An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation
Michael Schoof; Bryan Faust; Reuben A Saunders; Smriti Sangwan; Veronica V Rezelj; Nick Hoppe; Morgane Boone; Christian Billesboelle; Cristina Puchades; Caleigh M Azumaya; Huong T Kratochvil; Marcell Zimanyi; Ishan Deshpande; Jiahao Liang; Sasha Dickinson; Henry C Nguyen; Cynthia M Chio; Gregory E Merz; Michael C Thompson; Devan Diwanji; Kaitlin Schaefer; Aditya A Anand; Niv Dobzinski; Beth Shoshana Zha; Camille R. Simoneau; Kristoffer Leon; Kris M. White; Un Seng Chio; Meghna Gupta; Mingliang Jin; Fei Li; Yanxin Liu; Kaihua Zhang; David Bulkley; Ming Sun; Amber M Smith; Alexandrea N. Rizo; Frank Moss; Axel F. Brilot; Sergei Pourmal; Raphael Trenker; Thomas Pospiech; Sayan Gupta; Benjamin Barsi-Rhyne; Vladislav Belyy; Andrew W Barile-Hill; Silke Nock; Yuwei Liu; Nevan J. Krogan; Corie Y Ralston; Danielle L Swaney; Adolfo Garcia-Sastre; Melanie Ott; Marco Vignuzzi; - Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium; Peter Walter; Aashish Manglik.
Preprint
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| PREPRINT-BIORXIV | ID: ppbiorxiv-238469
Without an effective prophylactic solution, infections from SARS-CoV-2 continue to rise worldwide with devastating health and economic costs. SARS-CoV-2 gains entry into host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). Disruption of this interaction confers potent neutralization of viral entry, providing an avenue for vaccine design and for therapeutic antibodies. Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. By screening a yeast surface-displayed library of synthetic nanobody sequences, we identified a panel of nanobodies that bind to multiple epitopes on Spike and block ACE2 interaction via two distinct mechanisms. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for SARS-CoV-2 Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains stability and function after aerosolization, lyophilization, and heat treatment. These properties may enable aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia, promising to yield a widely deployable, patient-friendly prophylactic and/or early infection therapeutic agent to stem the worst pandemic in a century.
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