The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2

Fu, Y.; da Fonseca Rezende e Mello, J.; Fleming, B. D.; Renn, A.; Chen, C. Z.; Hu, X.; Xu, M.; Gorshkov, K.; Hanson, Q.; Zheng, W.; Lee, E. M.; Perera, L.; Petrovich, R.; Pradhan, M.; Eastman, R. T.; Itkin, Z.; Stanley, T.; Hsu, A.; Dandey, V.; Gillette, W.; Taylor, T.; Ramakrishnan, N.; Perkins, S.; Esposito, D.; Oh, E.; Susumu, K.; Wolak, M.; Ferrer, M.; Hall, M. D.; Borgnia, M. J.; Simeonov, A.

doi:10.1101/2021.10.22.465476

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bioRxiv · 10.1101/2021.10.22.465476

The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2

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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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Fu, Y., da Fonseca Rezende e Mello, J., Fleming, B. D., Renn, A., Chen, C. Z., Hu, X., Xu, M., Gorshkov, K., Hanson, Q., Zheng, W., Lee, E. M., Perera, L., Petrovich, R., Pradhan, M., Eastman, R. T., Itkin, Z., Stanley, T., Hsu, A., Dandey, V., Gillette, W., Taylor, T., Ramakrishnan, N., Perkins, S., Esposito, D., Oh, E., Susumu, K., Wolak, M., Ferrer, M., Hall, M. D., Borgnia, M. J., Simeonov, A.. 2021-10-24. The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2. https://doi.org/10.1101/2021.10.22.465476

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