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Published December 24, 2020 | Supplemental Material + Accepted Version
Journal Article Open

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

Abstract

The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein show promise therapeutically and are being evaluated clinically. Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and 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 to 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 and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.

Additional Information

© 2020 Nature Publishing Group. Received 30 August 2020; Accepted 06 October 2020; Published 12 October 2020. We thank J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance, J. Vielmetter and J. Keeffe for setting up automated polyreactivity assays, J. Keeffe for construct design, and N. 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 S. Chen. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory (J. Kaiser, director), and S. Russi, A. Cohen and C. 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 US 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. Data availability: The atomic models generated from X-ray crystallographic studies of the C102–RBD complex, C102 Fab, C002 Fab, C110 Fab, C121 Fab and C135 Fab have been deposited at the Protein Data Bank (PDB) under accession codes 7K8M, 7K8N, 7K8O, 7K8P, 7K8Q and 7K8R, respectively. The atomic models and cryo-EM maps generated from cryo-EM studies of the C002–S 2P (state 1), C002–S 2P (state 2), C104–S 2P, C110–S 2P, C119–S 2P, C121–S 2P (state 1), C121–S 2P (state 2), C135–S 2P and C144–S 6P complexes have been deposited at the PDB and the Electron Microscopy Data Bank (EMDB) under the following accession codes: PDB 7K8S, 7K8T, 7K8U, 7K8V, 7K8W, 7K8X, 7K8Y, 7K8Z and 7K90; EMD EMD-22729, EMD-22730, EMD-22731, EMD-22372, EMD-22733, EMD-22734, EMD-22735, EMD-22736 and EMD-22737. Author Contributions: C.O.B., M.C.N., A.P.W. and P.J.B. conceived the study and analysed 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.E.A., K.A.D., S.R.E., A.G.M. and N.G.S. C.A.J. and C.O.B. performed and analysed crystallographic structures, with refinement assistance from M.E.A. and K.M.D. Y.E.L. performed polyreactivity assays. H.B.G. performed and analysed SPR experiments. A.P.W. analysed antibody sequences. C.O.B., M.C.N., A.P.W. and P.J.B. wrote the paper with contributions from other authors. Competing interests: The Rockefeller University has filed a provisional patent application in connection with this work on which D.F.R. and M.C.N. are inventors (US 63/021,387). Peer review information: Nature thanks the anonymous reviewer(s) for their contribution to the peer review of this work.

Attached Files

Accepted Version - nihms-1688197.pdf

Supplemental Material - 41586_2020_2852_Fig10_ESM.webp

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Created:
September 25, 2023
Modified:
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