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Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Dadonaite B, Petersen BK, Engdahl TB, Chen E, Handal LS, Hall L, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JKY, Rubinfeld B, Saada EA, Weisenberger T, Lee TH, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Earnhart CG, Hopkins S, Bates TW, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Bloom JD, Diamond MS, Crowe JE, Carnahan RH, Faissol DM. Computationally restoring the potency of a clinical antibody against Omicron. Nature 2024; 629:878-885. [PMID: 38720086 PMCID: PMC11111397 DOI: 10.1038/s41586-024-07385-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/04/2024] [Indexed: 05/21/2024]
Abstract
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3 and revealed how quickly viral escape can curtail effective options4,5. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab4-6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.
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MESH Headings
- SARS-CoV-2/immunology
- Humans
- COVID-19/immunology
- COVID-19/virology
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- Antibodies, Viral/pharmacology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Neutralizing/pharmacology
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal/pharmacology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Neutralization Tests
- Mice
- Mutation
- Female
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Affiliation(s)
- Thomas A Desautels
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kathryn T Arrildt
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Adam T Zemla
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Edmond Y Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Fangqiang Zhu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Dante Ricci
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Stephanie Cronin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne M Scheaffer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brenden K Petersen
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Taylor B Engdahl
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elaine Chen
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura S Handal
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynn Hall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John W Goforth
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Denis Vashchenko
- Applications Simulations and Quality Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Sam Nguyen
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Google, Alphabet Inc., Mountain View, CA, USA
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jacky Kai-Yin Lo
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Bonnee Rubinfeld
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Edwin A Saada
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Tracy Weisenberger
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Tek-Hyung Lee
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Vir Biotechnology, San Francisco, CA, USA
| | - James B Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexander Ladd
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Mary S Silva
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Rebecca M Haluska
- Applications Simulations and Quality Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Emilia A Grzesiak
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christopher G Earnhart
- Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense, US Department of Defense, Frederick, MD, USA
| | | | - Thomas W Bates
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brent W Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Shivshankar Sundaram
- Center for Bioengineering, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel M Faissol
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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2
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Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Dadonaite B, Petersen BK, Engdahl TB, Chen E, Handal LS, Hall L, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JKY, Rubinfeld B, Saada EA, Weisenberger T, Lee TH, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Earnhart CG, Hopkins S, Bates TW, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Bloom J, Diamond MS, Crowe JE, Carnahan RH, Faissol DM. Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants. bioRxiv 2023:2022.10.21.513237. [PMID: 36324800 PMCID: PMC9628197 DOI: 10.1101/2022.10.21.513237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3, but also revealed how quickly viral escape can curtail effective options4,5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including Evusheld™ and its constituent, cilgavimab4,6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protection in vivo against the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.
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Affiliation(s)
- Thomas A Desautels
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Kathryn T Arrildt
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Adam T Zemla
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Edmond Y Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Fangqiang Zhu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dante Ricci
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Seth J Zost
- Vanderbilt Vaccine Center, Nashville, TN 37232, USA
| | | | - Suzanne M Scheaffer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Brenden K Petersen
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Elaine Chen
- Vanderbilt Vaccine Center, Nashville, TN 37232, USA
| | | | - Lynn Hall
- Vanderbilt Vaccine Center, Nashville, TN 37232, USA
| | - John W Goforth
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Denis Vashchenko
- Applications Simulations and Quality Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sam Nguyen
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Jacky Kai-Yin Lo
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Bonnee Rubinfeld
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Edwin A Saada
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Tracy Weisenberger
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Tek-Hyung Lee
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James B Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexander Ladd
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Mary S Silva
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Rebecca M Haluska
- Applications Simulations and Quality Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Emilia A Grzesiak
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Christopher G Earnhart
- Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense, US, Department of Defense, Frederick, MD 21703, USA
| | | | - Thomas W Bates
- Global Security Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brent W Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Shivshankar Sundaram
- Center for Bioengineering, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Jesse Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daniel M Faissol
- Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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