Design ofthe SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response

Dickey, Thayne H.; Tang, Wai Kwan; Butler, Brandi; Ouahes, Tarik; Orr-Gonzalez, Sachy; Salinas, Nichole D.; Lambert, Lynn E.; Tolia, Niraj H.

doi:10.1126/sciadv.abq8276

Design ofthe SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response

Journal Article · 01 September 2022 · Sci. Advances

DOI:https://doi.org/10.1126/sciadv.abq8276· OSTI ID:1901137

Dickey, Thayne H.; Tang, Wai Kwan; Butler, Brandi; Ouahes, Tarik; Orr-Gonzalez, Sachy; Salinas, Nichole D.; Lambert, Lynn E.; Tolia, Niraj H.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIAID; NIH

OSTI ID:: 1901137

Journal Information:: Sci. Advances, Journal Name: Sci. Advances Journal Issue: (37) Vol. 8

Country of Publication:: United States

Language:: ENGLISH

References (68)

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion Walls, Alexandra C.; Xiong, Xiaoli; Park, Young-Jun Cell, Vol. 176, Issue 5 https://doi.org/10.1016/j.cell.2018.12.028	journal	February 2019
Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability Brouwer, Philip J. M.; Caniels, Tom G.; van der Straten, Karlijn Science, Vol. 369, Issue 6504 https://doi.org/10.1126/science.abc5902	journal	June 2020
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
An interactive web-based dashboard to track COVID-19 in real time Dong, Ensheng; Du, Hongru; Gardner, Lauren The Lancet Infectious Diseases, Vol. 20, Issue 5 https://doi.org/10.1016/S1473-3099(20)30120-1	journal	May 2020
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Lan, Jun; Ge, Jiwan; Yu, Jinfang Nature, Vol. 581, Issue 7807 https://doi.org/10.1038/s41586-020-2180-5	journal	March 2020
The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic Hoffmann, Markus; Krüger, Nadine; Schulz, Sebastian Cell, Vol. 185, Issue 3 https://doi.org/10.1016/j.cell.2021.12.032	journal	February 2022
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
Structure of Severe Acute Respiratory Syndrome Coronavirus Receptor-binding Domain Complexed with Neutralizing Antibody Prabakaran, Ponraj; Gan, Jianhua; Feng, Yang Journal of Biological Chemistry, Vol. 281, Issue 23 https://doi.org/10.1074/jbc.M600697200	journal	April 2006
An mRNA Vaccine against SARS-CoV-2 — Preliminary Report Jackson, Lisa A.; Anderson, Evan J.; Rouphael, Nadine G. New England Journal of Medicine, Vol. 383, Issue 20 https://doi.org/10.1056/NEJMoa2022483	journal	November 2020
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody Pinto, Dora; Park, Young-Jun; Beltramello, Martina Nature, Vol. 583, Issue 7815 https://doi.org/10.1038/s41586-020-2349-y	journal	May 2020
Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Walls, Alexandra C.; Park, Young-Jun; Tortorici, M. Alejandra Cell, Vol. 181, Issue 2 https://doi.org/10.1016/j.cell.2020.02.058	journal	April 2020
The antigenic anatomy of SARS-CoV-2 receptor binding domain Dejnirattisai, Wanwisa; Zhou, Daming; Ginn, Helen M. Cell, Vol. 184, Issue 8 https://doi.org/10.1016/j.cell.2021.02.032	journal	April 2021
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S. Proceedings of the National Academy of Sciences, Vol. 114, Issue 35 https://doi.org/10.1073/pnas.1707304114	journal	August 2017
SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness Corbett, Kizzmekia S.; Edwards, Darin K.; Leist, Sarah R. Nature, Vol. 586, Issue 7830 https://doi.org/10.1038/s41586-020-2622-0	journal	August 2020
Neutralization of SARS-CoV-2 Omicron by BNT162b2 mRNA vaccine–elicited human sera Muik, Alexander; Lui, Bonny Gaby; Wallisch, Ann-Kathrin Science, Vol. 375, Issue 6581 https://doi.org/10.1126/science.abn7591	journal	February 2022
Phase 1–2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine Keech, Cheryl; Albert, Gary; Cho, Iksung New England Journal of Medicine, Vol. 383, Issue 24 https://doi.org/10.1056/NEJMoa2026920	journal	December 2020
Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity Liu, Hejun; Wu, Nicholas C.; Yuan, Meng Immunity, Vol. 53, Issue 6 https://doi.org/10.1016/j.immuni.2020.10.023	journal	December 2020
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
Safety and Immunogenicity of Two RNA-Based Covid-19 Vaccine Candidates Walsh, Edward E.; Frenck, Robert W.; Falsey, Ann R. New England Journal of Medicine, Vol. 383, Issue 25 https://doi.org/10.1056/NEJMoa2027906	journal	December 2020
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Influence of protein fold stability on immunogenicity and its implications for vaccine design Scheiblhofer, Sandra; Laimer, Josef; Machado, Yoan Expert Review of Vaccines, Vol. 16, Issue 5 https://doi.org/10.1080/14760584.2017.1306441	journal	March 2017
Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants ter Meulen, Jan; van den Brink, Edward N.; Poon, Leo L. M. PLoS Medicine, Vol. 3, Issue 7 https://doi.org/10.1371/journal.pmed.0030237	journal	July 2006
Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2 Chan, Kui K.; Dorosky, Danielle; Sharma, Preeti Science, Vol. 369, Issue 6508 https://doi.org/10.1126/science.abc0870	journal	August 2020
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2 Liu, Lihong; Iketani, Sho; Guo, Yicheng Nature, Vol. 602, Issue 7898 https://doi.org/10.1038/s41586-021-04388-0	journal	December 2021
Rapid Development of SARS-CoV-2 Spike Protein Receptor-Binding Domain Self-Assembled Nanoparticle Vaccine Candidates Kang, Yin-Feng; Sun, Cong; Zhuang, Zhen ACS Nano, Vol. 15, Issue 2 https://doi.org/10.1021/acsnano.0c08379	journal	January 2021
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S. Science, Vol. 367, Issue 6483 https://doi.org/10.1126/science.abb2507	journal	February 2020
Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies Wrapp, Daniel; De Vlieger, Dorien; Corbett, Kizzmekia S. Cell, Vol. 181, Issue 5 https://doi.org/10.1016/j.cell.2020.04.031	journal	May 2020
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
A single intranasal dose of a live-attenuated parainfluenza virus-vectored SARS-CoV-2 vaccine is protective in hamsters Liu, Xueqiao; Luongo, Cindy; Matsuoka, Yumiko Proceedings of the National Academy of Sciences, Vol. 118, Issue 50 https://doi.org/10.1073/pnas.2109744118	journal	December 2021
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes Hsieh, Ching-Lin; Goldsmith, Jory A.; Schaub, Jeffrey M. Science, Vol. 369, Issue 6510 https://doi.org/10.1126/science.abd0826	journal	July 2020
A time- and cost-efficient system for high-level protein production in mammalian cells Aricescu, A. Radu; Lu, Weixian; Jones, E. Yvonne Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 10 https://doi.org/10.1107/S0907444906029799	journal	September 2006
A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses Tan, Tiong Kit; Rijal, Pramila; Rahikainen, Rolle Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20654-7	journal	January 2021
Ad26 vector-based COVID-19 vaccine encoding a prefusion-stabilized SARS-CoV-2 Spike immunogen induces potent humoral and cellular immune responses Bos, Rinke; Rutten, Lucy; van der Lubbe, Joan E. M. npj Vaccines, Vol. 5, Issue 1 https://doi.org/10.1038/s41541-020-00243-x	journal	September 2020
Accurate design of megadalton-scale two-component icosahedral protein complexes Bale, J. B.; Gonen, S.; Liu, Y. Science, Vol. 353, Issue 6297 https://doi.org/10.1126/science.aaf8818	journal	July 2016
De novo protein design enables the precise induction of RSV-neutralizing antibodies Sesterhenn, Fabian; Yang, Che; Bonet, Jaume Science, Vol. 368, Issue 6492 https://doi.org/10.1126/science.aay5051	journal	May 2020
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability Goldenzweig, Adi; Goldsmith, Moshe; Hill, Shannon E. Molecular Cell, Vol. 63, Issue 2 https://doi.org/10.1016/j.molcel.2016.06.012	journal	July 2016
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies Barnes, Christopher O.; Jette, Claudia A.; Abernathy, Morgan E. Nature, Vol. 588, Issue 7839 https://doi.org/10.1038/s41586-020-2852-1	journal	October 2020
Introduction of Two Prolines and Removal of the Polybasic Cleavage Site Lead to Higher Efficacy of a Recombinant Spike-Based SARS-CoV-2 Vaccine in the Mouse Model Amanat, Fatima; Strohmeier, Shirin; Rathnasinghe, Raveen mBio, Vol. 12, Issue 2 https://doi.org/10.1128/mBio.02648-20	journal	April 2021
Interim Results of a Phase 1–2a Trial of Ad26.COV2.S Covid-19 Vaccine Sadoff, Jerald; Le Gars, Mathieu; Shukarev, Georgi New England Journal of Medicine, Vol. 384, Issue 19 https://doi.org/10.1056/NEJMoa2034201	journal	May 2021
Durability of mRNA-1273 vaccine–induced antibodies against SARS-CoV-2 variants Pegu, Amarendra; O’Connell, Sarah E.; Schmidt, Stephen D. Science, Vol. 373, Issue 6561 https://doi.org/10.1126/science.abj4176	journal	September 2021
Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Sui, J.; Li, W.; Murakami, A. Proceedings of the National Academy of Sciences, Vol. 101, Issue 8 https://doi.org/10.1073/pnas.0307140101	journal	February 2004
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Proof of principle for epitope-focused vaccine design Correia, Bruno E.; Bates, John T.; Loomis, Rebecca J. Nature, Vol. 507, Issue 7491 https://doi.org/10.1038/nature12966	journal	February 2014
A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV Yuan, Meng; Wu, Nicholas C.; Zhu, Xueyong Science, Vol. 368, Issue 6491 https://doi.org/10.1126/science.abb7269	journal	April 2020
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike Liu, Lihong; Wang, Pengfei; Nair, Manoj S. Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2571-7	journal	July 2020
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains Zhou, Tongqing; Tsybovsky, Yaroslav; Gorman, Jason Cell Host & Microbe, Vol. 28, Issue 6 https://doi.org/10.1016/j.chom.2020.11.004	journal	December 2020
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Nanoparticle Vaccines Based on the Receptor Binding Domain (RBD) and Heptad Repeat (HR) of SARS-CoV-2 Elicit Robust Protective Immune Responses Ma, Xiancai; Zou, Fan; Yu, Fei Immunity, Vol. 53, Issue 6 https://doi.org/10.1016/j.immuni.2020.11.015	journal	December 2020
One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen Campeotto, Ivan; Goldenzweig, Adi; Davey, Jack Proceedings of the National Academy of Sciences, Vol. 114, Issue 5 https://doi.org/10.1073/pnas.1616903114	journal	January 2017
ExPASy: the proteomics server for in-depth protein knowledge and analysis Gasteiger, E. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg563	journal	July 2003
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
A Universal Design of Betacoronavirus Vaccines against COVID-19, MERS, and SARS Dai, Lianpan; Zheng, Tianyi; Xu, Kun Cell, Vol. 182, Issue 3 https://doi.org/10.1016/j.cell.2020.06.035	journal	August 2020
Structural Basis of Neutralization by a Human Anti-severe Acute Respiratory Syndrome Spike Protein Antibody, 80R Hwang, William C.; Lin, Yaqiong; Santelli, Eugenio Journal of Biological Chemistry, Vol. 281, Issue 45 https://doi.org/10.1074/jbc.M603275200	journal	September 2006
Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody Lv, Zhe; Deng, Yong-Qiang; Ye, Qing Science, Vol. 369, Issue 6510 https://doi.org/10.1126/science.abc5881	journal	July 2020
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants Wang, Zijun; Schmidt, Fabian; Weisblum, Yiska Nature, Vol. 592, Issue 7855 https://doi.org/10.1038/s41586-021-03324-6	journal	February 2021
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 Wang, Pengfei; Nair, Manoj S.; Liu, Lihong Nature, Vol. 593, Issue 7857 https://doi.org/10.1038/s41586-021-03398-2	journal	March 2021
Extremely potent human monoclonal antibodies from COVID-19 convalescent patients Andreano, Emanuele; Nicastri, Emanuele; Paciello, Ida Cell, Vol. 184, Issue 7 https://doi.org/10.1016/j.cell.2021.02.035	journal	April 2021
Convergent antibody responses to SARS-CoV-2 in convalescent individuals Robbiani, Davide F.; Gaebler, Christian; Muecksch, Frauke Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2456-9	journal	June 2020
Structural Insights into Immune Recognition of the Severe Acute Respiratory Syndrome Coronavirus S Protein Receptor Binding Domain Pak, John E.; Sharon, Chetna; Satkunarajah, Malathy Journal of Molecular Biology, Vol. 388, Issue 4 https://doi.org/10.1016/j.jmb.2009.03.042	journal	May 2009
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing Whitehead, Timothy A.; Chevalier, Aaron; Song, Yifan Nature Biotechnology, Vol. 30, Issue 6 https://doi.org/10.1038/nbt.2214	journal	May 2012
Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors Jardine, J.; Julien, J. -P.; Menis, S. Science, Vol. 340, Issue 6133 https://doi.org/10.1126/science.1234150	journal	March 2013
An engineered vaccine of the Plasmodium vivax Duffy binding protein enhances induction of broadly neutralizing antibodies Ntumngia, Francis B.; Pires, Camilla V.; Barnes, Samantha J. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-13891-2	journal	October 2017
Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody Rappazzo, C. Garrett; Tse, Longping V.; Kaku, Chengzi I. Science, Vol. 371, Issue 6531 https://doi.org/10.1126/science.abf4830	journal	February 2021
Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2 Walls, Alexandra C.; Fiala, Brooke; Schäfer, Alexandra Cell, Vol. 183, Issue 5 https://doi.org/10.1016/j.cell.2020.10.043	journal	November 2020
Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail Hansen, Johanna; Baum, Alina; Pascal, Kristen E. Science https://doi.org/10.1126/science.abd0827	journal	June 2020
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
Human neutralizing antibodies elicited by SARS-CoV-2 infection Ju, Bin; Zhang, Qi; Ge, Jiwan Nature, Vol. 584, Issue 7819 https://doi.org/10.1038/s41586-020-2380-z	journal	May 2020

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