it indicates that the neutralizing ability is limited and no IC50 calculation is performed.
  • the AINNL0011 antibody has an inhibition rate of 91.98% at a working concentration of 20 ⁇ g/ml and can significantly inhibit the SARS-CoV-2 Spike pseudovirus.
  • the IC50 of the antibody is 8.03 ⁇ g/ml, indicating that the AINNL0011 antibody has a high Neutralizing activity.
  • MEM minimum essential medium
  • HI FBS heat-inactivated fetal bovine serum
  • the experiment consists of two steps. First, virus neutralization is completed by mixing a fixed number of infectious virus particles and serially diluted antibodies, and then cell viability is detected through a CPE experiment. Add 5 ⁇ l of serum-diluted antibody to each well of a 384-well plate, then add 5 ⁇ l of virus containing 1000 half tissue culture infectious dose (TCID), and incubate at 37°C for 1 hour. For CPE experiments, 20 ⁇ l of the above cell suspension was added. The blank control contains only cells, while the virus control contains no antibodies.
  • TCID tissue culture infectious dose
  • Inhibition rate (%) 100x [(test value - average value of only virus test values) / (average value of blank test values - average value of only virus test values)]
  • the experiment was conducted in a level 3 safety laboratory, and the well plate reading was sealed with a transparent sealing film.
  • the antibody was gradient diluted in the same medium as the CPE experiment. 20 ⁇ l of cells and 10 ⁇ l of antibody were added to each well of the multi-well plate, except that cells were used as blank controls and only cells treated with benzethonium chloride (final concentration 100 ⁇ M) were used as negative controls. After culturing for 72 hours at 37 degrees Celsius/5% carbon dioxide/90% humidity, add 30 ⁇ l of Promega Cell Titer-Glo luminescence cell viability detection reagent to each well, and read in the same way as the CPE experiment.
  • Table 7 shows the results of the CPE experiment. As shown in Table 7 below, when no antibody is added, the value is 0. When the addition of the antibody can significantly improve the growth curve (see Figure 2), it is considered that there is activity, and the growth curve can be fitted. Find the half inhibition rate IC50 value. A low IC50 indicates that the antibody at low concentration has good attenuation activity. There is a certain error in this value, but in general, the lower the IC50, the better the effect. For example, the IC50 of the AINNL0031 antibody is 2.704, indicating that the AINNL0031 antibody has good attenuation activity. toxic activity.
  • the toxicity test is a test for the toxicity of the antibody itself. The results are shown in Table 8 and Figure 3. When no antibody is added, the value is 100%. If the antibody is toxic, the curve will shift downward. As can be seen from Table 8 and Figure 3, this None of the inventive antibodies was significantly toxic.

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Abstract

提供了一种分离的单克隆抗体或其抗原结合片段，其结合SARS-CoV-2病毒刺突蛋白的受体结合区域RBD,该抗体或其抗原结合片段包含：选自表1任意一组的VHCDRKVHCDR2、VHCDR3及VLCDR1、VLCDR2、VLCDR3的氨基酸序列。还提供了上述单克隆抗体或其抗原结合片段在制备治疗或预防病毒感染的药物中的用途。所述抗新型冠状病毒SARS-CoV-2的抗体，能高效特异地与SARS-CoV-2刺突蛋白的受体结合区域RBD相结合，并抑制新冠病毒SARS-CoV-2的感染，对于新冠病毒疫情的防控具有重要意义，应用前景广阔。

Description

冠状病毒抗体及其用途 技术领域
本发明涉及抗体技术领域，尤其涉及一种与冠状病毒刺突蛋白的受体结合区域RBD特异性结合的抗体或其抗原结合片段、以及所述抗体或片段用于治疗和/或预防冠状病毒感染的用途。
背景技术
从2019年12月底以来，在全球爆发了大规模的新型冠状病毒感染性肺炎(COVID-19)的疫情。COVID-19是由一种新型冠状病毒SARS-CoV-2感染所致的全球性流行病。COVID-19的临床特征包含发烧、干咳和疲劳，并且疾病可能会导致呼吸衰竭，从而导致死亡。该流行病传播迅速，已造成巨大的人身健康损害和重大的社会经济危害。
新冠病毒(SARS-CoV-2)有四种主要的结构蛋白：刺突蛋白(Spike protein，S蛋白)，核衣壳蛋白(Nucleocapsid，N蛋白)，膜蛋白(Membrane protein，M蛋白)，包膜蛋白(Envelope protein，E蛋白)。新冠病毒刺突蛋白(S蛋白)有两个亚基：S1和S2，受体结合区域(RBD)位于S1亚基上。该S蛋白以三聚体的形式组成病毒粒子外膜表面的刺突，其主要功能是识别宿主细胞表面受体，介导与宿主细胞的融合。
迄今为止，还没有能够有效预防或治疗SARS-CoV-2感染的疫苗或治疗剂。鉴于对人类健康的持续威胁，迫切需要开发用于防控SARS-CoV-2感染的具有预防性和治疗性的抗病毒药物。由于这种病毒使用其刺突蛋白与细胞受体ACE2(血管紧张素转换酶2)和丝氨酸蛋白酶TMPRSS2相互作用进入靶细胞，所以该刺突蛋白是抗体治疗的关键靶标。具体地，以高亲和力与SARS-CoV-2刺突蛋白特异性结合并抑制病毒感染的全人抗体，对于预防和治疗COVID-19是重要的。
发明内容
本发明要解决目前临床上缺乏新型冠状病毒抗体的技术问题，提供一种抗新型冠状病毒SARS-CoV-2的抗体，该抗体能高效特异地与SARS-CoV-2病毒刺突蛋白的受体结合区域RBD相结合，并能抑制新冠病毒SARS-CoV-2的感染。
为了解决上述技术问题，本发明通过如下技术方案实现:
在本发明的一个方面，提供了一种分离的单克隆抗体或其抗原结合片段，其结合SARS-CoV-2病毒刺突蛋白的受体结合区域RBD，该抗体或其抗原结合片段包含：选自下述表1任意一组的VHCDR1、VHCDR2、VHCDR3及VLCDR1、VLCDR2、VLCDR3的氨基酸序列。
表1 VHCDR1～VHCDR3及VLCDR1～VLCDR3的氨基酸序列编号
Figure PCTCN2022094029-appb-000001
Figure PCTCN2022094029-appb-000002
优选的，所述抗体或其抗原结合片段包含：选自下述表2任意一组的重链可变区VH和轻链可变区VL的氨基酸序列。
表2 VH和VL的氨基酸序列编号
Figure PCTCN2022094029-appb-000003
Figure PCTCN2022094029-appb-000004
Figure PCTCN2022094029-appb-000005
所述抗体或其抗原结合片段还包含：如SEQ ID NO.9、SEQ ID NO.162、或SEQ ID NO.164所示氨基酸序列的重链恒定区。
所述抗体或其抗原结合片段还包含：如SEQ ID NO.10或SEQ ID NO.163所示氨基酸序列的轻链恒定区。
在本发明的另一方面，还提供了一种双特异性抗体，包含上述抗体或其抗原结合片段、和第二抗体或其抗原结合片段。
双特异性抗体拥有两种特异性抗原结合位点，可以同时与靶细胞和功能细胞(一般为T细胞)相互作用，进而增强对靶细胞的杀伤作用。
在本发明的另一方面，还提供了一种药物组合物，该组合物包含上述单克隆抗体或其抗原结合片段、以及药学上可接受的载体或稀释剂。
优选的，所述药物组合物还包括第二治疗剂，所述第二治疗剂选自：结合SARS-CoV-2病毒刺突蛋白的第二抗体或其抗原结合片段、抗炎剂、抗疟疾剂、以及结合TMPRSS2的抗体或其抗原结合片段。
在本发明的另一方面，还提供了一种分离的核酸，其编码上述单克隆抗体或其抗原结合片段的重链或轻链可变区。
在本发明的另一方面，还提供了一种包含上述核酸的重组表达载体。
在本发明的另一方面，还提供了一种包含重组表达载体的宿主细胞。
在本发明的另一方面，还提供了一种检测病毒的试剂盒，包含上述的单克隆抗体或其抗原结合片段。
在本发明的另一方面，还提供了一种检测芯片，包含上述的单克隆抗体或其抗原结合部分。
在本发明的另一方面，还提供了一种上述单克隆抗体或其抗原结合片段在制备治疗病毒感染的药物中的用途。
在本发明的另一方面，还提供了一种上述单克隆抗体或其抗原结合片段在制备预防病毒感染的药物中的用途。
所述病毒感染包括冠状病毒感染。
本发明抗体可治疗或预防多种会免疫逃逸的病毒如新冠病毒SARS-CoV-2等，具有广谱 抗病毒活性。
在本发明的另一方面，还提供了一种上述单克隆抗体或其抗原结合片段在制备诊断病毒感染的产品中的用途。
本发明抗新型冠状病毒SARS-CoV-2的抗体，能高效特异地与SARS-CoV-2刺突蛋白的受体结合区域RBD相结合，并抑制新冠病毒SARS-CoV-2的感染，对于新冠病毒感染性肺炎(COVID-19)疫情的防控具有重要意义。
附图说明
下面结合附图和具体实施方式对本发明作进一步详细的说明。
图1是本发明实施例2通过ELISA实验测定抗体与SARS-CoV-2病毒及各个突变株的刺突蛋白受体结合区(RBD)的结合能力结果图；
图2是本发明实施例4的细胞病变效应(CPE)降低实验中抗体加入后的细胞生长曲线图；
图3是本发明实施例4的检测抗体的细胞毒性结果图。
具体实施方式
在描述本发明方法之前，应当理解本发明不限于所描述的具体方法和实验条件，因为此类方法和条件可以变化。还应理解，本文所使用的术语仅出于描述具体实施例的目的，而不是限制性的，因为本发明的范围仅受所附权利要求限制。
除非另外定义，否则本文所使用的所有技术术语和科学术语均具有与本发明所属领域普通技术人员通常所理解的含义相同的含义。尽管在本发明的实践或测试中可以使用类似于或等同于本文所描述的方法和材料的任何方法和材料，但现在描述优选的方法和材料。本文所提到的所有出版物均通过全文引用的方式并入本文中。
术语“冠状病毒”或“CoV”是指冠状病毒家族的任何病毒，包含但不限于SARS-CoV-2、MERS-CoV和SARS-CoV。SARS-CoV-2是指被鉴定为新出现的冠状病毒。SARS-CoV-2也被称为2019-nCoV。其通过病毒刺突蛋白与人宿主细胞受体血管紧张素转换酶2(ACE2)结合。刺突蛋白还与活化纤突蛋白以对病毒进行膜融合的TMPRSS2结合并由其切割。
术语“CoV-S”(也被称为“S”或“S蛋白”)是指冠状病毒的刺突蛋白，并且可以是指特异性S蛋白，如SARS-CoV-2-S、MERS-CoV S和SARS-CoV S。SARS-CoV-2刺突蛋白是组装成构成包膜冠状病毒颗粒的表面上的刺突或膜粒的三聚体的1273氨基酸类型I膜糖蛋白。S蛋白具有N端(S1)部分和C端(S2)部分的两个重要功能：宿主受体结合和膜融合。CoV-S通过S1亚基中存在的受体结合区域(RBD)与其同源受体结合。术语“CoV-S”包含从不同的CoV分离物分离的CoV刺突蛋白的蛋白质变异体以及重组CoV刺突蛋白或其片段。
术语“冠状病毒感染”是指感染冠状病毒，如SARSCoV-2、MERS-CoV或SARS-CoV，包含通常在下呼吸道中的冠状病毒呼吸道感染。症状可以包含高烧、干咳、呼吸短促、肺炎、胃肠道症状(如腹泻)、器官衰竭(肾衰竭和肾功能障碍)、脓毒性休克和严重病例的死亡。
术语“病毒”包含其在受试者体内的感染可通过施用抗CoV-S抗体或其抗原结合片段来治疗或预防的任何病毒(例如，其中病毒的感染性至少部分地依赖于CoV-S)。在本发明的实施例中，“病毒”是表达刺突蛋白(例如，CoV-S)的任何病毒。术语“病毒”还包含CoV-S依赖性呼吸道病毒，其是使受试者的呼吸组织(例如，上和/或下呼吸道、气管、细支气管、肺)感染并且可通过施用抗CoV-S抗体或其抗原结合片段治疗或预防的病毒。例如，在本发明的实施例中，病毒包含冠状病毒、SARS-CoV-2(严重急性呼吸综合征冠状病毒2)、SARS-CoV(严重急性呼吸综合征冠状病毒)和MERS-CoV(中东呼吸综合征(MERS)冠状病毒)。冠状病毒可以包含α冠状病毒、β冠状病毒、γ冠状病毒和δ冠状病毒的属。在一些实施例中，本发明所提供的抗体或抗原结合片段可以与α冠状病毒、β冠状病毒、γ冠状病毒和/或δ冠状病毒结合和/或中和α冠状病毒、β冠状病毒、γ冠状病毒和/或δ冠状病毒。在某些实施例中，这种结合和/或中和可以对特定冠状病毒属或对属的特定亚群具有特异性。“病毒感染”是指病毒在受试者体内的侵袭和繁殖。
冠状病毒是球形的，其直径为大约125nm。冠状病毒最显著的特征是从病毒体的表面产生的棒状刺突突出。这些刺突是病毒体的定义性特征并且给予其日冕的外观，这促使其具有冠状病毒这一名称。在病毒体的包膜内是核衣壳。冠状病毒具有螺旋对称的核衣壳，这在正义RNA病毒不常见，但对于负义RNA病毒而言更加常见。SARS-CoV-2、MERS-CoV和SARS-CoV属于冠状病毒家族。病毒体到宿主细胞的初始附着是通过S蛋白与其受体之间的相互作用而引发。受体结合区域(RBD)在冠状病毒S蛋白的S1区内的位点取决于病毒而变化，其中一些病毒的RBD在S1的C端处。S蛋白/受体相互作用是冠状病毒使宿主物种感染的主要决定因素并且还控制病毒的组织向性。许多冠状病毒将肽酶用作其细胞受体。受体结合后，病毒接下来必须获得进入宿主细胞细胞质的途径。这通常通过组织蛋白酶、TMPRRS2或另一种蛋白酶对S蛋白进行酸依赖性蛋白切割、然后将病毒和细胞膜融合来完成。
在本发明中，术语“抗体”应该解释为涵盖具有所需特异性的结合结构域的任意特异性结合因子。因而，这个术语涵盖了与之同源的抗体片段、衍生物以及抗体的功能等同物和同源物，也包括含有抗原结合结构域的任何多肽，无论是天然的还是合成产生的。抗体的实例是免疫球蛋白亚型(如IgG，IgE，IgM，IgD和IgA)及其亚型亚类；也可以是包含抗原结合结构域的片段如Fab、scFv、Fv、dAb或Fd，或者双链抗体(diabodies)。融合至另一多肽的、包含抗原结合结构域的嵌合体分子或者等同物也包括在其中。
本发明所述单克隆抗体可以是单价的或是单链抗体、双链抗体、嵌合抗体以及上述抗体的衍生物、功能等同物和同源物，也包括抗体片段和含有抗原结合结构域的任何多肽。
抗体可以通过许多方式修饰，可用DNA重组技术来产生保留原来抗体特异性的其它抗体或嵌合分子。这种技术可以包括将编码抗体的免疫球蛋白可变区或互补性决定区(CDRs)的DNA引入不同免疫球蛋白的恒定区或恒定区加框架区。
本发明所述单克隆抗体除了重链和轻链中的高度可变区CDR1、CDR2和CDR3和连接序列外，其它为框架区。框架区可在结合所需的三维结构不受影响的条件下被其他序列置换，抗体特异性的分子基础主要来自于它的高度可变区CDR1、CDR2和CDR3，这些区域是与抗原结合的关键部位。为维持优选的结合特性，CDR的序列应尽可能保留，然而，可能需要一些氨基酸改变使结合特性最优化，本领域的技术人员可以用标准做法来达到此目的。
术语抗体或抗原结合蛋白的“抗原结合部分”或“抗原结合片段”等包含任何与抗原特异性结合以形成复合物的天然存在的、可酶促获得的、合成的或基因工程化的多肽或糖蛋白。抗原结合片段的非限制性实例包含：(i)Fab片段；(ii)F(ab')2片段；(iii)Fd片段；(iv)Fv片段；(v)单链Fv(scFv)分子；(vi)dAb片段；以及(vii)由模拟抗体的高变区的氨基酸残基组成的最小识别单位(例如，分离的互补决定区(CDR)，如CDR3肽)或受约束的FR3-CDR3-FR4肽。其它工程化分子如结构域特异性抗体、单结构域抗体、结构域缺失抗体、嵌合抗体、CDR移植抗体、双抗体、三抗体、四抗体、微抗体、纳米抗体、小型模块化免疫药物(SMIP)和鲨鱼可变IgNAR结构域也包含在如本发明所述的“抗原结合片段”内。在本发明的实施例中，抗原结合片段包括表3抗体的三个或更多个CDR(例如，VHCDR1、VHCDR2和VHCDR3；或VLCDR1、VLCDR2和VLCDR3)。
在本发明的实施例中，抗体的抗原结合片段将包括至少一个可变结构域。可变结构域可以具有任何大小或氨基酸组成，可变区可以是二聚体并且含有VH-VH、VH-VL或VL-VL二聚体。可替代地，抗体的抗原结合片段可以含有单体VH或VL结构域。
通常，以某种方式修饰的本发明的抗体或抗原结合片段保留与CoV-S特异性结合的能力，例如，当以摩尔为基础表达其CoV-S结合活性时，保留所述活性的至少10％(在与亲本抗体相比时)。优选地，本发明的抗体或抗原结合片段与亲本抗体相比保留CoV-S结合亲和力的至少20％、50％、70％、80％、90％、95％或100％或更多。本发明的抗体或抗原结合片段还可以包含基本上不改变其生物活性的保守或非保守氨基酸取代(称为抗体的“保守变异体”或“功能保守变异体”)。
多肽(如免疫球蛋白链)的“变异体”是指包括与本发明所述的(例如，SEQ ID NO:22、50、114、134、162、170、178、186、194、186、206、210、或214中所示)参考氨基酸序列至少 约70-99.9％(例如，70％、72％、74％、75％、76％、79％、80％、81％、82％、83％、84％、85％、86％、87％、88％、89％、90％、91％、92％、93％、94％、95％、96％、97％、98％、99％、99.5％、99.9％)相同或类似的氨基酸序列的多肽；当通过BLAST算法进行比较时，其中算法的参数被选择成给出在相应参考序列的整个长度内的相应序列之间的最大匹配(例如，预期阈值：10；字号：3；查询范围内的最大匹配数：0；BLOSUM 62矩阵；空位罚分：存在11，扩展1；条件组成得分矩阵调整)。
保守修饰变异体抗CoV-S抗体和其抗原结合片段也是本发明的一部分。“保守修饰的变异体”或“保守取代”是指其中多肽中的氨基酸被具有类似特性(例如，电荷、侧链大小、疏水性/亲水性、主链构象和刚性等)的其它氨基酸取代一次或多次的变异体。在不显著破坏抗体或片段的生物活性的情况下可以经常进行此类改变。本领域技术人员认识到，通常，多肽的非必需区中的单个氨基酸取代基本上不会改变生物活性。另外，结构或功能上类似的氨基酸的取代不太可能显著破坏生物活性。
抗CoV-S抗体和其抗原结合片段的功能保守变异体也是本发明的一部分。抗CoV-S抗体和其抗原结合片段的任何变异体可以是“功能保守变异体”。在一些情况下，此类功能保守变异体也可以被表征为保守修饰的变异体。如本发明所使用的“功能保守变异体”是指其中一个或多个氨基酸残基在没有显著改变抗体或片段的一个或多个功能性质的情况下已经变化的抗CoV-S抗体或其抗原结合片段的变异体。在本发明的实施例中，本发明的功能保守变异体抗CoV-S抗体或其抗原结合片段包括变异体氨基酸序列，并且表现出以下功能性质中的一个或多个功能性质：
抑制冠状病毒(例如，SARS-CoV-2、SARS-CoV和/或MERS-CoV)在表达ACE2和/或TMPRSS2的细胞(例如，Calu-3细胞)中的生长；
不会与没有表达ACE2和/或TMPRSS2的MDCK/Tet-on细胞显著结合；
显示细胞(例如，Calu-3)的冠状病毒感染(例如，通过SARS-CoV-2、SARS-CoV和/或MERS-CoV)的体外传播；和/或
任选地，当与第二治疗剂组合时，保护表达人TMPRSS2和/或ACE2蛋白的小鼠免于冠状病毒感染(例如，SARS-CoV-2、SARS-CoV或MERS-CoV)所引起的死亡。
任选地，当与第二治疗剂组合时，保护表达人TMPRSS2和/或ACE2蛋白的小鼠免于冠状病毒感染(例如，SARS-CoV-2、SARS-CoV或MERS-CoV)所引起的体重。
示例性抗SARS-CoV-2刺突蛋白(SARS-CoV-2-S)抗体的氨基酸序列如下述的示例性序列表所示，表中举例列明本发明部分抗体重链和轻链可变区的氨基酸序列，本发明70个抗体的重链和轻链可变区序列详见后面的序列表。在本发明中，优选的抗体包括：AINNL0002， AINNL0004，AINNL0010，AINNL0011，AINNL0014，AINNL0017，AINNL0031，AINNL0051，AINNL0053，AINNL0054，AINNL0057，AINNL0060，AINNL0061，AINNL0066，AINNL0068。
示例性序列表
Figure PCTCN2022094029-appb-000006
Figure PCTCN2022094029-appb-000007
Figure PCTCN2022094029-appb-000008
Figure PCTCN2022094029-appb-000009
实施例1针对SARS-CoV-2刺突蛋白(SARS-CoV-2-S)的人抗体的产生和筛选
利用人工智能技术，结合数据分析策略，可实现针对大分子的功能性改造(包括抗体以及融合蛋白)，本发明的Ainnocence大分子虚拟筛选计算平台TM是自主研发的基于数据驱动和深度网络的大分子人工智能模型。其中，抗体亲和力成熟模块可用于抗体-抗原的亲和力改造。在针对SARS-CoV-2的广谱中和抗体分子设计中，具体计算流程如下：
1)基于GISAID[Khare,S.,et al(2021)GISAID’s Role in Pandemic Response.China CDC Weekly,3(49):1049-1051.doi:10.46234/ccdcw2021.255 PMCID:8668406]数据库，收集数据库中截至2021年8月26日的SARS-CoV-2病毒突变株历史数据，并进一步筛选在病毒受体结合区(RBD)产生突变的病毒突变株序列(共64种)，包含野生型SARS-CoV-2病毒及其Delta变种。
2)基于平台计算模块，筛选出与SARS-CoV-2刺突蛋白的受体结合区(RBD)具有结合潜力的模板抗体CR3022[US20100172917A1]，REGN10933，REGN10987[US20210395345A1]。
3)对于每一病毒变种序列，将抗体模版序列与病毒序列作为输入，使用Ainnocence大分子虚拟筛选计算平台，进行基于单点突变及多点突变的抗体亲和力提升改造，对改造后的抗体序列进行记录，定义为此病毒突变株的优选抗体库。
4)对于所有64种病毒突变株(及野生型)，分别执行步骤3)。
5)对64种病毒突变株(及野生型)的优选抗体库进行横向比对，观察64组优选序列中是否存在重叠，即是否存在某一/某些抗体序列，对病毒突变株均表现出较高的结合能力，以此推断此抗体序列对SARS-CoV-2病毒的已知突变株及未知突变株均具有较高的广谱中和概率。对所有计算推测的广谱中和抗体进行记录，形成优选广谱中和抗体库。
6)基于下游验证实验成本及时间评估，在优选库中选择排名前70条(即广谱中和概率最高的前70)序列开展下游验证实验。
本发明70个抗体的重链和轻链可变区的氨基酸序列编号如下表3所示，其中CDR氨基酸序列按Kabat命名系统编号。
表3 70个抗体的重链和轻链可变区的氨基酸序列编号
Figure PCTCN2022094029-appb-000010
Figure PCTCN2022094029-appb-000011
Figure PCTCN2022094029-appb-000012
实施例2通过ELISA实验测定抗体与SARS-CoV-2病毒及各个突变株的刺突蛋白受体结合区(RBD)的结合能力
1.实验方法
ELISA板制备：包被缓冲液为每500ml中含CBS 0.75g，NaCO 3/NaHCO 3,1.46g，调pH至9.6，三种毒株(wuhan、delta、omicron)病毒RBD蛋白配置成0.03μg/ml或1μg/ml，每孔加入100μl，4℃包被过夜。板内液体甩净拍干，每孔加入2％BSA封闭，室温孵育一小时，弃去并用300μl洗脱缓冲液(含0.2％Tween20的PBS缓冲液，pH＝7.2-7.4)洗两次。拍干。
ELISA反应：抗体使用含0.1％BSA的上述洗脱缓冲液稀释至1μg/ml，每孔加入100μl稀释的抗体，混合均匀，室温反应2h，弃去并用300μl洗脱缓冲液洗三次，拍干。每孔加入工作浓度的Jackson：Goat Anti-Human IgG(H+L)/HRP二抗100μl，混合均匀，室温孵育1h。弃去并用300μl洗脱缓冲液洗三次，拍干。将TMB显色液A和B按1:1混匀后，每孔加入200μl，室温避光孵育20min，每孔加入50μl 2M硫酸终止液，立即在450nm波长处测量OD值。
2.实验结果：
如下表4和图1所示，本发明抗体与不同浓度的各个毒株RBD蛋白发生结合作用，由测得的OD450值可知，本发明多个抗体与SARS-CoV-2刺突蛋白的受体结合区(RBD)具有较强的结合能力，达到过饱和状态(OD值大于2.0)，有些抗体与低浓度的SARS-CoV-2病毒RBD蛋白(0.03μg/ml)也能很好结合，OD值在0.1-2.0之间。表4底部所列为阴性和阳性对照。
表4 ELISA实验结果
Figure PCTCN2022094029-appb-000013
Figure PCTCN2022094029-appb-000014
Figure PCTCN2022094029-appb-000015
Figure PCTCN2022094029-appb-000016
实施例3假病毒中和实验
假病毒为表达特定糖蛋白的脂质包膜(例如来自新型冠状病毒)和替换的病毒核心组成。通常病毒核心经过基因调整，使其不能表达自己的表面蛋白。假病毒能够感染不同物种的易感细胞，具有更高的滴度和对血清补体的抗性，但它们仅在受感染的宿主细胞中复制1轮。假病毒较其对应的真病毒安全，用于病毒中和实验更加容易操作。对于新型冠状病毒、非典病毒、埃博拉病毒、H5N1型高致病性禽流感病毒等高感染性和致病性的病毒，基于假病毒的中和试验平台可以安全地进行血清学研究，快速评估和筛选中和抗体或血清中和活性。本实验通过假病毒平台进行抗体中和能力测试。
1.实验方法
1)材料
宿主细胞：293T-ACE2
SARS-CoV-2(2019-nCoV)Spike假病毒：使用HIV-1(人类免疫缺陷I型病毒)为基础 载体转染293T细胞后，包装成SARS-CoV-2(2019-nCoV)Spike假病毒，表面表达SARS-CoV-2(2019-nCoV)Spike蛋白，并携带有荧光素酶报告基因，可用于感染过表达ACE2的细胞，荧光素酶在细胞内表达。此假病毒无自主复制能力，具有安全性高、可操作性强等特点。
2)中和实验步骤
用SARS-CoV-2 Spike假病毒与待测抗体孵育后感染293T-ACE2细胞，采用化学发光法检测荧光素酶的相对光强度值RLU，根据RLU读值计算待测抗体的假病毒抑制率，评价待测抗体的中和效果。
具体步骤如下：
将抗体于96孔板中按表5稀释浓度进行梯度稀释，加入确定浓度的假病毒与抗体混合，37℃孵育1小时使假病毒与抗体结合，然后，加入到提前铺板的293T-ACE2细胞上，每个梯度2个复孔。
表5抗体稀释浓度表
序号 稀释浓度(μg/mL)
① 100
② 20
④ 4
⑤ 0.8
⑥ 0.16
⑦ 0.032
37℃，5％CO 2培养箱中继续培养48-72小时后，加入荧光素酶底物，并测定相对光强度值(RLU)。依据RLU值计算抗体的中和能力：
抑制率(％)＝1-(待测抗体RLU平均值-阴性对照RLU平均值)/(阳性对照RLU平均值-阴性对照RLU值)
使用Reed-Muench法计算IC50值。
2.实验结果
假病毒中和实验结果如下表6所示，表中所列数据为各个抗体浓度下的抑制率，以及有效抑制条件下的IC50，其中，AINNL0001-AINNL0050是delta变异株假病毒的中和结果，AINNL0051-AINNL0070是omicron变异株假病毒的中和结果。考虑到实验误差，在没有中和信号或数值过低时，抑制率很可能为负值。当最高浓度下抑制率小于50％时，说明中和能力有限，不进行IC50计算。
由表6可知，AINNL0011抗体在20μg/ml的工作浓度下抑制率为91.98％，能显著抑制SARS-CoV-2 Spike假病毒，该抗体的IC50是8.03μg/ml，说明AINNL0011抗体具有较高的 中和活性。
表6假病毒中和实验结果
Figure PCTCN2022094029-appb-000017
Figure PCTCN2022094029-appb-000018
实施例4冠状病毒细胞病变效应降低实验
病毒劫持供其复制的细胞机制导致宿主细胞死亡，抗体或抗病毒药物的加入则促进了细胞生存。细胞病变效应(CPE)降低实验通过测定细胞生存能力从而确定抗体的中和活性。本实验采用可以表达ACE2受体的非洲绿猴肾细胞vero E6进行，冠状病毒可以通过该受体感 染细胞。
1.实验方法
1)细胞培养：
采用含10％热失活胎牛血清(HI FBS)的最低基本培养基(MEM)培养细胞。对于CPE和毒性实验，细胞收集自含1％青霉素链霉素谷氨酰胺(PSG)和2％HI FBS的MEM培养基，并重悬至每毫升200,000细胞。每孔加入20ul细胞悬液(约4000细胞)。
2)检测抗体中和能力：
实验包括两个步骤，首先通过混合固定数量的感染性病毒颗粒和梯度稀释的抗体完成病毒中和，再通过CPE实验检测细胞活性。于384孔板的每孔中加入5μl血清稀释的抗体，随即加入5μl含1000半数组织培养感染量(TCID)的病毒，37摄氏度孵育1小时。CPE实验则加入20μl上述细胞悬液进行。空白对照只含有细胞，病毒对照则不加入抗体。于37摄氏度/5％二氧化碳/90％湿度条件下培养72小时后，每孔加入30μl Promega Cell Titer-Glo发光法细胞活力检测试剂并室温孵育10分钟，使用Perkin Elmer Envision或者BMG CLARIOstar微孔板读取器进行细胞活性测定。每孔的原始信号按照无抗体抑制率为100％，空白对照抑制率为0进行归一化，计算CPE抑制率。公式为：
抑制率(％)＝100x[(测试值-仅病毒测试值的平均值)/(空白测试值的平均值-仅病毒测试值的平均值)]
实验在三级安全实验室中进行，孔板读取采用透明封口膜密封。
3)检测抗体的细胞毒活性：
抗体采用与CPE实验相同的介质梯度稀释，多孔板中每孔加入20μl细胞和10μl抗体，只是用细胞作为空白对照，而只使用苄索氯铵(最终浓度100μM)处理的细胞作为阴性对照。于37摄氏度/5％二氧化碳/90％湿度条件下培养72小时后，每孔加入30μl每孔加入30μl Promega Cell Titer-Glo发光法细胞活力检测试剂，并如CPE实验相同的方式进行读取。
2.实验结果：
表7为CPE实验结果，如下表7所示，在无抗体加入情况下，数值为0，当抗体加入可明显提升生长曲线时(见图2)，认为存在活性，对生长曲线进行拟合可以求得半数抑制率IC50值。IC50低说明低浓度的抗体即具有很好的减毒活性，该数值存在一定误差，但总体来说，IC50越低效果越好，如AINNL0031抗体的IC50为2.704，说明AINNL0031抗体具有很好的减毒活性。
表7 CPE实验结果列表
Figure PCTCN2022094029-appb-000019
毒性实验是针对抗体本身毒性的测试，结果如表8和图3所示，无抗体加入时数值为100％，抗体具有毒性则会使曲线下移，由表8和图3可以看出，本发明各个抗体均不具有显著毒性。
表8毒性实验结果列表
Figure PCTCN2022094029-appb-000020
以上所述实施例仅表达了本发明的实施方式，其描述较为具体和详细，但并不能因此而理解为对本发明专利范围的限制。应当指出的是，对于本领域的普通技术人员来说，在不脱离本发明构思的前提下，还可以做出若干变形和改进，这些都属于本发明的保护范围。因此，本发明专利的保护范围应以所附权利要求为准。

Claims (15)

  1. 一种分离的单克隆抗体或其抗原结合片段，其结合SARS-CoV-2病毒刺突蛋白的受体结合区域RBD，该抗体或其抗原结合片段包含：选自下述表1任意一组的VHCDR1、VHCDR2、VHCDR3及VLCDR1、VLCDR2、VLCDR3的氨基酸序列。
    表1 VHCDR1～VHCDR3及VLCDR1～VLCDR3的氨基酸序列编号
    Figure PCTCN2022094029-appb-100001
    Figure PCTCN2022094029-appb-100002
  2. 根据权利要求1所述的单克隆抗体或其抗原结合片段，其特征在于，所述抗体或其抗原结合片段包含：选自下述表2任意一组的重链可变区VH和轻链可变区VL的氨基酸序列。
    表2 VH和VL的氨基酸序列编号
    Figure PCTCN2022094029-appb-100003
    Figure PCTCN2022094029-appb-100004
    Figure PCTCN2022094029-appb-100005
  3. 根据权利要求1或2所述的单克隆抗体或其抗原结合片段，其特征在于，所述抗体或其抗原结合片段还包含：如SEQ ID NO.9、SEQ ID NO.162、或SEQ ID NO.164所示氨基酸序列的重链恒定区。
  4. 根据权利要求1或2所述的单克隆抗体或其抗原结合片段，其特征在于，所述抗体或其抗原结合片段还包含：如SEQ ID NO.10或SEQ ID NO.163所示氨基酸序列的轻链恒定区。
  5. 一种双特异性抗体，包含权利要求1所述抗体或其抗原结合片段、和第二抗体或其抗原结合片段。
  6. 一种药物组合物，其特征在于，包含权利要求1所述的单克隆抗体或其抗原结合片段、以及药学上可接受的载体或稀释剂。
  7. 根据权利要求6所述的药物组合物，其特征在于，还包括第二治疗剂，所述第二治疗剂选自：结合SARS-CoV-2病毒刺突蛋白的第二抗体或其抗原结合片段、抗炎剂、抗疟疾剂、以及结合TMPRSS2的抗体或其抗原结合片段。
  8. 一种分离的核酸，其编码权利要求1所述单克隆抗体或其抗原结合片段的重链或轻链可变区。
  9. 一种重组表达载体，其包含权利要求8所述的核酸。
  10. 一种宿主细胞，其包含权利要求9所述的重组表达载体。
  11. 一种检测病毒的试剂盒，其特征在于，包含权利要求1所述的单克隆抗体或其抗原结合片段。
  12. 一种检测芯片，其特征在于，包含权利要求1所述的单克隆抗体或其抗原结合片段。
  13. 权利要求1～4任一项所述单克隆抗体或其抗原结合片段在制备治疗病毒感染的药物中的用途。
  14. 权利要求1～4任一项所述单克隆抗体或其抗原结合片段在制备预防病毒感染的药物中的用途。
  15. 权利要求1～4任一项所述单克隆抗体或其抗原结合片段在制备诊断病毒感染的产品中的用途。
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