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

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 pot...

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Published in:bioRxiv 2022-03
Main Authors: Fu, Ying, Juliana Da Fonseca Rezende E Mello, Fleming, Bryan D, Renn, Alex, Chen, Catherine Z, Hu, Xin, Xu, Miao, Gorshkov, Kirill, Hanson, Quinlin, Zheng, Wei, Lee, Emily M, Perera, Lalith, Petrovich, Robert, Pradhan, Manisha, Eastman, Richard T, Itkin, Zina, Stanley, Thomas, Hsu, Allen, Dandey, Venkata, Gillette, William, Taylor, Troy, Ramakrishnan, Nitya, Perkins, Shelley, Esposito, Dominic, Oh, Eunkeu, Kimihiro Susumu, Wolak, Mason, Ferrer, Marc, Hall, Matthew D, Borgnia, Mario J, Simeonov, Anton
Format: Article
Language:English
Subjects:
ACE2
Angiotensin-converting enzyme 2
Mutation
Nanobodies
Patent applications
Phage display
Severe acute respiratory syndrome coronavirus 2
Spike protein
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Summary: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. Competing Interest Statement Y.F., A.R., B.D.F., M.H., and A.S. are listed as inventors on pending patent applications for the listed nanobodies in this work. The other authors declare that they have no competing interests. Footnotes * The title was changed and the formatting was updated.
DOI:10.1101/2021.10.22.465476