A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike

  1. Ying Fu
  2. Juliana da Fonseca Rezende e Mello
  3. Bryan D. Fleming
  4. Alex Renn
  5. Catherine Z. Chen
  6. Xin Hu
  7. Miao Xu
  8. Kirill Gorshkov
  9. Quinlin Hanson
  10. Wei Zheng
  11. Emily M. Lee
  12. Lalith Perera
  13. Robert Petrovich
  14. Manisha Pradhan
  15. Richard T. Eastman
  16. Zina Itkin
  17. Thomas B. Stanley
  18. Allen Hsu
  19. Venkata Dandey
  20. Kedar Sharma
  21. William Gillette
  22. Troy Taylor
  23. Nitya Ramakrishnan
  24. Shelley Perkins
  25. Dominic Esposito
  26. Eunkeu Oh
  27. Kimihiro Susumu
  28. Mason Wolak
  29. Marc Ferrer
  30. Matthew D. Hall
  31. Mario J. Borgnia
  32. Anton Simeonov

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Abstract

Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.

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  1. Version published to 10.1371/journal.pone.0272364
  2. Version published to 10.1101/2021.10.22.465476v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.10.22.465476: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    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:
    • 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.

    Results from scite Reference Check: We found no unreliable references.

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  4. Version published to 10.1101/2021.10.22.465476v1 on bioRxiv