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An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation #MMPMID32817938
Schoof M; Faust B; Saunders RA; Sangwan S; Rezelj V; Hoppe N; Boone M; Billesbolle CB; Puchades C; Azumaya CM; Kratochvil HT; Zimanyi M; Deshpande I; Liang J; Dickinson S; Nguyen HC; Chio CM; Merz GE; Thompson MC; Diwanji D; Schaefer K; Anand AA; Dobzinski N; Zha BS; Simoneau CR; Leon K; White KM; Chio US; Gupta M; Jin M; Li F; Liu Y; Zhang K; Bulkley D; Sun M; Smith AM; Rizo AN; Moss F; Brilot AF; Pourmal S; Trenker R; Pospiech T; Gupta S; Barsi-Rhyne B; Belyy V; Barile-Hill AW; Nock S; Liu Y; Krogan NJ; Ralston CY; Swaney DL; Garcia-Sastre A; Ott M; Vignuzzi M; Walter P; Manglik A
bioRxiv 2020[Aug]; ä (ä): ä PMID32817938show ga
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.