Journal Article

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

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

2022

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: ACE2 / Analysis / Angiotensin-converting enzyme 2 / Antibodies / Antibodies, Neutralizing / Antibodies, Viral / Antigens / Bacteriophages - metabolism / Binders / Binding sites / Biological markers / Biology and life sciences / Coronaviruses / COVID-19 / Development strategies / Engineering and Technology / Glycerol / Humans / Medicine and health sciences / Molecular dynamics / Mutation / Nanobodies / Neutralization / Neutralizing / Pandemics / Phage display / Phages / Physical Sciences / Protein Binding / Proteins / Research and Analysis Methods / SARS-CoV-2 / Severe acute respiratory syndrome / Severe acute respiratory syndrome coronavirus 2 / Single-Domain Antibodies / Spike Glycoprotein, Coronavirus / Spike protein / Structural analysis