Neutralization of SARS-CoV-2 by destruction of the prefusion Spike

  1. Jiandong Huo
  2. Yuguang Zhao
  3. Jingshan Ren
  4. Daming Zhou
  5. Helen ME Duyvesteyn
  6. Helen M Ginn
  7. Loic Carrique
  8. Tomas Malinauskas
  9. Reinis R Ruza
  10. Pranav NM Shah
  11. Tiong Kit Tan
  12. Pramila Rijal
  13. Naomi Coombes
  14. Kevin Bewley
  15. Julika Radecke
  16. Neil G Paterson
  17. Piyasa Supasa
  18. Juthathip Mongkolsapaya
  19. Gavin R Screaton
  20. Miles Carroll
  21. Alain Townsend
  22. Elizabeth E Fry
  23. Raymond J Owens
  24. David I Stuart

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Abstract

There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment.

Highlights

  • CR3022 neutralises SARS-CoV-2

  • Neutralisation is by destroying the prefusion SPIKE conformation

  • This antibody may have therapeutic potential alone or with one blocking receptor attachment

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    SciScore for 10.1101/2020.05.05.079202: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All curves were plotted using GraphPad Prism 8.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Structural comparisons used SHP (Stuart et al., 1979), residues forming the RBD/Fab interface were identified with PISA (Krissinel and Henrick, 2007), figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    CTF-estimation with GCTF (v1.06) (Zhang, 2016) and non-template-driven particle picking was then performed within cryoSPARC v2.14.1-live followed by multiple rounds of 2D classification (Punjani et al., 2017).
    GCTF
    suggested: (GCTF, RRID:SCR_016500)
    Both structures were then sharpened in cryoSPARC.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    An initial model for the spike (structure-A) was generated using PDB ID, 6VYB (Walls et al., 2020) and rigid body fitted into the final map using COOT (Emsley and Cowtan, 2004).
    COOT
    suggested: (Coot, RRID:SCR_014222)
    The model was further refined in real space with PHENIX (Liebschner et al., 2019) which resulted in a correlation coefficient of 0.84.
    PHENIX
    suggested: (Phenix, RRID:SCR_014224)

    Results from OddPub: Thank you for sharing your data.

    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:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.05.05.079202 on bioRxiv