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Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies

Barnes, Christopher O. and Jette, Claudia A. and Abernathy, Morgan E. and Dam, Kim-Marie A. and Esswein, Shannon R. and Gristick, Harry B. and Malyutin, Andrey G. and Sharaf, Naima G. and Huey-Tubman, Kathryn E. and Lee, Yu E. and Robbiani, Davide F. and Nussenzweig, Michel C. and West, Anthony P., Jr. and Bjorkman, Pamela J. (2020) Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies. . (Unpublished)

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The COVID-19 pandemic presents an urgent health crisis. Human neutralizing antibodies (hNAbs) that target the host ACE2 receptor-binding domain (RBD) of the SARS-CoV-2 spike show therapeutic promise and are being evaluated clincally. To determine structural correlates of SARS-CoV-2 neutralization, we solved 8 new structures of distinct COVID-19 hNAbs in complex with SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed classification into categories: (1) VH3-53 hNAbs with short CDRH3s that block ACE2 and bind only to “up” RBDs, (2) ACE2-blocking hNAbs that bind both “up” and “down” RBDs and can contact adjacent RBDs, (3) hNAbs that bind outside the ACE2 site and recognize “up” and “down” RBDs, and (4) Previously-described antibodies that do not block ACE2 and bind only “up” RBDs. Class 2 comprised four hNAbs whose epitopes bridged RBDs, including a VH3-53 hNAb that used a long CDRH3 with a hydrophobic tip to bridge between adjacent “down” RBDs, thereby locking spike into a closed conformation. Epitope/paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, suggesting combinations for clinical use, and providing insight into immune responses against SARS-CoV-2.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Barnes, Christopher O.0000-0003-2754-5951
Jette, Claudia A.0000-0002-5085-8027
Esswein, Shannon R.0000-0002-5142-0190
Gristick, Harry B.0000-0002-1957-2821
Sharaf, Naima G.0000-0002-3662-9228
Huey-Tubman, Kathryn E.0000-0002-4683-8138
Robbiani, Davide F.0000-0001-7379-3484
Nussenzweig, Michel C.0000-0003-0592-8564
Bjorkman, Pamela J.0000-0002-2277-3990
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. Posted August 30, 2020. We thank Dr. Jost Vielmetter, Pauline Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance, Drs. Jost Vielmetter and Jennifer Keeffe for setting up automated polyreactivity assays, Dr. Jennifer Keeffe for construct design, and Nicholas Koranda for help with cloning and protein purification. Electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy with assistance from Dr. Songye Chen. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory (Dr. Jens Kaiser, director), and Drs. Silvia Russi, Aina Cohen, and Clyde Smith and the beamline staff at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-c76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. This work was supported by NIH grant P01-AI138938-S1 (P.J.B. and M.C.N.), the Caltech Merkin Institute for Translational Research (P.J.B.), NIH grant P50 8 P50 AI150464-13 (P.J.B.), and a George Mason University Fast Grant (P.J.B.). C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. M.C.N. is a Howard Hughes Medical Institute Investigator. Author contributions: C.O.B., M.C.N., A.P.W., and P.J.B. conceived the study and analyzed data; D.F.R. and M.C.N. provided monoclonal antibody sequences and plasmids derived from COVID-19 convalescent donors. C.O.B. and K.H.T. performed protein purifications and C.O.B. assembled complexes for cryo-EM and X-ray crystallography studies. C.O.B. performed cryo-EM and interpreted structures with assistance from M.A.E., K.A.D, S.R.E., A.G.M., and N.G.S. C.A.J. and C.O.B. performed and analyzed crystallographic structures, with refinement assistance from M.A.E and K.M.D. Y.E.L. performed polyreactivity assays. H.B.G. performed and analyzed SPR experiments. A.P.W. analyzed antibody sequences. C.O.B., M.C.N., A.P.W., and P.J.B. wrote the paper with contributions from other authors. Competing Interest Statement: The Rockefeller University has filed a provisional patent application for monoclonal antibodies described in this work, on which D.F.R. and M.C.N. are inventors. Data availability: The cryo-EM maps and atomic models will be deposited at the EMDB and the PDB. Crystal structure data will be deposited in the PDB. Described materials will be available upon request, in some cases after completion of a materials transfer agreement.
Group:Richard N. Merkin Institute for Translational Research, COVID-19
Funding AgencyGrant Number
Gordon and Betty Moore FoundationUNSPECIFIED
Arnold and Mabel Beckman FoundationUNSPECIFIED
Department of Energy (DOE)DE-AC02-76SF00515
Caltech Merkin Institute for Translational ResearchUNSPECIFIED
NIHP50 8 P50 AI150464-13
George Mason UniversityUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Burroughs Wellcome FundUNSPECIFIED
Record Number:CaltechAUTHORS:20200908-082702811
Persistent URL:
Official Citation:Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies. Christopher O. Barnes, Claudia A. Jette, Morgan E. Abernathy, Kim-Marie A. Dam, Shannon R. Esswein, Harry B. Gristick, Andrey G. Malyutin, Naima G. Sharaf, Kathryn E. Huey-Tubman, Yu E. Lee, Davide F. Robbiani, Michel C. Nussenzweig, Anthony P. West Jr., Pamela J. Bjorkman. bioRxiv 2020.08.30.273920; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:105265
Deposited By: Tony Diaz
Deposited On:08 Sep 2020 15:45
Last Modified:16 Nov 2021 18:41

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