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Schoof M, Faust B, Saunders RA, et al. An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation. bioRxiv. 2020;doi: 10.1101/2020.08.08.238469.
Schoof, M., Faust, B., Saunders, R. A., Sangwan, S., Rezelj, V., Hoppe, N., Boone, M., Billesbølle, C. B., Puchades, C., Azumaya, C. M., Kratochvil, H. T., Zimanyi, M., Deshpande, I., Liang, J., Dickinson, S., Nguyen, H. C., Chio, C. M., Merz, G. E., Thompson, M. C., Diwanji, D., Schaefer, K., Anand, A. A., Dobzinski, N., Zha, B. S., Simoneau, C. R., Leon, K., White, K. M., Chio, U. S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D., Sun, M., Smith, A. M., Rizo, A. N., Moss, F., Brilot, A. F., Pourmal, S., Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill, A. W., Nock, S., Liu, Y., Krogan, N. J., Ralston, C. Y., Swaney, D. L., García-Sastre, A., Ott, M., Vignuzzi, M., Walter, P., & Manglik, A. (2020). An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.08.08.238469
Schoof, Michael, et al. "An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.08.08.238469
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle 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, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation. bioRxiv. 2020 Aug 17; doi: 10.1101/2020.08.08.238469. PMID: 32817938; PMCID: PMC7430568.
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bioRxiv. 2020 Aug 17; doi: 10.1101/2020.08.08.238469.

An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation.

bioRxiv : the preprint server for biology

Michael Schoof, Bryan Faust, Reuben A Saunders, Smriti Sangwan, Veronica Rezelj, Nick Hoppe, Morgane Boone, Christian B Billesbølle, 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 García-Sastre, Melanie Ott, Marco Vignuzzi, Peter Walter, Aashish Manglik

Affiliations

  1. Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.
  2. Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.
  3. Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.
  4. Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.
  5. Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA.
  6. Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, Cedex 15, France.
  7. Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA 94158, USA.
  8. Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
  9. J. David Gladstone Institutes, San Francisco, CA, USA.
  10. Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
  11. Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  12. Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  13. Molecular Biophysics and Integrated Bioimaging and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  14. Cytiva Life Sciences, Marlborough, MA, USA.
  15. Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  16. The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  17. Department of Anesthesia and Perioperative Care, University of California at San Francisco, San Francisco, CA, USA.

PMID: 32817938 PMCID: PMC7430568 DOI: 10.1101/2020.08.08.238469

Abstract

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.

Conflict of interest statement

Competing Interests M.Schoof, B.Faust, R.A.Saunders, N.Hoppe, P.Walter, and A.Manglik are inventors on a provisional patent describing anti-Spike nanobodies described in this manuscript.

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