PLoS ONE (Jan 2022)

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

  • Ying Fu,
  • Juliana da Fonseca Rezende E Mello,
  • Bryan D Fleming,
  • Alex Renn,
  • Catherine Z Chen,
  • Xin Hu,
  • Miao Xu,
  • Kirill Gorshkov,
  • Quinlin Hanson,
  • Wei Zheng,
  • Emily M Lee,
  • Lalith Perera,
  • Robert Petrovich,
  • Manisha Pradhan,
  • Richard T Eastman,
  • Zina Itkin,
  • Thomas B Stanley,
  • Allen Hsu,
  • Venkata Dandey,
  • Kedar Sharma,
  • William Gillette,
  • Troy Taylor,
  • Nitya Ramakrishnan,
  • Shelley Perkins,
  • Dominic Esposito,
  • Eunkeu Oh,
  • Kimihiro Susumu,
  • Mason Wolak,
  • Marc Ferrer,
  • Matthew D Hall,
  • Mario J Borgnia,
  • Anton Simeonov

DOI
https://doi.org/10.1371/journal.pone.0272364
Journal volume & issue
Vol. 17, no. 8
p. e0272364

Abstract

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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.