SARS-CoV-2 and SARS-CoV Spike-RBD Structure and Receptor Binding Comparison and Potential Implications on Neutralizing Antibody and Vaccine Development

  1. Chunyun Sun
  2. Long Chen
  3. Ji Yang
  4. Chunxia Luo
  5. Yanjing Zhang
  6. Jing Li
  7. Jiahui Yang
  8. Jie Zhang
  9. Liangzhi Xie

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Abstract

SARS-CoV-2 and SARS-CoV share a common human receptor ACE2. Protein-protein interaction structure modeling indicates that spike-RBD of the two viruses also has similar overall binding conformation and binding free energy to ACE2. In vitro assays using recombinant ACE2 proteins and ACE2 expressing cells confirmed the two coronaviruses’ similar binding affinities to ACE2. The above studies provide experimental supporting evidences and possible explanation for the high transmissibility observed in the SARS-CoV-2 outbreak. Potent ACE2-blocking SARS-CoV neutralizing antibodies showed limited cross-binding and neutralizing activities to SARS-CoV-2. ACE2-non-blocking SARS-CoV RBD antibodies, though with weaker neutralizing activities against SARS-CoV, showed positive cross-neutralizing activities to SARS-CoV-2 with an unknown mechanism. These findings suggest a trade-off between the efficacy and spectrum for therapeutic antibodies to different coronaviruses, and hence highlight the possibilities and challenges in developing broadly protecting antibodies and vaccines against SARS-CoV-2 and its future mutants.

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  1. ScreenIT

    SciScore for 10.1101/2020.02.16.951723: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    , transfection reagent Sinofection (Cat: STF02), mammalian expression plasmids of full length S or RBD protein of SARS-CoV-2 (Cat: VG40589-UT, Wuhan/IVDC-HB-01/2019) and SARS-CoV (Cat: VG40150-G-N, CUHK-W1), ACE2 (Cat: HG10108-UT), polyclonal antibodies against SARS-CoV RP01 (Cat: 40150-RP01) and T52 (Cat: 40150-T52) were purchased from Sino Biological.
    SARS-CoV
    suggested: None
    ACE2
    suggested: None
    RP01
    suggested: None
    T52
    suggested: (Rockland Cat# 600-401-W94, RRID:AB_2614544)
    SARS-CoV neutralizing antibodies were generated from mice (M103, M127) or rabbits (R314, R301, R325, R302, R258, R348) immunized with recombinant S1 protein of SARS-CoV.
    R302
    suggested: None
    After washing away the unbound proteins, cells were incubated withPE labelled anti-his-tag antibody for 20 min and went through flow cytometer for detection of cellular binding.
    anti-his-tag
    suggested: None
    Then 100μL/well of the antibody-PSV mixture was added onto the 293T/ACE2 cell wells and incubated for 37°C, 5% CO2.
    antibody-PSV
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Both 293T and 293T-ACE2 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) FBS.
    293T-ACE2
    suggested: RRID:CVCL_YZ65)
    Pseudovirus production in 293T adherent cells: 6-8 hours before transfection, 293T cells were pre-plate on T75 flask in DMEM+10% FBS at 100,000 cells/cm2. 13μg of Luciferase-expressing HIV-1 lentiviral transfer genome (pWPXL-luc), 13μg of packaging plasmid (PSD) and 13μg of expression plasmid encoding either SARS-CoV-2-S protein (pCMV-whCoV-Spike) or SARS-S protein (pCMV-SARS-Spike) were co-transfected into pre-plated 293T cells using Sinofection transfection reagent according to the procedure recommended by manufacturer.
    293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    Then 100μL/well of the antibody-PSV mixture was added onto the 293T/ACE2 cell wells and incubated for 37°C, 5% CO2.
    293T/ACE2
    suggested: RRID:CVCL_YZ65)
    Software and Algorithms
    SentencesResources
    Flowjo and Graphpad softwares were used for data analysis.
    Flowjo
    suggested: (FlowJo, RRID:SCR_008520)
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)
    Software PyMol was used for preparing structural figures39.
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    Alignment of 111 SARS-CoV RBD sequence, used for the generation of sequence conservation, was collected by BLAST via NCBI website34.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    NCBI
    suggested: (NCBI, RRID:SCR_006472)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.02.16.951723v1 on bioRxiv