1
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Rexhepaj M, Park YJ, Perruzza L, Asarnow D, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Starr TN, Corti D, Benigni F, Veesler D. Broadly neutralizing antibodies against emerging delta-coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586411. [PMID: 38617231 PMCID: PMC11014491 DOI: 10.1101/2024.03.27.586411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Porcine deltacoronavirus (PDCoV) spillovers were recently detected in children with acute undifferentiated febrile illness, underscoring recurrent zoonoses of divergent coronaviruses. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated human spike (S)-directed monoclonal antibodies from transgenic mice and found that two of them, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryo-electron microscopy structures of PD33 and PD41 in complex with the PDCoV receptor-binding domain and S ectodomain trimer provide a blueprint of the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs inhibit PDCoV by competitively interfering with host APN binding to the PDCoV receptor-binding loops, explaining the mechanism of viral neutralization. PD33 and PD41 are candidates for clinical advancement, which could be stockpiled to prepare for possible future PDCoV outbreaks.
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Affiliation(s)
- Megi Rexhepaj
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lisa Perruzza
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Mathew Mccallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Katja Culap
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Giada Leoni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Alessio Balmelli
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Miles S. Dickinson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jack Taylor Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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2
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Winiger RR, Perez L. Therapeutic antibodies and alternative formats against SARS-CoV-2. Antiviral Res 2024; 223:105820. [PMID: 38307147 DOI: 10.1016/j.antiviral.2024.105820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) heavily burdened the entire world. Despite a prompt generation of vaccines and therapeutics to confront infection, the virus remains a threat. The ancestor viral strain has evolved into several variants of concern, with the Omicron variant now having many distinct sublineages. Consequently, most available antibodies targeting the spike went obsolete and thus new therapies or therapeutic formats are needed. In this review we focus on antibody targets, provide an overview of the therapeutic progress made so far, describe novel formats being explored, and lessons learned from therapeutic antibodies that can enhance pandemic preparedness.
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Affiliation(s)
- Rahel R Winiger
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
| | - Laurent Perez
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
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3
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Hueting D, Schriever K, Sun R, Vlachiotis S, Zuo F, Du L, Persson H, Hofström C, Ohlin M, Walldén K, Buggert M, Hammarström L, Marcotte H, Pan-Hammarström Q, Andréll J, Syrén PO. Design, structure and plasma binding of ancestral β-CoV scaffold antigens. Nat Commun 2023; 14:6527. [PMID: 37845250 PMCID: PMC10579346 DOI: 10.1038/s41467-023-42200-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 Å) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma.
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Affiliation(s)
- David Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stelios Vlachiotis
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Helena Persson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Camilla Hofström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Mats Ohlin
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Karin Walldén
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juni Andréll
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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4
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Wrobel AG. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Curr Opin Struct Biol 2023; 81:102619. [PMID: 37285618 PMCID: PMC10183628 DOI: 10.1016/j.sbi.2023.102619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023]
Abstract
Spike glycoprotein of SARS-CoV-2 mediates viral entry into host cells by facilitating virus attachment and membrane fusion. ACE2 is the main receptor of SARS-CoV-2 and its interaction with spike has shaped the virus' emergence from an animal reservoir and subsequent evolution in the human host. Many structural studies on the spike:ACE2 interaction have provided insights into mechanisms driving viral evolution during the on-going pandemic. This review describes the molecular basis of spike binding to ACE2, outlines mechanisms that have optimised this interaction during viral evolution, and suggests directions for future research.
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Affiliation(s)
- Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom.
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5
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Kumru OS, Bajoria S, Kaur K, Hickey JM, Van Slyke G, Doering J, Berman K, Richardson C, Lien H, Kleanthous H, Mantis NJ, Joshi SB, Volkin DB. Effects of aluminum-salt, CpG and emulsion adjuvants on the stability and immunogenicity of a virus-like particle displaying the SARS-CoV-2 receptor-binding domain (RBD). Hum Vaccin Immunother 2023; 19:2264594. [PMID: 37932241 PMCID: PMC10760504 DOI: 10.1080/21645515.2023.2264594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 11/08/2023] Open
Abstract
Second-generation COVID-19 vaccines with improved immunogenicity (e.g., breadth, duration) and availability (e.g., lower costs, refrigerator stable) are needed to enhance global coverage. In this work, we formulated a clinical-stage SARS-CoV-2 receptor-binding domain (RBD) virus-like particle (VLP) vaccine candidate (IVX-411) with widely available adjuvants. Specifically, we assessed the in vitro storage stability and in vivo mouse immunogenicity of IVX-411 formulated with aluminum-salt adjuvants (Alhydrogel™, AH and Adjuphos™, AP), without or with the TLR-9 agonist CpG-1018™ (CpG), and compared these profiles to IVX-411 adjuvanted with an oil-in-water nano-emulsion (AddaVax™, AV). Although IVX-411 bound both AH and AP, lower binding strength of antigen to AP was observed by Langmuir binding isotherms. Interestingly, AH- and AP-adsorbed IVX-411 had similar storage stability profiles as measured by antigen-binding assays (competitive ELISAs), but the latter displayed higher pseudovirus neutralizing titers (pNT) in mice, at levels comparable to titers elicited by AV-adjuvanted IVX-411. CpG addition to alum (AP or AH) resulted in a marginal trend of improved pNTs in stressed samples only, yet did not impact the storage stability profiles of IVX-411. In contrast, previous work with AH-formulations of a monomeric RBD antigen showed greatly improved immunogenicity and decreased stability upon CpG addition to alum. At elevated temperatures (25, 37°C), IVX-411 formulated with AH or AP displayed decreased in vitro stability compared to AV-formulated IVX-411and this rank-ordering correlated with in vivo performance (mouse pNT values). This case study highlights the importance of characterizing antigen-adjuvant interactions to develop low cost, aluminum-salt adjuvanted recombinant subunit vaccine candidates.
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Affiliation(s)
- Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - John M. Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Greta Van Slyke
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jennifer Doering
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Katherine Berman
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | | | | | - Harry Kleanthous
- Discovery & Translational Sciences, Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Nicholas J. Mantis
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
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6
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Hunt AC, Vögeli B, Hassan AO, Guerrero L, Kightlinger W, Yoesep DJ, Krüger A, DeWinter M, Diamond MS, Karim AS, Jewett MC. A rapid cell-free expression and screening platform for antibody discovery. Nat Commun 2023; 14:3897. [PMID: 37400446 DOI: 10.1038/s41467-023-38965-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/23/2023] [Indexed: 07/05/2023] Open
Abstract
Antibody discovery is bottlenecked by the individual expression and evaluation of antigen-specific hits. Here, we address this bottleneck by developing a workflow combining cell-free DNA template generation, cell-free protein synthesis, and binding measurements of antibody fragments in a process that takes hours rather than weeks. We apply this workflow to evaluate 135 previously published antibodies targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including all 8 antibodies previously granted emergency use authorization for coronavirus disease 2019 (COVID-19), and demonstrate identification of the most potent antibodies. We also evaluate 119 anti-SARS-CoV-2 antibodies from a mouse immunized with the SARS-CoV-2 spike protein and identify neutralizing antibody candidates, including the antibody SC2-3, which binds the SARS-CoV-2 spike protein of all tested variants of concern. We expect that our cell-free workflow will accelerate the discovery and characterization of antibodies for future pandemics and for research, diagnostic, and therapeutic applications more broadly.
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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
| | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Ahmed O Hassan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura Guerrero
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Danielle J Yoesep
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Madison DeWinter
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, 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
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, 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.
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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7
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Dash S, Farnós O, Yang Z, Perumal AS, Chaves Fulber JP, Venereo-Sánchez A, Leclerc D, Kamen AA. A rapid procedure to generate stably transfected HEK293 suspension cells for recombinant protein manufacturing: Yield improvements, bioreactor production and downstream processing. Protein Expr Purif 2023; 210:106295. [PMID: 37201590 DOI: 10.1016/j.pep.2023.106295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/20/2023]
Abstract
The human cell line HEK293 is one of the preferred choices for manufacturing therapeutic proteins and viral vectors for human applications. Despite its increased use, it is still considered in disadvantage in production aspects compared to cell lines such as the CHO cell line. We provide here a simple workflow for the rapid generation of stably transfected HEK293 cells expressing an engineered variant of the SARS-CoV-2 Receptor Binding Domain (RBD) carrying a coupling domain for linkage to VLPs through a bacterial transpeptidase-sortase (SrtA). To generate stable suspension cells expressing the RBD-SrtA, a single two plasmids transfection was performed, with hygromycin selection. The suspension HEK293 were grown in adherent conditions, with 20% FBS supplementation. These transfection conditions increased cell survival, allowing the selection of stable cell pools, which was otherwise not possible with standard procedures in suspension. Six pools were isolated, expanded and successfully re-adapted to suspension with a gradual increase of serum-free media and agitation. The complete process lasted four weeks. Stable expression with viability over 98% was verified for over two months in culture, with cell passages every 4-5 days. With process intensification, RBD-SrtA yields reached 6.4 μg/mL and 13.4 μg/mL in fed-batch and perfusion-like cultures, respectively. RBD-SrtA was further produced in fed-batch stirred tank 1L-bioreactors, reaching 10-fold higher yields than perfusion flasks. The trimeric antigen displayed the conformational structure and functionality expected. This work provides a series of steps for stable cell pool development using suspension HEK293 cells aimed at the scalable production of recombinant proteins.
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Affiliation(s)
- Shantoshini Dash
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0E9, Canada
| | - Omar Farnós
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0E9, Canada
| | - Zeyu Yang
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0E9, Canada
| | | | | | | | - Denis Leclerc
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Amine A Kamen
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0E9, Canada.
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8
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Dynesen LT, Fernandez I, Coquin Y, Delaplace M, Montange T, Njouom R, Bilounga-Ndongo C, Rey FA, Gessain A, Backovic M, Buseyne F. Neutralization of zoonotic retroviruses by human antibodies: Genotype-specific epitopes within the receptor-binding domain from simian foamy virus. PLoS Pathog 2023; 19:e1011339. [PMID: 37093892 PMCID: PMC10159361 DOI: 10.1371/journal.ppat.1011339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/04/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Infection with viruses of animal origin pose a significant threat to human populations. Simian foamy viruses (SFVs) are frequently transmitted to humans, in which they establish a life-long infection, with the persistence of replication-competent virus. However, zoonotic SFVs do not induce severe disease nor are they transmitted between humans. Thus, SFVs represent a model of zoonotic retroviruses that lead to a chronic infection successfully controlled by the human immune system. We previously showed that infected humans develop potent neutralizing antibodies (nAbs). Within the viral envelope (Env), the surface protein (SU) carries a variable region that defines two genotypes, overlaps with the receptor binding domain (RBD), and is the exclusive target of nAbs. However, its antigenic determinants are not understood. Here, we characterized nAbs present in plasma samples from SFV-infected individuals living in Central Africa. Neutralization assays were carried out in the presence of recombinant SU that compete with SU at the surface of viral vector particles. We defined the regions targeted by the nAbs using mutant SU proteins modified at the glycosylation sites, RBD functional subregions, and genotype-specific sequences that present properties of B-cell epitopes. We observed that nAbs target conformational epitopes. We identified three major epitopic regions: the loops at the apex of the RBD, which likely mediate interactions between Env protomers to form Env trimers, a loop located in the vicinity of the heparan binding site, and a region proximal to the highly conserved glycosylation site N8. We provide information on how nAbs specific for each of the two viral genotypes target different epitopes. Two common immune escape mechanisms, sequence variation and glycan shielding, were not observed. We propose a model according to which the neutralization mechanisms rely on the nAbs to block the Env conformational change and/or interfere with binding to susceptible cells. As the SFV RBD is structurally different from known retroviral RBDs, our data provide fundamental knowledge on the structural basis for the inhibition of viruses by nAbs. Trial registration: The study was registered at www.clinicaltrials.gov: https://clinicaltrials.gov/ct2/show/NCT03225794/.
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Affiliation(s)
- Lasse Toftdal Dynesen
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Ignacio Fernandez
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Manon Delaplace
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Thomas Montange
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | | | | | - Félix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
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9
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Christensen D, Polacek C, Sheward DJ, Hanke L, McInerney G, Murrell B, Hartmann KT, Jensen HE, Zimmermann J, Jungersen G, Illigen KE, Isling LK, Fernandez-Antunez C, Ramirez S, Bukh J, Pedersen GK. SARS-CoV-2 spike HexaPro formulated in aluminium hydroxide and administered in an accelerated vaccination schedule partially protects Syrian Hamsters against viral challenge despite low neutralizing antibody responses. Front Immunol 2023; 14:941281. [PMID: 36756130 PMCID: PMC9900178 DOI: 10.3389/fimmu.2023.941281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2 continues to pose a threat to human health as new variants emerge and thus a diverse vaccine pipeline is needed. We evaluated SARS-CoV-2 HexaPro spike protein formulated in Alhydrogel® (aluminium oxyhydroxide) in Syrian hamsters, using an accelerated two dose regimen (given 10 days apart) and a standard regimen (two doses given 21 days apart). Both regimens elicited spike- and RBD-specific IgG antibody responses of similar magnitude, but in vitro virus neutralization was low or undetectable. Despite this, the accelerated two dose regimen offered reduction in viral load and protected against lung pathology upon challenge with homologous SARS-CoV-2 virus (Wuhan-Hu-1). This highlights that vaccine-induced protection against SARS-CoV-2 disease can be obtained despite low neutralizing antibody levels and suggests that accelerated vaccine schedules may be used to confer rapid protection against SARS-CoV-2 disease.
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Affiliation(s)
- Dennis Christensen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus Research and Development Laboratory, Department of Microbial Diagnostic and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Katrine Top Hartmann
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie Zimmermann
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Gregers Jungersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Louise Krag Isling
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Kristian Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark,*Correspondence: Gabriel Kristian Pedersen,
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10
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Wu Y, Wang S, Zhang Y, Yuan L, Zheng Q, Wei M, Shi Y, Wang Z, Ma J, Wang K, Nie M, Xiao J, Huang Z, Chen P, Guo H, Lan M, Xu J, Hou W, Hong Y, Chen D, Sun H, Xiong H, Zhou M, Liu C, Guo W, Guo H, Gao J, Gan C, Li Z, Zhang H, Wang X, Li S, Cheng T, Zhao Q, Chen Y, Wu T, Zhang T, Zhang J, Cao H, Zhu H, Yuan Q, Guan Y, Xia N. Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine. Cell Host Microbe 2022; 30:1732-1744.e7. [PMID: 36323313 PMCID: PMC9576691 DOI: 10.1016/j.chom.2022.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/31/2022] [Accepted: 10/14/2022] [Indexed: 01/26/2023]
Abstract
SARS-CoV-2 spread in humans results in continuous emergence of new variants, highlighting the need for vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation-patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x) that contains key regions and residues across multiple SAR-CoV-2 variants. STFK1628x demonstrated high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine composed of STFK and STFK1628x elicited high titers of broad-spectrum neutralizing antibodies to 19 circulating SARS-CoV-2 variants, including Omicron sublineages BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, and BA.4/5. Furthermore, this vaccine conferred robust protection against intranasal challenges by either SARS-CoV-2 ancestral strain or immune-evasive Beta and Omicron BA.1. Strikingly, vaccination with the bivalent vaccine in hamsters effectively blocked within-cage virus transmission of ancestral SARS-CoV-2, Beta variant, and Omicron BA.1 to unvaccinated sentinels. Thus, our study provided insight and antigen candidates for the development of next-generation COVID-19 vaccines.
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Affiliation(s)
- Yangtao Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shaojuan Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yali Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Lunzhi Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Min Wei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yang Shi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zikang Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jian Ma
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kai Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Meifeng Nie
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jin Xiao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zehong Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Peiwen Chen
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong 515063, China
- EKIH Pathogen Research Institute, Futian District, Shenzhen, Guangdong 518045, China
| | - Huilin Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Miaolin Lan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jingjing Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wangheng Hou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yunda Hong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Dabing Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hualong Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Ming Zhou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Che Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wenjie Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Huiyu Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiahua Gao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Congling Gan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zhixiong Li
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health Commission, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350013, China
| | - Haitao Zhang
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health Commission, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350013, China
| | - Xinrui Wang
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health Commission, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350013, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yixin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Ting Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tianying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hua Cao
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health Commission, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350013, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong 515063, China
- EKIH Pathogen Research Institute, Futian District, Shenzhen, Guangdong 518045, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong 515063, China
- EKIH Pathogen Research Institute, Futian District, Shenzhen, Guangdong 518045, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, Fujian 361102, China
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11
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Liu Y, Arase H. Neutralizing and enhancing antibodies against SARS-CoV-2. Inflamm Regen 2022; 42:58. [PMID: 36471381 PMCID: PMC9720987 DOI: 10.1186/s41232-022-00233-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
The high transmissibility and rapid global spread of SARS-CoV-2 since 2019 has led to a huge burden on healthcare worldwide. Anti-SARS-CoV-2 neutralizing antibodies play an important role in not only protecting against infection but also in clearing the virus and are essential to providing long-term immunity. On the other hand, antibodies against the virus are not always protective. With the emergence of SARS-CoV-2 immune escape variants, vaccine design strategies as well as antibody-mediated therapeutic approaches have become more important. We review some of the findings on SARS-CoV-2 antibodies, focusing on both basic research and clinical applications.
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Affiliation(s)
- Yafei Liu
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
| | - Hisashi Arase
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
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12
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Antigenic mapping reveals sites of vulnerability on α-HCoV spike protein. Commun Biol 2022; 5:1179. [PMID: 36333470 PMCID: PMC9636267 DOI: 10.1038/s42003-022-04160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Understanding the antigenic signatures of all human coronaviruses (HCoVs) Spike (S) proteins is imperative for pan-HCoV epitopes identification and broadly effective vaccine development. To depict the currently elusive antigenic signatures of α-HCoVs S proteins, we isolated a panel of antibodies against the HCoV-229E S protein and characterized their epitopes and neutralizing potential. We found that the N-terminal domain of HCoV-229E S protein is antigenically dominant wherein an antigenic supersite is present and appears conserved in HCoV-NL63, which holds potential to serve as a pan-α-HCoVs epitope. In the receptor binding domain, a neutralizing epitope is captured in the end distal to the receptor binding site, reminiscent of the locations of the SARS-CoV-2 RBD cryptic epitopes. We also identified a neutralizing antibody that recognizes the connector domain, thus representing the first S2-directed neutralizing antibody against α-HCoVs. The unraveled HCoVs S proteins antigenic similarities and variances among genera highlight the challenges faced by pan-HCoV vaccine design while supporting the feasibility of broadly effective vaccine development against a subset of HCoVs. The antigenic landscape of α-HCoVs S proteins is revealed, highlighting the challenges faced by pan-HCoV vaccine design but also revealing opportunities for development of broadly effective vaccines against a subset of HCoVs.
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13
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Abstract
Despite effective spike-based vaccines and monoclonal antibodies, the SARS-CoV-2 pandemic continues more than two and a half years post-onset. Relentless investigation has outlined a causative dynamic between host-derived antibodies and reciprocal viral subversion. Integration of this paradigm into the architecture of next generation antiviral strategies, predicated on a foundational understanding of the virology and immunology of SARS-CoV-2, will be critical for success. This review aims to serve as a primer on the immunity endowed by antibodies targeting SARS-CoV-2 spike protein through a structural perspective. We begin by introducing the structure and function of spike, polyclonal immunity to SARS-CoV-2 spike, and the emergence of major SARS-CoV-2 variants that evade immunity. The remainder of the article comprises an in-depth dissection of all major epitopes on SARS-CoV-2 spike in molecular detail, with emphasis on the origins, neutralizing potency, mechanisms of action, cross-reactivity, and variant resistance of representative monoclonal antibodies to each epitope.
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Lucas J Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, United States.
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14
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Wang S, Sun H, Zhang Y, Yuan L, Wang Y, Zhang T, Wang S, Zhang J, Yu H, Xiong H, Tang Z, Liu L, Huang Y, Chen X, Li T, Ying D, Liu C, Chen Z, Yuan Q, Zhang J, Cheng T, Li S, Guan Y, Zheng Q, Zheng Z, Xia N. Three SARS-CoV-2 antibodies provide broad and synergistic neutralization against variants of concern, including Omicron. Cell Rep 2022; 39:110862. [PMID: 35594869 PMCID: PMC9080080 DOI: 10.1016/j.celrep.2022.110862] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/22/2022] [Accepted: 05/02/2022] [Indexed: 12/05/2022] Open
Abstract
The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel of human nAbs from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent patients show diverse neutralization against Omicron, of which XMA01 and XMA04 maintain nanomolar affinities and excellent neutralization (half maximal inhibitory concentration [IC50]: ∼20 ng/mL). nAb XMA09 shows weak but unattenuated neutralization against all variants of concern (VOCs) as well as SARS-CoV. Structural analysis reveals that the above three antibodies could synergistically bind to the receptor-binding domains (RBDs) of both wild-type and Omicron spikes and defines the critical determinants for nAb-mediated broad neutralizations. Three nAbs confer synergistic neutralization against Omicron, resulting from the inter-antibody interaction between XMA04 and XMA01(or XMA09). Furthermore, the XMA01/XMA04 cocktail provides synergistic protection against Beta and Omicron variant infections in hamsters. In summary, our results provide insights for the rational design of antibody cocktail therapeutics or universal vaccines against Omicron.
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Affiliation(s)
- Siling Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yali Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Lunzhi Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yizhen Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tianying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shaojuan Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jinlei Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hualong Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zimin Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Liqin Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiuting Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Dong Ying
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Chang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zihao Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen 361102, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China
- Joint Institute of Virology (Shantou University and University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou 515063, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen 361102, China
| | - Zizheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen 361102, China
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15
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Gruell H, Vanshylla K, Weber T, Barnes CO, Kreer C, Klein F. Antibody-Mediated Neutralization of SARS-CoV-2. Immunity 2022; 55:925-944. [PMID: 35623355 PMCID: PMC9118976 DOI: 10.1016/j.immuni.2022.05.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their development, function, and potential use to prevent and treat COVID-19 have been revealed. With the emergence of SARS-CoV-2 immune escape variants, humoral immunity is being challenged, and a detailed understanding of neutralizing antibodies is essential to guide vaccine design strategies as well as antibody-mediated therapies. In this review, we summarize some of the key findings on SARS-CoV-2 neutralizing antibodies, with a focus on their clinical application.
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Affiliation(s)
- Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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16
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High predictive QSAR models for predicting the SARS coronavirus main protease inhibition activity of ketone-based covalent inhibitors. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [PMCID: PMC8547569 DOI: 10.1007/s13738-021-02426-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this research, a dataset including 29 ketone-based covalent inhibitors with SARS-CoV-1 3CLpro inhibition activity was used to develop high predictive QSAR models. Twenty-two molecules were put in train set and seven molecules in test set. By using stepwise MLR method for molecules in train set, four molecular descriptors including Mor26p, Hy, GATS7p and Mor04v were selected to build QSAR models. MLR and ANN methods were used to create QSAR models for predicting the activity of molecules in both train and test sets. Both QSAR models were validated by calculating several statistical parameters. R2 values for the test set of MLR and ANN models were 0.93 and 0.95, respectively, and RMSE values for their test sets were 0.24 and 0.17, respectively. Other calculated statistical parameters (especially \documentclass[12pt]{minimal}
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\begin{document}$$Q_{F3}^{2}$$\end{document}QF32 parameter) show that created ANN model has more predictive power with respect to developed MLR model (with four descriptor). Calculated leverages for all molecules show that predicted pIC50 (by both QSAR models) for all molecules is acceptable, and drawn residuals plots show that there is no systematic error in building both QSAR modes. Also, based on developed MLR model, used molecular descriptors were interpreted.
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17
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Staufer O, Gupta K, Hernandez Bücher JE, Kohler F, Sigl C, Singh G, Vasileiou K, Yagüe Relimpio A, Macher M, Fabritz S, Dietz H, Cavalcanti Adam EA, Schaffitzel C, Ruggieri A, Platzman I, Berger I, Spatz JP. Synthetic virions reveal fatty acid-coupled adaptive immunogenicity of SARS-CoV-2 spike glycoprotein. Nat Commun 2022; 13:868. [PMID: 35165285 PMCID: PMC8844029 DOI: 10.1038/s41467-022-28446-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection is a major global public health concern with incompletely understood pathogenesis. The SARS-CoV-2 spike (S) glycoprotein comprises a highly conserved free fatty acid binding pocket (FABP) with unknown function and evolutionary selection advantage1,2. Deciphering FABP impact on COVID-19 progression is challenged by the heterogenous nature and large molecular variability of live virus. Here we create synthetic minimal virions (MiniVs) of wild-type and mutant SARS-CoV-2 with precise molecular composition and programmable complexity by bottom-up assembly. MiniV-based systematic assessment of S free fatty acid (FFA) binding reveals that FABP functions as an allosteric regulatory site enabling adaptation of SARS-CoV-2 immunogenicity to inflammation states via binding of pro-inflammatory FFAs. This is achieved by regulation of the S open-to-close equilibrium and the exposure of both, the receptor binding domain (RBD) and the SARS-CoV-2 RGD motif that is responsible for integrin co-receptor engagement. We find that the FDA-approved drugs vitamin K and dexamethasone modulate S-based cell binding in an FABP-like manner. In inflammatory FFA environments, neutralizing immunoglobulins from human convalescent COVID-19 donors lose neutralization activity. Empowered by our MiniV technology, we suggest a conserved mechanism by which SARS-CoV-2 dynamically couples its immunogenicity to the host immune response.
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Affiliation(s)
- Oskar Staufer
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.
- Institute for Molecular Systems Engineering, University of Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany.
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany.
| | - Kapil Gupta
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol, BS8 1TQ, UK
| | - Jochen Estebano Hernandez Bücher
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering, University of Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
| | - Fabian Kohler
- Department of Physics, Technical University of Munich, 85748, Garching, Germany
| | - Christian Sigl
- Department of Physics, Technical University of Munich, 85748, Garching, Germany
| | - Gunjita Singh
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
| | - Kate Vasileiou
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
| | - Ana Yagüe Relimpio
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering, University of Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
| | - Meline Macher
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering, University of Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Sebastian Fabritz
- Department for Chemical Biology, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Hendrik Dietz
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Department of Physics, Technical University of Munich, 85748, Garching, Germany
| | - Elisabetta Ada Cavalcanti Adam
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christiane Schaffitzel
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol, BS8 1TQ, UK
- Halo Therapeutics Ltd, Science Creates, Albert Road St. Philips Central, Bristol, BS2 0XJ, UK
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrated Infectious Disease Research, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Ilia Platzman
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering, University of Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
| | - Imre Berger
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol, BS8 1TQ, UK.
- Halo Therapeutics Ltd, Science Creates, Albert Road St. Philips Central, Bristol, BS2 0XJ, UK.
| | - Joachim P Spatz
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.
- Institute for Molecular Systems Engineering, University of Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany.
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany.
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18
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Bozdaganyan ME, Shaitan KV, Kirpichnikov MP, Sokolova OS, Orekhov PS. Computational Analysis of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike and Their Effects on Antibody Binding. Viruses 2022; 14:v14020295. [PMID: 35215888 PMCID: PMC8874930 DOI: 10.3390/v14020295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represent a potential danger. Here, we analyzed the diversity of neutralizing Ab epitopes and assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding affinity to various antibodies and the human ACE2 receptor using bioinformatics approaches. The RBD-Ab complexes with experimentally resolved structures were grouped into four clusters with distinct features at sequence and structure level. The performed computational analysis indicates that while single amino acid replacements in RBD may only cause partial impairment of the Abs binding, moreover, limited to specific epitopes, the variants of SARS-CoV-2 with multiple mutations, including some which were already detected in the population, may potentially result in a much broader antigenic escape. Further analysis of the existing RBD variants pointed to the trade-off between ACE2 binding and antigenic escape as a key limiting factor for the emergence of novel SAR-CoV-2 strains, as the naturally occurring mutations in RBD tend to reduce its binding affinity to Abs but not to ACE2. The results provide guidelines for further experimental studies aiming to identify high-risk RBD mutations that allow for an antigenic escape.
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Affiliation(s)
- Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Correspondence: (O.S.S.); (P.S.O.)
| | - Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (K.V.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (O.S.S.); (P.S.O.)
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19
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022; 13:155. [PMID: 35013189 PMCID: PMC8748511 DOI: 10.1038/s41467-021-27610-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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20
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022. [PMID: 35013189 DOI: 10.1101/2021.03.20.436243v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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21
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Yuan TZ, Garg P, Wang L, Willis JR, Kwan E, Hernandez AGL, Tuscano E, Sever EN, Keane E, Soto C, Mucker EM, Fouch ME, Davidson E, Doranz BJ, Kailasan S, Aman MJ, Li H, Hooper JW, Saphire EO, Crowe JE, Liu Q, Axelrod F, Sato AK. Rapid discovery of diverse neutralizing SARS-CoV-2 antibodies from large-scale synthetic phage libraries. MAbs 2022; 14:2002236. [PMID: 34967699 PMCID: PMC8726723 DOI: 10.1080/19420862.2021.2002236] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 12/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an evolving global public health crisis in need of therapeutic options. Passive immunization of monoclonal antibodies (mAbs) represents a promising therapeutic strategy capable of conferring immediate protection from SARS-CoV-2 infection. Herein, we describe the discovery and characterization of neutralizing SARS-CoV-2 IgG and VHH antibodies from four large-scale phage libraries. Each library was constructed synthetically with shuffled complementarity-determining region loops from natural llama and human antibody repertoires. While most candidates targeted the receptor-binding domain of the S1 subunit of SARS-CoV-2 spike protein, we also identified a neutralizing IgG candidate that binds a unique epitope on the N-terminal domain. A select number of antibodies retained binding to SARS-CoV-2 variants Alpha, Beta, Gamma, Kappa and Delta. Overall, our data show that synthetic phage libraries can rapidly yield SARS-CoV-2 S1 antibodies with therapeutically desirable features, including high affinity, unique binding sites, and potent neutralizing activity in vitro, and a capacity to limit disease in vivo.
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MESH Headings
- Animals
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Specificity
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/metabolism
- COVID-19/prevention & control
- COVID-19/virology
- Cell Surface Display Techniques
- Chlorocebus aethiops
- Disease Models, Animal
- Epitopes
- Female
- Host-Pathogen Interactions
- Immunoglobulin G/genetics
- Immunoglobulin G/immunology
- Immunoglobulin G/metabolism
- Immunoglobulin G/pharmacology
- Mesocricetus
- Peptide Library
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/immunology
- Vero Cells
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Affiliation(s)
- Tom Z. Yuan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | | | - Linya Wang
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Jordan R. Willis
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, USA
| | - Eric Kwan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | | | - Emily Tuscano
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Emily N. Sever
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Erica Keane
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric M. Mucker
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | | | | | | | | | | | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jay W. Hooper
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiang Liu
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Fumiko Axelrod
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Aaron K. Sato
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
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22
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Shalash AO, Azuar A, Madge HYR, Modhiran N, Amarilla AA, Liang B, Khromykh AA, Watterson D, Young PR, Toth I, Skwarczynski M. Detection and Quantification of SARS-CoV-2 Receptor Binding Domain Neutralization by a Sensitive Competitive ELISA Assay. Vaccines (Basel) 2021; 9:vaccines9121493. [PMID: 34960239 PMCID: PMC8705285 DOI: 10.3390/vaccines9121493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 12/11/2022] Open
Abstract
This protocol describes an ELISA-based procedure for accurate measurement of SARS-CoV-2 spike protein-receptor binding domain (RBD) neutralization efficacy by murine immune serum. The procedure requires a small amount of S-protein/RBD and angiotensin converting enzyme-2 (ACE2). A high-throughput, simple ELISA technique is employed. Plate-coated-RBDs are allowed to interact with the serum, then soluble ACE2 is added, followed by secondary antibodies and substrate. The key steps in this procedure include (1) serum heat treatment to prevent non-specific interactions, (2) proper use of blank controls to detect side reactions and eliminate secondary antibody cross-reactivity, (3) the addition of an optimal amount of saturating ACE2 to maximize sensitivity and prevent non-competitive co-occurrence of RBD-ACE2 binding and neutralization, and (4) mechanistically derived neutralization calculation using a calibration curve. Even manually, the protocol can be completed in 16 h for >30 serum samples; this includes the 7.5 h of incubation time. This automatable, high-throughput, competitive ELISA assay can screen a large number of sera, and does not require sterile conditions or special containment measures, as live viruses are not employed. In comparison to the ‘gold standard’ assays (virus neutralization titers (VNT) or plaque reduction neutralization titers (PRNT)), which are laborious and time consuming and require special containment measures due to their use of live viruses. This simple, alternative neutralization efficacy assay can be a great asset for initial vaccine development stages. The assay successfully passed conventional validation parameters (sensitivity, specificity, precision, and accuracy) and results with moderately neutralizing murine sera correlated with VNT assay results (R2 = 0.975, n = 25), demonstrating high sensitivity.
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Affiliation(s)
- Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
| | - Armira Azuar
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
| | - Harrison Y. R. Madge
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
| | - Benjamin Liang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Paul R. Young
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.O.S.); (A.A.); (H.Y.R.M.); (N.M.); (A.A.A.); (B.L.); (A.A.K.); (D.W.); (P.R.Y.); (I.T.)
- Correspondence:
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23
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Modeling coronavirus spike protein dynamics: implications for immunogenicity and immune escape. Biophys J 2021; 120:5592-5618. [PMID: 34767789 PMCID: PMC8577870 DOI: 10.1016/j.bpj.2021.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/19/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing COVID-19 pandemic is a global public health emergency requiring urgent development of efficacious vaccines. While concentrated research efforts have focused primarily on antibody-based vaccines that neutralize SARS-CoV-2, and several first-generation vaccines have either been approved or received emergency use authorization, it is forecasted that COVID-19 will become an endemic disease requiring updated second-generation vaccines. The SARS-CoV-2 surface spike (S) glycoprotein represents a prime target for vaccine development because antibodies that block viral attachment and entry, i.e., neutralizing antibodies, bind almost exclusively to the receptor-binding domain. Here, we develop computational models for a large subset of S proteins associated with SARS-CoV-2, implemented through coarse-grained elastic network models and normal mode analysis. We then analyze local protein domain dynamics of the S protein systems and their thermal stability to characterize structural and dynamical variability among them. These results are compared against existing experimental data and used to elucidate the impact and mechanisms of SARS-CoV-2 S protein mutations and their associated antibody binding behavior. We construct a SARS-CoV-2 antigenic map and offer predictions about the neutralization capabilities of antibody and S mutant combinations based on protein dynamic signatures. We then compare SARS-CoV-2 S protein dynamics to SARS-CoV and MERS-CoV S proteins to investigate differing antibody binding and cellular fusion mechanisms that may explain the high transmissibility of SARS-CoV-2. The outbreaks associated with SARS-CoV, MERS-CoV, and SARS-CoV-2 over the last two decades suggest that the threat presented by coronaviruses is ever-changing and long term. Our results provide insights into the dynamics-driven mechanisms of immunogenicity associated with coronavirus S proteins and present a new, to our knowledge, approach to characterize and screen potential mutant candidates for immunogen design, as well as to characterize emerging natural variants that may escape vaccine-induced antibody responses.
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24
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, Di Iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Fregni CS, Abdelnabi R, Foo SYC, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Virgin HW, Whelan SPJ, Snell G, Bloom JD, Corti D, Veesler D, Pizzuto MS. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature 2021; 597:103-108. [PMID: 34280951 PMCID: PMC9341430 DOI: 10.1038/s41586-021-03817-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023]
Abstract
The recent emergence of SARS-CoV-2 variants of concern1-10 and the recurrent spillovers of coronaviruses11,12 into the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here we describe a human monoclonal antibody designated S2X259, which recognizes a highly conserved cryptic epitope of the receptor-binding domain and cross-reacts with spikes from all clades of sarbecovirus. S2X259 broadly neutralizes spike-mediated cell entry of SARS-CoV-2, including variants of concern (B.1.1.7, B.1.351, P.1, and B.1.427/B.1.429), as well as a wide spectrum of human and potentially zoonotic sarbecoviruses through inhibition of angiotensin-converting enzyme 2 (ACE2) binding to the receptor-binding domain. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. We show that prophylactic and therapeutic administration of S2X259 protects Syrian hamsters (Mesocricetus auratus) against challenge with the prototypic SARS-CoV-2 and the B.1.351 variant of concern, which suggests that this monoclonal antibody is a promising candidate for the prevention and treatment of emergent variants and zoonotic infections. Our data reveal a key antigenic site that is targeted by broadly neutralizing antibodies and will guide the design of vaccines that are effective against all sarbecoviruses.
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Affiliation(s)
- M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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25
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Au L, Fendler A, Shepherd STC, Rzeniewicz K, Cerrone M, Byrne F, Carlyle E, Edmonds K, Del Rosario L, Shon J, Haynes WA, Ward B, Shum B, Gordon W, Gerard CL, Xie W, Joharatnam-Hogan N, Young K, Pickering L, Furness AJS, Larkin J, Harvey R, Kassiotis G, Gandhi S, Swanton C, Fribbens C, Wilkinson KA, Wilkinson RJ, Lau DK, Banerjee S, Starling N, Chau I, Turajlic S. Cytokine release syndrome in a patient with colorectal cancer after vaccination with BNT162b2. Nat Med 2021; 27:1362-1366. [PMID: 34040262 PMCID: PMC8363501 DOI: 10.1038/s41591-021-01387-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
Patients with cancer are currently prioritized in coronavirus disease 2019 (COVID-19) vaccination programs globally, which includes administration of mRNA vaccines. Cytokine release syndrome (CRS) has not been reported with mRNA vaccines and is an extremely rare immune-related adverse event of immune checkpoint inhibitors. We present a case of CRS that occurred 5 d after vaccination with BTN162b2 (tozinameran)-the Pfizer-BioNTech mRNA COVID-19 vaccine-in a patient with colorectal cancer on long-standing anti-PD-1 monotherapy. The CRS was evidenced by raised inflammatory markers, thrombocytopenia, elevated cytokine levels (IFN-γ/IL-2R/IL-18/IL-16/IL-10) and steroid responsiveness. The close temporal association of vaccination and diagnosis of CRS in this case suggests that CRS was a vaccine-related adverse event; with anti-PD1 blockade as a potential contributor. Overall, further prospective pharmacovigillence data are needed in patients with cancer, but the benefit-risk profile remains strongly in favor of COVID-19 vaccination in this population.
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Affiliation(s)
- Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Maddalena Cerrone
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - Barry Ward
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Ben Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - William Gordon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Camille L Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Precision Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Wenyi Xie
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | | | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charlotte Fribbens
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, UK
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | | | - Robert J Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - David K Lau
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, UK
| | - Naureen Starling
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Ian Chau
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK.
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26
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Riahi S, Lee JH, Wei S, Cost R, Masiero A, Prades C, Olfati-Saber R, Wendt M, Park A, Qiu Y, Zhou Y. Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers. Antib Ther 2021; 4:109-122. [PMID: 34396040 PMCID: PMC8344454 DOI: 10.1093/abt/tbab011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
As the COVID-19 pandemic continues to spread, hundreds of new initiatives including
studies on existing medicines are running to fight the disease. To deliver a potentially
immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new
collaborations and ways of sharing are required to create as many paths forward as
possible. Here, we leverage our expertise in computational antibody engineering to
rationally design/engineer three previously reported SARS-CoV neutralizing antibodies and
share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing
antibodies, m396, 80R and CR-3022 were chosen as templates due to their diversified
epitopes and confirmed neutralization potency against SARS-CoV (but not SARS-CoV-2 except
for CR3022). Structures of variable fragment (Fv) in complex with receptor binding domain
(RBD) from SARS-CoV or SARS-CoV-2 were subjected to our established in silico antibody
engineering platform to improve their binding affinity to SARS-CoV-2 and developability
profiles. The selected top mutations were ensembled into a focused library for each
antibody for further screening. In addition, we convert the selected binders with
different epitopes into the trispecific format, aiming to increase potency and to prevent
mutational escape. Lastly, to avoid antibody-induced virus activation or enhancement, we
suggest application of NNAS and DQ mutations to the Fc region to eliminate effector
functions and extend half-life.
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Affiliation(s)
- Saleh Riahi
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Jae Hyeon Lee
- Data & Data Science, Sanofi, Cambridge, MA, United States
| | - Shuai Wei
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Robert Cost
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | | | | | | | - Maria Wendt
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Anna Park
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Yu Qiu
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Yanfeng Zhou
- Large Molecule Research, Sanofi, Framingham, MA, United States
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27
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Rey F. Structure-function relations of the SARS-CoV-2 spike protein and impact of mutations in the variants of concern. C R Biol 2021; 344:77-110. [PMID: 34213849 DOI: 10.5802/crbiol.53] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review covers the main features of the severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, its interaction with the main entry receptor, the human angiotensin converting enzyme 2 (ACE2), and the subsequent membrane fusion step. The focus is on the structural organization of these proteins and mechanistic aspects of their interactions that lead to cytoplasmic release of the viral genome. The most potently neutralizing antibodies against SARS-CoV-2 were shown to interfere with the spike/ACE2 interaction. I thus also review the location and the potential impact of mutations in the spike protein observed in the variants of concern that emerged concomitantly with acquired immunity in the population after one year of virus circulation. Understanding how these interactions affect the spike/ACE2 interactions and the subsequent spike-protein-induced membrane fusion reaction is important to stay one step ahead of the virus evolution and develop efficient countermeasures.
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Affiliation(s)
- Félix Rey
- Unité de Virologie Structurale, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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28
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Torrente-López A, Hermosilla J, Navas N, Cuadros-Rodríguez L, Cabeza J, Salmerón-García A. The Relevance of Monoclonal Antibodies in the Treatment of COVID-19. Vaccines (Basel) 2021; 9:557. [PMID: 34073559 PMCID: PMC8229508 DOI: 10.3390/vaccines9060557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Major efforts have been made in the search for effective treatments since the outbreak of the COVID-19 infection in December 2019. Extensive research has been conducted on drugs that are already available and new treatments are also under development. Within this context, therapeutic monoclonal antibodies (mAbs) have been the subject of widespread investigation focusing on two target-based groups, i.e., non-SARS-CoV-2 specific mAbs, that target immune system responses, and SARS-CoV-2 specific mAbs, designed to neutralize the virus protein structure. Here we review the latest literature about the use of mAbs in order to describe the state of the art of the clinical trials and the benefits of using these biotherapeutics in the treatment of COVID-19. The clinical trials considered in the present review include both observational and randomized studies. We begin by presenting the studies conducted using non-SARS-CoV-2 specific mAbs for treating different immune disorders that were already on the market. Within this group of mAbs, we focus particularly on anti-IL-6/IL-6R. This is followed by a discussion of the studies on SARS-CoV-2 specific mAbs. Our findings indicate that SARS-CoV-2 specific mAbs are significantly more effective than non-specific ones.
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Affiliation(s)
- Anabel Torrente-López
- Department of Analytical Chemistry, Science Faculty, Biohealth Research Institute (ibs.GRANADA), University of Granada, E-18071 Granada, Spain; (A.T.-L.); (J.H.); (L.C.-R.)
| | - Jesús Hermosilla
- Department of Analytical Chemistry, Science Faculty, Biohealth Research Institute (ibs.GRANADA), University of Granada, E-18071 Granada, Spain; (A.T.-L.); (J.H.); (L.C.-R.)
| | - Natalia Navas
- Department of Analytical Chemistry, Science Faculty, Biohealth Research Institute (ibs.GRANADA), University of Granada, E-18071 Granada, Spain; (A.T.-L.); (J.H.); (L.C.-R.)
| | - Luis Cuadros-Rodríguez
- Department of Analytical Chemistry, Science Faculty, Biohealth Research Institute (ibs.GRANADA), University of Granada, E-18071 Granada, Spain; (A.T.-L.); (J.H.); (L.C.-R.)
| | - José Cabeza
- Department of Clinical Pharmacy, Biohealth Research Institute (ibs.GRANADA), San Cecilio University Hospital, E-18012 Granada, Spain; (J.C.); (A.S.-G.)
| | - Antonio Salmerón-García
- Department of Clinical Pharmacy, Biohealth Research Institute (ibs.GRANADA), San Cecilio University Hospital, E-18012 Granada, Spain; (J.C.); (A.S.-G.)
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29
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Case JB, Winkler ES, Errico JM, Diamond MS. On the road to ending the COVID-19 pandemic: Are we there yet? Virology 2021; 557:70-85. [PMID: 33676349 PMCID: PMC7908885 DOI: 10.1016/j.virol.2021.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into the human population in late 2019 and caused the global COVID-19 pandemic. SARS-CoV-2 has spread to more than 215 countries and infected many millions of people. Despite the introduction of numerous governmental and public health measures to control disease spread, infections continue at an unabated pace, suggesting that effective vaccines and antiviral drugs will be required to curtail disease, end the pandemic, and restore societal norms. Here, we review the current developments in antibody and vaccine countermeasures to limit or prevent disease.
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MESH Headings
- Animals
- Antibodies, Viral/biosynthesis
- COVID-19/epidemiology
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/biosynthesis
- COVID-19 Vaccines/immunology
- Clinical Trials as Topic
- Disease Models, Animal
- Genetic Vectors/chemistry
- Genetic Vectors/immunology
- Humans
- Immunity, Innate/drug effects
- Immunization, Passive/methods
- Immunogenicity, Vaccine
- Pandemics
- Patient Safety
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Vaccines, Attenuated
- Vaccines, DNA
- Vaccines, Subunit
- Vaccines, Virus-Like Particle/administration & dosage
- Vaccines, Virus-Like Particle/biosynthesis
- Vaccines, Virus-Like Particle/immunology
- COVID-19 Serotherapy
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Affiliation(s)
- James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA; Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John M Errico
- Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA; Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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30
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McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SYC, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 2021; 184:2332-2347.e16. [PMID: 33761326 PMCID: PMC7962585 DOI: 10.1016/j.cell.2021.03.028] [Citation(s) in RCA: 644] [Impact Index Per Article: 214.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/17/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023]
Abstract
The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alex Chen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - 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
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Agostino Riva
- III Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, 20157 Milan, Italy
| | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - 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.
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31
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Dejnirattisai W, Zhou D, Ginn HM, Duyvesteyn HME, Supasa P, Case JB, Zhao Y, Walter TS, Mentzer AJ, Liu C, Wang B, Paesen GC, Slon-Campos J, López-Camacho C, Kafai NM, Bailey AL, Chen RE, Ying B, Thompson C, Bolton J, Fyfe A, Gupta S, Tan TK, Gilbert-Jaramillo J, James W, Knight M, Carroll MW, Skelly D, Dold C, Peng Y, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Temperton N, Hall DR, Williams MA, Paterson NG, Bertram FKR, Siebert CA, Clare DK, Howe A, Radecke J, Song Y, Townsend AR, Huang KYA, Fry EE, Mongkolsapaya J, Diamond MS, Ren J, Stuart DI, Screaton GR. The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell 2021; 184:2183-2200.e22. [PMID: 33756110 PMCID: PMC7891125 DOI: 10.1016/j.cell.2021.02.032] [Citation(s) in RCA: 266] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/03/2021] [Accepted: 02/13/2021] [Indexed: 12/26/2022]
Abstract
Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50 < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
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Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Yuguang Zhao
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Thomas S Walter
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Guido C Paesen
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Jose Slon-Campos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Natasha M Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Adam L Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Craig Thompson
- Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Jai Bolton
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Alex Fyfe
- Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Sunetra Gupta
- Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - William James
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael Knight
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury SP4 0JG, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Andrew J Pollard
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham ME4 4TB, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Felicity K R Bertram
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - C Alistair Siebert
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Daniel K Clare
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Andrew Howe
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Julika Radecke
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Yun Song
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Kuan-Ying A Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, St. Louis, MO 63110 USA.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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32
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, di iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Silacci Fregni C, Abdelnabi R, Caroline Foo SY, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Snell G, Virgin HW, Whelan SP, Bloom JD, Corti D, Veesler D, Pizzuto MS. Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.07.438818. [PMID: 33851169 PMCID: PMC8043460 DOI: 10.1101/2021.04.07.438818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2X259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2X259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2X259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.
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Affiliation(s)
- M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- 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, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | - Michael A. Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - 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
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | | | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Finkelstein MT, Mermelstein AG, Parker Miller E, Seth PC, Stancofski ESD, Fera D. Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies. Viruses 2021; 13:134. [PMID: 33477902 PMCID: PMC7833398 DOI: 10.3390/v13010134] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/01/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus research has gained tremendous attention because of the COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus (nCoV or SARS-CoV-2). In this review, we highlight recent studies that provide atomic-resolution structural details important for the development of monoclonal antibodies (mAbs) that can be used therapeutically and prophylactically and for vaccines against SARS-CoV-2. Structural studies with SARS-CoV-2 neutralizing mAbs have revealed a diverse set of binding modes on the spike's receptor-binding domain and N-terminal domain and highlight alternative targets on the spike. We consider this structural work together with mAb effects in vivo to suggest correlations between structure and clinical applications. We also place mAbs against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses in the context of the SARS-CoV-2 spike to suggest features that may be desirable to design mAbs or vaccines capable of conferring broad protection.
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Affiliation(s)
| | | | | | | | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA; (M.T.F.); (A.G.M.); (E.P.M.); (P.C.S.); (E.-S.D.S.)
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34
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McCallum M, Marco AD, Lempp F, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Caroline Foo SY, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.14.426475. [PMID: 33469588 PMCID: PMC7814825 DOI: 10.1101/2021.01.14.426475] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.
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