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Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display

Tanaka, Shiho and Olson, C. Anders and Barnes, Christopher O. and Higashide, Wendy and Gonzales, Marcos and Taft, Justin and Richardson, Ashley and Martin-Fernandez, Marta and Bogunovic, Dusan and Gnanapragasam, Priyanthi N. P. and Bjorkman, Pamela J. and Spilman, Patricia and Niazi, Kayvan and Rabizadeh, Shahrooz and Soon-Shiong, Patrick (2021) Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210915-214123136

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Abstract

The increasing prevalence of SARS-CoV-2 variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly-reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identified a set of antibodies against SARS-CoV-2 spike (S) proteins and characterized the structures of nAbs that recognized epitopes in the S1 subunit of the S glycoprotein. These structural studies revealed distinct binding modes for several antibodies, including targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interacts with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. A potent ACE2-blocking nAb was further engineered to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is a promising approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.09.14.460356DOIDiscussion Paper
ORCID:
AuthorORCID
Tanaka, Shiho0000-0002-2562-9660
Barnes, Christopher O.0000-0003-2754-5951
Taft, Justin0000-0002-9998-0429
Martin-Fernandez, Marta0000-0003-2714-8120
Bogunovic, Dusan0000-0002-9277-3232
Bjorkman, Pamela J.0000-0002-2277-3990
Rabizadeh, Shahrooz0000-0002-8609-7645
Soon-Shiong, Patrick0000-0002-4682-8298
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This version posted September 15, 2021. We thank J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance and K. Huey-Tubman for assistance with soluble spike purification. Electron microscopy was performed in the Caltech Cryo-EM Center with assistance from S. Chen and A. Malyutin. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory. We thank J. Kaiser, director of the Molecular Observatory at Caltech, and beamline staff C. Smith and S. Russi 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-AC02-76SF00515. 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 (P30GM133894). 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 (P01-AI138938-S1 to P.J.B.), the Caltech Merkin Institute for Translational Research (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. Author Contributions: Experimental designs: C.A.O., S.T, C.O.B, K.N., S.R., and P.S.S; mRNA library display: C.A.O; Cloning: C.A.O and W.H.; Protein Expression and Purification: C.A.O., S.T. and M.G.; Kinetic Analysis, ACE2 Blocking Assay, Epitope Binning, and ELISA ACE2 blocking assay: S.T., cryo-EM and X-ray crystallography: C.O.B and P.J.B.; Vero E6 Live Virus Neutralization Assay: J.T., A.R., M.M.F. and D.B.; pseudo-typed virus neutralization assay: P.G.. Manuscript preparation: S.T., C.O.B., C.A.O., and P.S. Declaration of interests: C.A.O., S.T., W.H., K.N., and P.S.S. are inventors for an international patent application with this work.
Group:COVID-19, Richard N. Merkin Institute for Translational Research
Funders:
Funding AgencyGrant Number
Gordon and Betty Moore FoundationUNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
Department of Energy (DOE)DE-AC02-76SF00515
NIHP30GM133894
NIHP01-AI138938-S1
Caltech Merkin Institute for Translational ResearchUNSPECIFIED
George Mason UniversityUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Burroughs Wellcome FundUNSPECIFIED
Subject Keywords:SARS-CoV-2, mRNA display, antibody, antibody design, neutralizing antibody, anti-spike antibody, SARS-CoV-2 variants
Record Number:CaltechAUTHORS:20210915-214123136
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210915-214123136
Official Citation:Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display. Shiho Tanaka, C. Anders Olson, Christopher O. Barnes, Wendy Higashide, Marcos Gonzales, Justin Taft, Ashley Richardson, Marta Martin-Fernandez, Dusan Bogunovic, Priyanthi N. P. Gnanapragasam, Pamela Bjorkman, Patricia R Spilman, Kayvan Niazi, Shahrooz Rabizadeh, Patrick Soon-Shiong bioRxiv 2021.09.14.460356; doi: https://doi.org/10.1101/2021.09.14.460356
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:110909
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 Sep 2021 22:15
Last Modified:15 Sep 2021 22:15

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