1. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike
- Author
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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, and Anton Simeonov
- Subjects
Mutation ,Multidisciplinary ,biology ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,COVID-19 ,Spike Protein ,Human airway ,Single-Domain Antibodies ,Antibodies, Viral ,medicine.disease_cause ,Antibodies, Neutralizing ,Virology ,Article ,Neutralization ,Spike Glycoprotein, Coronavirus ,medicine ,biology.protein ,Humans ,Bacteriophages ,Spike (software development) ,Antibody ,Ex vivo ,Protein Binding - 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. ONE-SENTENCE SUMMARY: A cost-effective, high-throughput, adaptable pipeline capable of identifying effective humanized nanobodies against SARS-CoV-2.
- Published
- 2021