1
|
Sharma D, Rawat P, Janakiraman V, Gromiha MM. Elucidating important structural features for the binding affinity of spike - SARS-CoV-2 neutralizing antibody complexes. Proteins 2022; 90:824-834. [PMID: 34761442 PMCID: PMC8661754 DOI: 10.1002/prot.26277] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/04/2021] [Accepted: 11/07/2021] [Indexed: 12/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) has affected the lives of millions of people around the world. In an effort to develop therapeutic interventions and control the pandemic, scientists have isolated several neutralizing antibodies against SARS-CoV-2 from the vaccinated and convalescent individuals. These antibodies can be explored further to understand SARS-CoV-2 specific antigen-antibody interactions and biophysical parameters related to binding affinity, which can be utilized to engineer more potent antibodies for current and emerging SARS-CoV-2 variants. In the present study, we have analyzed the interface between spike protein of SARS-CoV-2 and neutralizing antibodies in terms of amino acid residue propensity, pair preference, and atomic interaction energy. We observed that Tyr residues containing contacts are highly preferred and energetically favorable at the interface of spike protein-antibody complexes. We have also developed a regression model to relate the experimental binding affinity for antibodies using structural features, which showed a correlation of 0.93. Moreover, several mutations at the spike protein-antibody interface were identified, which may lead to immune escape (epitope residues) and improved affinity (paratope residues) in current/emerging variants. Overall, the work provides insights into spike protein-antibody interactions, structural parameters related to binding affinity and mutational effects on binding affinity change, which can be helpful to develop better therapeutics against COVID-19.
Collapse
Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| | - Puneet Rawat
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| | - Vani Janakiraman
- Infection Biology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| | - M. Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| |
Collapse
|
2
|
Lusvarghi S, Wang W, Herrup R, Neerukonda SN, Vassell R, Bentley L, Eakin AE, Erlandson KJ, Weiss CD. Key Substitutions in the Spike Protein of SARS-CoV-2 Variants Can Predict Resistance to Monoclonal Antibodies, but Other Substitutions Can Modify the Effects. J Virol 2022; 96:e0111021. [PMID: 34668774 PMCID: PMC8754225 DOI: 10.1128/jvi.01110-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
Mutations in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants can compromise the effectiveness of therapeutic antibodies. Most clinical-stage therapeutic antibodies target the spike receptor binding domain (RBD), but variants often have multiple mutations in several spike regions. To help predict antibody potency against emerging variants, we evaluated 25 clinical-stage therapeutic antibodies for neutralization activity against 60 pseudoviruses bearing spikes with single or multiple substitutions in several spike domains, including the full set of substitutions in B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma), B.1.429 (epsilon), B.1.526 (iota), A.23.1, and R.1 variants. We found that 14 of 15 single antibodies were vulnerable to at least one RBD substitution, but most combination and polyclonal therapeutic antibodies remained potent. Key substitutions in variants with multiple spike substitutions predicted resistance, but the degree of resistance could be modified in unpredictable ways by other spike substitutions that may reside outside the RBD. These findings highlight the importance of assessing antibody potency in the context of all substitutions in a variant and show that epistatic interactions in spike can modify virus susceptibility to therapeutic antibodies. IMPORTANCE Therapeutic antibodies are effective in preventing severe disease from SARS-CoV-2 infection (COVID-19), but their effectiveness may be reduced by virus variants with mutations affecting the spike protein. To help predict resistance to therapeutic antibodies in emerging variants, we profiled resistance patterns of 25 antibody products in late stages of clinical development against a large panel of variants that include single and multiple substitutions found in the spike protein. We found that the presence of a key substitution in variants with multiple spike substitutions can predict resistance against a variant but that other substitutions can affect the degree of resistance in unpredictable ways. These findings highlight complex interactions among substitutions in the spike protein affecting virus neutralization and, potentially, virus entry into cells.
Collapse
Affiliation(s)
- Sabrina Lusvarghi
- Division of Viral Product, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Wei Wang
- Division of Viral Product, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rachel Herrup
- Division of Viral Product, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sabari Nath Neerukonda
- Division of Viral Product, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Russell Vassell
- Division of Viral Product, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Lisa Bentley
- Office of the Assistant Secretary for Preparedness and Response, U.S. Department of Human Health and Services, Washington, DC, USA
| | - Ann E. Eakin
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Karl J. Erlandson
- Influenza and Emerging Infectious Diseases Division, Biomedical Advanced Research and Development Authority, U.S. Department of Health and Human Services, Washington, DC, United States of America
| | - Carol D. Weiss
- Division of Viral Product, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| |
Collapse
|
3
|
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have become a major concern in the containment of current pandemic. The variants, including B.1.1.7 (Alpha), B.1.351 (Beta), P1 (Gamma) and B.1.617.2 (Delta) have shown reduced sensitivity to monoclonal antibodies, plasma and/or sera obtained from convalescent patients and vaccinated individuals. Development of potent therapeutic monoclonal antibodies (mAbs) with broad neutralizing breadth have become a priority for alleviating the devastating effects of this pandemic. Here, we review some of the most promising broadly neutralizing antibodies obtained from plasma of patients that recovered from early variants of SARS-CoV-2 that may be effective against emerging new variants of the virus. This review summarizes several mAbs, that have been discovered to cross-neutralize across Sarbecoviruses and SARS-CoV-2 escape mutants. Understanding the characteristics that confer this broad and cross-neutralization functions of these mAbs would inform on the development of therapeutic antibodies and guide the discovery of second-generation vaccines.
Collapse
Affiliation(s)
- Lok Bahadur Shrestha
- School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Medicine, Sydney, NSW, Australia
| | - Nicodemus Tedla
- School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
| | - Rowena A. Bull
- School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Medicine, Sydney, NSW, Australia
| |
Collapse
|
4
|
Pinto D, Sauer MM, Czudnochowski N, Low JS, Tortorici MA, Housley MP, Noack J, Walls AC, Bowen JE, Guarino B, Rosen LE, di Iulio J, Jerak J, Kaiser H, Islam S, Jaconi S, Sprugasci N, Culap K, Abdelnabi R, Foo C, Coelmont L, Bartha I, Bianchi S, Silacci-Fregni C, Bassi J, Marzi R, Vetti E, Cassotta A, Ceschi A, Ferrari P, Cippà PE, Giannini O, Ceruti S, Garzoni C, Riva A, Benigni F, Cameroni E, Piccoli L, Pizzuto MS, Smithey M, Hong D, Telenti A, Lempp FA, Neyts J, Havenar-Daughton C, Lanzavecchia A, Sallusto F, Snell G, Virgin HW, Beltramello M, Corti D, Veesler D. Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science 2021; 373:1109-1116. [PMID: 34344823 PMCID: PMC9268357 DOI: 10.1126/science.abj3321] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/29/2021] [Indexed: 12/11/2022]
Abstract
The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.
Collapse
Affiliation(s)
- Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Coelmont
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Pietro E. Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Faculty of Medicine, University of Zurich, 8057 Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
| | - Samuele Ceruti
- Intensive Care Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Matteo S. Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - David Hong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- UT Southwestern Medical Center, Dallas, TX 75390, USA
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
5
|
Abstract
Prophylactic and therapeutic drugs are urgently needed to combat coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Over the past year, SARS-CoV-2 neutralizing antibodies have been developed for preventive or therapeutic uses. While neutralizing antibodies target the spike protein, their neutralization potency and breadth vary according to recognition epitopes. Several potent SARS-CoV-2 antibodies have shown degrees of success in preclinical or clinical trials, and the US Food and Drug Administration has issued emergency use authorization for two neutralizing antibody cocktails. Nevertheless, antibody therapy for SARS-CoV-2 still faces potential challenges, including emerging viral variants of concern that have antibody-escape mutations and the potential for antibody-mediated enhancement of infection or inflammation. This review summarizes representative SARS-CoV-2 neutralizing antibodies that have been reported and discusses prospects and challenges for the development of the next generation of COVID-19 preventive or therapeutic antibodies. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Surgery, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Surgery, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA; .,Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| |
Collapse
|
6
|
McCallum M, Bassi J, De Marco A, Chen A, Walls AC, Di Iulio J, Tortorici MA, Navarro MJ, Silacci-Fregni C, Saliba C, Sprouse KR, Agostini M, Pinto D, Culap K, Bianchi S, Jaconi S, Cameroni E, Bowen JE, Tilles SW, Pizzuto MS, Guastalla SB, Bona G, Pellanda AF, Garzoni C, Van Voorhis WC, Rosen LE, Snell G, Telenti A, Virgin HW, Piccoli L, Corti D, Veesler D. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 2021; 373:648-654. [PMID: 34210893 PMCID: PMC9835956 DOI: 10.1126/science.abi7994] [Citation(s) in RCA: 293] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/25/2021] [Indexed: 01/16/2023]
Abstract
A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies.
Collapse
MESH Headings
- 2019-nCoV Vaccine mRNA-1273
- Amino Acid Substitution
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- BNT162 Vaccine
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Conformation
- Protein Domains
- Protein Interaction Domains and Motifs
- Protein Subunits/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
Collapse
Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alex Chen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | - Giovanni Bona
- Clinical Research Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
7
|
Abstract
The COVID-19 pandemic has put healthcare infrastructures and our social and economic lives under unprecedented strain. Effective solutions are needed to end the pandemic while significantly lessening its further impact on mortality and social and economic life. Effective and widely-available vaccines have appropriately long been seen as the best way to end the pandemic. Indeed, the current availability of several effective vaccines are already making a significant progress towards achieving that goal. Nevertheless, concerns have risen due to new SARS-CoV-2 variants that harbor mutations against which current vaccines are less effective. Furthermore, some individuals are unwilling or unable to take the vaccine. As health officials across the globe scramble to vaccinate their populations to reach herd immunity, the challenges noted above indicate that COVID-19 therapeutics are still needed to work alongside the vaccines. Here we describe the impact that neutralizing antibodies have had on those with early or mild COVID-19, and what their approval for early management of COVID-19 means for other viral entry inhibitors that have a similar mechanism of action. Importantly, we also highlight studies that show that therapeutic strategies involving various viral entry inhibitors such as multivalent antibodies, recombinant ACE2 and miniproteins can be effective not only for pre-exposure prophylaxis, but also in protecting against SARS-CoV-2 antigenic drift and future zoonotic sarbecoviruses.
Collapse
Affiliation(s)
- Lennox Chitsike
- Department of Basic Sciences, Loma Linda University School of Medicine, 11021 Campus Street, 101 Alumni Hall, Loma Linda, CA, 92354, USA
| | - Penelope Duerksen-Hughes
- Department of Basic Sciences, Loma Linda University School of Medicine, 11021 Campus Street, 101 Alumni Hall, Loma Linda, CA, 92354, USA.
| |
Collapse
|
8
|
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. bioRxiv 2021:2021.07.07.451375. [PMID: 34268509 PMCID: PMC8282097 DOI: 10.1101/2021.07.07.451375] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/27/2022]
Abstract
Escape variants of SARS-CoV-2 are threatening to prolong the COVID-19 pandemic. To address this challenge, we developed multivalent protein-based minibinders as potential prophylactic and therapeutic agents. Homotrimers of single minibinders and fusions of three distinct minibinders were designed to geometrically match the SARS-CoV-2 spike (S) trimer architecture and were optimized by cell-free expression and found to exhibit virtually no measurable dissociation upon binding. Cryo-electron microscopy (cryoEM) showed that these trivalent minibinders engage all three receptor binding domains on a single S trimer. The top candidates neutralize SARS-CoV-2 variants of concern with IC 50 values in the low pM range, resist viral escape, and provide protection in highly vulnerable human ACE2-expressing transgenic mice, both prophylactically and therapeutically. Our integrated workflow promises to accelerate the design of mutationally resilient therapeutics for pandemic preparedness. ONE-SENTENCE SUMMARY We designed, developed, and characterized potent, trivalent miniprotein binders that provide prophylactic and therapeutic protection against emerging SARS-CoV-2 variants of concern.
Collapse
Affiliation(s)
- Andrew C. Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Louisa Helms
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology and Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | | | | | | | - Bastain Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Antje Krüger-Gericke
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Natasha Edman
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron Chow
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- The Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin S. Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology and Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, 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
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
9
|
Ellis D, Brunette N, Crawford KHD, Walls AC, Pham MN, Chen C, Herpoldt KL, Fiala B, Murphy M, Pettie D, Kraft JC, Malone KD, Navarro MJ, Ogohara C, Kepl E, Ravichandran R, Sydeman C, Ahlrichs M, Johnson M, Blackstone A, Carter L, Starr TN, Greaney AJ, Lee KK, Veesler D, Bloom JD, King NP. Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design. Front Immunol 2021; 12:710263. [PMID: 34267764 PMCID: PMC8276696 DOI: 10.3389/fimmu.2021.710263] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
The unprecedented global demand for SARS-CoV-2 vaccines has demonstrated the need for highly effective vaccine candidates that are thermostable and amenable to large-scale manufacturing. Nanoparticle immunogens presenting the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein (S) in repetitive arrays are being advanced as second-generation vaccine candidates, as they feature robust manufacturing characteristics and have shown promising immunogenicity in preclinical models. Here, we used previously reported deep mutational scanning (DMS) data to guide the design of stabilized variants of the RBD. The selected mutations fill a cavity in the RBD that has been identified as a linoleic acid binding pocket. Screening of several designs led to the selection of two lead candidates that expressed at higher yields than the wild-type RBD. These stabilized RBDs possess enhanced thermal stability and resistance to aggregation, particularly when incorporated into an icosahedral nanoparticle immunogen that maintained its integrity and antigenicity for 28 days at 35-40°C, while corresponding immunogens displaying the wild-type RBD experienced aggregation and loss of antigenicity. The stabilized immunogens preserved the potent immunogenicity of the original nanoparticle immunogen, which is currently being evaluated in a Phase I/II clinical trial. Our findings may improve the scalability and stability of RBD-based coronavirus vaccines in any format and more generally highlight the utility of comprehensive DMS data in guiding vaccine design.
Collapse
Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, United States
| | - Natalie Brunette
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Katharine H. D. Crawford
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Minh N. Pham
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Chengbo Chen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
| | - Karla-Luise Herpoldt
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Brooke Fiala
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - John C. Kraft
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Keara D. Malone
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Cassandra Ogohara
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Elizabeth Kepl
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Claire Sydeman
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Max Johnson
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Alyssa Blackstone
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Tyler N. Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Allison J. Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Howard Hughes Medical Institute, Seattle, WA, United States
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| |
Collapse
|
10
|
Westendorf K, Žentelis S, Foster D, Vaillancourt P, Wiggin M, Lovett E, Hendle J, Pustilnik A, Sauder JM, Kraft L, Hwang Y, Siegel RW, Chen J, Heinz BA, Higgs RE, Kalleward N, Jepson K, Goya R, Smith MA, Collins DW, Pellacani D, Xiang P, de Puyraimond V, Ricicova M, Devorkin L, Pritchard C, O'Neill A, Cohen C, Dye J, Huie KI, Badger CV, Kobasa D, Audet J, Freitas JJ, Hassanali S, Hughes I, Munoz L, Palma HC, Ramamurthy B, Cross RW, Geisbert TW, Borisevich V, Lanz I, Anderson L, Sipahimalani P, Corbett KS, Wang L, Yang ES, Zhang Y, Shi W, Graham BS, Mascola JR, Fernandez TL, Hansen CL, Falconer E, Jones BE, Barnhart BC. LY-CoV1404 potently neutralizes SARS-CoV-2 variants. bioRxiv 2021. [PMID: 33972947 DOI: 10.1101/2021.04.30.442182] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
LY-CoV1404 is a highly potent, neutralizing, SARS-CoV-2 spike glycoprotein receptor binding domain (RBD)-specific antibody identified from a convalescent COVID-19 patient approximately 60 days after symptom onset. In pseudovirus studies, LY-CoV1404 retains potent neutralizing activity against numerous variants including B.1.1.7, B.1.351, B.1.427/B.1.429, P.1, and B.1.526 and binds to these variants in the presence of their underlying RBD mutations (which include K417N, L452R, E484K, and N501Y). LY-CoV1404 also neutralizes authentic SARS-CoV-2 in two different assays against multiple isolates. The RBD positions comprising the LY-CoV1404 epitope are highly conserved, with the exception of N439 and N501; notably the binding and neutralizing activity of LY-CoV1404 is unaffected by the most common mutations at these positions (N439K and N501Y). The breadth of variant binding, potent neutralizing activity and the relatively conserved epitope suggest that LY-CoV1404 is one in a panel of well-characterized, clinically developable antibodies that could be deployed rapidly to address current and emerging variants. New variant-resistant treatments such as LY-CoV1404 are desperately needed, given that some of the existing therapeutic antibodies are less effective or ineffective against certain variants and the impact of variants on vaccine efficacy is still poorly understood. In Brief LY-CoV1404 is a potent SARS-CoV-2-binding antibody that neutralizes all known variants of concern and whose epitope is rarely mutated. Highlights LY-CoV1404 potently neutralizes SARS-CoV-2 authentic virus and all known variants of concernNo loss of potency against current variantsBinding epitope on RBD of SARS-CoV-2 is rarely mutated in GISAID databaseBreadth of neutralizing activity and potency supports clinical development.
Collapse
|
11
|
Jette CA, Cohen AA, Gnanapragasam PN, Muecksch F, Lee YE, Huey-Tubman KE, Schmidt F, Hatziioannou T, Bieniasz PD, Nussenzweig MC, West AP, Keeffe JR, Bjorkman PJ, Barnes CO. Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies. bioRxiv 2021:2021.04.23.441195. [PMID: 33948592 PMCID: PMC8095199 DOI: 10.1101/2021.04.23.441195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly-emergent zoonotic sarbecoviruses and variants, but usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD β-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
Collapse
Affiliation(s)
- Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| |
Collapse
|
12
|
VanBlargan L, Adams L, Liu Z, Chen RE, Gilchuk P, Raju S, Smith B, Zhao H, Case JB, Winkler ES, Whitener B, Droit L, Aziati I, Shi PY, Creanga A, Pegu A, Handley S, Wang D, Boon A, Crowe JE, Whelan SPJ, Fremont D, Diamond M. A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope. bioRxiv 2021. [PMID: 33907753 DOI: 10.1101/2021.04.26.441501] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With the emergence of SARS-CoV-2 variants with increased transmissibility and potential resistance, antibodies and vaccines with broadly inhibitory activity are needed. Here we developed a panel of neutralizing anti-SARS-CoV-2 mAbs that bind the receptor binding domain of the spike protein at distinct epitopes and block virus attachment to cells and its receptor, human angiotensin converting enzyme-2 (hACE2). While several potently neutralizing mAbs protected K18-hACE2 transgenic mice against infection caused by historical SARS-CoV-2 strains, others induced escape variants in vivo and lost activity against emerging strains. We identified one mAb, SARS2-38, that potently neutralizes all SARS-CoV-2 variants of concern tested and protects mice against challenge by multiple SARS-CoV-2 strains. Structural analysis showed that SARS2-38 engages a conserved epitope proximal to the receptor binding motif. Thus, treatment with or induction of inhibitory antibodies that bind conserved spike epitopes may limit the loss of potency of therapies or vaccines against emerging SARS-CoV-2 variants.
Collapse
|