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Ahuja R, Vishwakarma P, Raj S, Kumar V, Khatri R, Lohiya B, Saxena S, Kaur G, Singh G, Asthana S, Ahmed S, Samal S. Characterization and immunogenicity assessment of MERS-CoV pre-fusion spike trimeric oligomers as vaccine immunogen. Hum Vaccin Immunother 2024; 20:2351664. [PMID: 38757508 PMCID: PMC11110700 DOI: 10.1080/21645515.2024.2351664] [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: 12/15/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a lethal beta-coronavirus that emerged in 2012. The virus is part of the WHO blueprint priority list with a concerning fatality rate of 35%. Scientific efforts are ongoing for the development of vaccines, anti-viral and biotherapeutics, which are majorly directed toward the structural spike protein. However, the ongoing effort is challenging due to conformational instability of the spike protein and the evasion strategy posed by the MERS-CoV. In this study, we have expressed and purified the MERS-CoV pre-fusion spike protein in the Expi293F mammalian expression system. The purified protein was extensively characterized for its biochemical and biophysical properties. Thermal stability analysis showed a melting temperature of 58°C and the protein resisted major structural changes at elevated temperature as revealed by fluorescence spectroscopy and circular dichroism. Immunological assessment of the MERS-CoV spike immunogen in BALB/c mice with AddaVaxTM and Imject alum adjuvants showed elicitation of high titer antibody responses but a more balanced Th1/Th2 response with AddaVaxTM squalene like adjuvant. Together, our results suggest the formation of higher-order trimeric pre-fusion MERS-CoV spike proteins, which were able to induce robust immune responses. The comprehensive characterization of MERS-CoV spike protein warrants a better understanding of MERS spike protein and future vaccine development efforts.
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MESH Headings
- Middle East Respiratory Syndrome Coronavirus/immunology
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Mice, Inbred BALB C
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Viral Vaccines/immunology
- Mice
- Female
- Coronavirus Infections/prevention & control
- Coronavirus Infections/immunology
- Immunogenicity, Vaccine
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Vaccine
- Humans
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Affiliation(s)
- Rahul Ahuja
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Preeti Vishwakarma
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Sneha Raj
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Varun Kumar
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Ritika Khatri
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Bharat Lohiya
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shikha Saxena
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Gurleen Kaur
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Gagandeep Singh
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shailendra Asthana
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shubbir Ahmed
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Centralized Core Research Facility (CCRF), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sweety Samal
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
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Li D, Li C, Chen Q, Zhou H, Zhong Z, Huang Z, Liu H, Li X. Generalizing a Ligation Site at the N-Glycosylation Sequon for Chemical Synthesis of N-Linked Glycopeptides and Glycoproteins. J Am Chem Soc 2024; 146:29017-29027. [PMID: 39390739 DOI: 10.1021/jacs.4c09996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Chemical synthesis can generate homogeneous glycoproteins with well-defined and modifiable glycan structures at designated sites. The precision and flexibility of the chemical synthetic approach provide a solution to the heterogeneity problem of glycopeptides/glycoproteins obtained through biological approaches. In this study, we reported that the conserved N-glycosylation sequon (Asn-Xaa-Ser/Thr) of glycoproteins can serve as a general site for performing Ser/Thr ligation to achieve N-linked glycoprotein synthesis. We developed an N + 2 strategy to prepare the corresponding glycopeptide salicylaldehyde esters for Ser/Thr ligation and demonstrated that Ser/Thr ligation at the sequon was not affected by the steric hindrance brought about by the large-sized glycan structures. The effectiveness of this strategy was showcased by the total synthesis of the glycosylated receptor-binding domain (RBD) of the SARS-CoV-2 spike protein.
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Affiliation(s)
- Dongfang Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
| | - Can Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
| | - Qiushi Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR 999077, P. R. China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515063, P. R. China
| | - Zhixiang Zhong
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515063, P. R. China
| | - Zirong Huang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong SAR 999077, P. R. China
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Rosen LE, Tortorici MA, De Marco A, Pinto D, Foreman WB, Taylor AL, Park YJ, Bohan D, Rietz T, Errico JM, Hauser K, Dang HV, Chartron JW, Giurdanella M, Cusumano G, Saliba C, Zatta F, Sprouse KR, Addetia A, Zepeda SK, Brown J, Lee J, Dellota E, Rajesh A, Noack J, Tao Q, DaCosta Y, Tsu B, Acosta R, Subramanian S, de Melo GD, Kergoat L, Zhang I, Liu Z, Guarino B, Schmid MA, Schnell G, Miller JL, Lempp FA, Czudnochowski N, Cameroni E, Whelan SPJ, Bourhy H, Purcell LA, Benigni F, di Iulio J, Pizzuto MS, Lanzavecchia A, Telenti A, Snell G, Corti D, Veesler D, Starr TN. A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification. Cell 2024:S0092-8674(24)01084-5. [PMID: 39383863 DOI: 10.1016/j.cell.2024.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/01/2024] [Accepted: 09/16/2024] [Indexed: 10/11/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has resulted in viral escape from clinically authorized monoclonal antibodies (mAbs), creating a need for mAbs that are resilient to epitope diversification. Broadly neutralizing coronavirus mAbs that are sufficiently potent for clinical development and retain activity despite viral evolution remain elusive. We identified a human mAb, designated VIR-7229, which targets the viral receptor-binding motif (RBM) with unprecedented cross-reactivity to all sarbecovirus clades, including non-ACE2-utilizing bat sarbecoviruses, while potently neutralizing SARS-CoV-2 variants since 2019, including the recent EG.5, BA.2.86, and JN.1. VIR-7229 tolerates extraordinary epitope variability, partly attributed to its high binding affinity, receptor molecular mimicry, and interactions with RBM backbone atoms. Consequently, VIR-7229 features a high barrier for selection of escape mutants, which are rare and associated with reduced viral fitness, underscoring its potential to be resilient to future viral evolution. VIR-7229 is a strong candidate to become a next-generation medicine.
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Affiliation(s)
| | | | - Anna De Marco
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Dora Pinto
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - William B Foreman
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ashley L Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Dana Bohan
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Tyson Rietz
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | - Ha V Dang
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Martina Giurdanella
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Giuseppe Cusumano
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Qiqing Tao
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Brian Tsu
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Rima Acosta
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barbara Guarino
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Michael A Schmid
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Florian A Lempp
- Vir Biotechnology, San Francisco, CA 94158, USA; Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Elisabetta Cameroni
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | | | - Fabio Benigni
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Antonio Lanzavecchia
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Davide Corti
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Asor R, Olerinyova A, Burnap SA, Kushwah MS, Soltermann F, Rudden LS, Hensen M, Vasiljevic S, Brun J, Hill M, Chang L, Dejnirattisai W, Supasa P, Mongkolsapaya J, Zhou D, Stuart DI, Screaton GR, Degiacomi MT, Zitzmann N, Benesch JLP, Struwe WB, Kukura P. Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition. Proc Natl Acad Sci U S A 2024; 121:e2403260121. [PMID: 39298475 PMCID: PMC11459207 DOI: 10.1073/pnas.2403260121] [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: 02/20/2024] [Accepted: 06/28/2024] [Indexed: 09/21/2024] Open
Abstract
Cellular processes are controlled by the thermodynamics of the underlying biomolecular interactions. Frequently, structural investigations use one monomeric binding partner, while ensemble measurements of binding affinities generally yield one affinity representative of a 1:1 interaction, despite the majority of the proteome consisting of oligomeric proteins. For example, viral entry and inhibition in SARS-CoV-2 involve a trimeric spike surface protein, a dimeric angiotensin-converting enzyme 2 (ACE2) cell-surface receptor and dimeric antibodies. Here, we reveal that cooperativity correlates with infectivity and inhibition as opposed to 1:1 binding strength. We show that ACE2 oligomerizes spike more strongly for more infectious variants, while exhibiting weaker 1:1 affinity. Furthermore, we find that antibodies use induced oligomerization both as a primary inhibition mechanism and to enhance the effects of receptor-site blocking. Our results suggest that naive affinity measurements are poor predictors of potency, and introduce an antibody-based inhibition mechanism for oligomeric targets. More generally, they point toward a much broader role of induced oligomerization in controlling biomolecular interactions.
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Affiliation(s)
- Roi Asor
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Anna Olerinyova
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Sean A. Burnap
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Manish S. Kushwah
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Fabian Soltermann
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Lucas S.P. Rudden
- Department of Physics, Durham University, DurhamDH1 3LE, United Kingdom
| | - Mario Hensen
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Snežana Vasiljevic
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Juliane Brun
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Michelle Hill
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Liu Chang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok10700, Thailand
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Daming Zhou
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
- Diamond Light Source (United Kingdom), Harwell Science and Innovation Campus, DidcotOX110DE, United Kingdom
| | - Gavin R. Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Oxford University Hospitals National Health Service Foundation Trust, OxfordOX3 7JH, United Kingdom
| | | | - Nicole Zitzmann
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Justin L. P. Benesch
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Weston B. Struwe
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Philipp Kukura
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, OxfordOX1 3QU, United Kingdom
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Wickenhagen A, van Tol S, Munster V. Molecular determinants of cross-species transmission in emerging viral infections. Microbiol Mol Biol Rev 2024; 88:e0000123. [PMID: 38912755 PMCID: PMC11426021 DOI: 10.1128/mmbr.00001-23] [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] [Indexed: 06/25/2024] Open
Abstract
SUMMARYSeveral examples of high-impact cross-species transmission of newly emerging or re-emerging bat-borne viruses, such as Sudan virus, Nipah virus, and severe acute respiratory syndrome coronavirus 2, have occurred in the past decades. Recent advancements in next-generation sequencing have strengthened ongoing efforts to catalog the global virome, in particular from the multitude of different bat species. However, functional characterization of these novel viruses and virus sequences is typically limited with regard to assessment of their cross-species potential. Our understanding of the intricate interplay between virus and host underlying successful cross-species transmission has focused on the basic mechanisms of entry and replication, as well as the importance of host innate immune responses. In this review, we discuss the various roles of the respective molecular mechanisms underlying cross-species transmission using different recent bat-borne viruses as examples. To delineate the crucial cellular and molecular steps underlying cross-species transmission, we propose a framework of overall characterization to improve our capacity to characterize viruses as benign, of interest, or of concern.
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Affiliation(s)
- Arthur Wickenhagen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Sarah van Tol
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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Nor Rashid N, Amrani L, Alwan A, Mohamed Z, Yusof R, Rothan H. Angiotensin-Converting Enzyme-2 (ACE2) Downregulation During Coronavirus Infection. Mol Biotechnol 2024:10.1007/s12033-024-01277-5. [PMID: 39266903 DOI: 10.1007/s12033-024-01277-5] [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: 10/09/2023] [Accepted: 08/29/2024] [Indexed: 09/14/2024]
Abstract
Angiotensin-converting enzyme-2 (ACE2) downregulation represents a detrimental factor in people with a baseline ACE2 deficiency associated with older age, hypertension, diabetes, and cardiovascular diseases. Human coronaviruses, including HCoV-NL63, SARS-CoV-1, and SARS CoV-2 infect target cells via binding of viral spike (S) glycoprotein to the ACE2, resulting in ACE2 downregulation through yet unidentified mechanisms. This downregulation disrupts the enzymatic activity of ACE2, essential in protecting against organ injury by cleaving and disposing of Angiotensin-II (Ang II), leading to the formation of Ang 1-7, thereby exacerbating the accumulation of Ang II. This accumulation activates the Angiotensin II type 1 receptor (AT1R) receptor, leading to leukocyte recruitment and increased proinflammatory cytokines, contributing to organ injury. The biological impacts and underlying mechanisms of ACE2 downregulation during SARS-CoV-2 infection have not been well defined. Therefore, there is an urgent need to establish a solid theoretical and experimental understanding of the mechanisms of ACE2 downregulation during SARS-CoV-2 entry and replication in the host cells. This review aims to discuss the physiological impact of ACE2 downregulation during coronavirus infection, the relationship between ACE2 decline and virus pathogenicity, and the possible mechanisms of ACE2 degradation, along with the therapeutic approaches.
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Affiliation(s)
- Nurshamimi Nor Rashid
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Lina Amrani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Zulqarnain Mohamed
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia.
| | - Hussin Rothan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Pfizer, Pearl River, NY, USA.
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7
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Yan Q, Gao X, Liu B, Hou R, He P, Ma Y, Zhang Y, Zhang Y, Li Z, Chen Q, Wang J, Huang X, Liang H, Zheng H, Yao Y, Chen X, Niu X, He J, Chen L, Zhao J, Xiong X. Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Nat Commun 2024; 15:7585. [PMID: 39217172 PMCID: PMC11366018 DOI: 10.1038/s41467-024-51770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 08/17/2024] [Indexed: 09/04/2024] Open
Abstract
Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruitian Hou
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Guangzhou National Laboratory, Guangzhou, China
| | - Yong Ma
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huiran Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yichen Yao
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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8
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Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi AN, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. Cell Rep 2024; 43:114530. [PMID: 39058596 DOI: 10.1016/j.celrep.2024.114530] [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: 03/26/2024] [Revised: 05/31/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts are limited by a poor understanding of antibody responses elicited by infection. Here, we analyze S-directed antibody responses in plasma collected from MERS-CoV-infected individuals. We observe that binding and neutralizing antibodies peak 1-6 weeks after symptom onset/hospitalization, persist for at least 6 months, and neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the receptor-binding domain (RBD), account for most plasma neutralizing activity. Antigenic site mapping reveals that plasma antibodies frequently target RBD epitopes, whereas targeting of S2 subunit epitopes is rare. Our data reveal the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Kyung Hee University, Seoul, South Korea
| | - Abeer N Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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9
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Mackin SR, Sariol A, Diamond MS. Antibody-mediated control mechanisms of viral infections. Immunol Rev 2024. [PMID: 39162394 DOI: 10.1111/imr.13383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Antibodies generated after vaccination or natural pathogen exposure are essential mediators of protection against many infections. Most studies with viruses have focused on antibody neutralization, in which protection is conferred by the fragment antigen binding region (Fab) through targeting of different steps in the viral lifecycle including attachment, internalization, fusion, and egress. Beyond neutralization, the fragment crystallizable (Fc) region of antibodies can integrate innate and adaptive immune responses by engaging complement components and distinct Fc gamma receptors (FcγR) on different host immune cells. In this review, we discuss recent advances in our understanding of antibody neutralization and Fc effector functions, and the assays used to measure them. Additionally, we describe the contexts in which these mechanisms are associated with protection against viruses and highlight how Fc-FcγR interactions can improve the potency of antibody-based therapies.
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Affiliation(s)
- Samantha R Mackin
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology & Immunology and Center for Genome Sciences, Lab & Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alan Sariol
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology & Immunology and Center for Genome Sciences, Lab & Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, Missouri, USA
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10
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Bai Y, Zhou M, Wang N, Yang Y, Wang D. Designing a Candidate Multi-Epitope Vaccine against Transmissible Gastroenteritis Virus Based on Immunoinformatic and Molecular Dynamics. Int J Mol Sci 2024; 25:8828. [PMID: 39201514 PMCID: PMC11354480 DOI: 10.3390/ijms25168828] [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: 06/28/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is an etiological agent of enteric disease that results in high mortality rates in piglets. The economic impact of the virus is considerable, causing significant losses to the pig industry. The development of an efficacious subunit vaccine to provide promising protection against TGEV is of the utmost importance. The viral antigen, spike glycoprotein (S), is widely regarded as one of the most effective antigenic components for vaccine research. In this study, we employed immunoinformatics and molecular dynamics approaches to develop an 'ideal' multi-epitope vaccine. Firstly, the dominant, non-toxic, highly antigenic T (Th, CTL) and B cell epitopes predicted from the TGEV S protein were artificially engineered in tandem to design candidate subunit vaccines. Molecular docking and dynamic simulation results demonstrate that it exhibits robust interactions with toll-like receptor 4 (TLR4). Of particular significance was the finding that the vaccine was capable of triggering an immune response in mammals, as evidenced by the immune simulation results. The humoral aspect is typified by elevated levels of IgG and IgM, whereas the cellular immune aspect is capable of eliciting the robust production of interleukins and cytokines (IFN-γ and IL-2). Furthermore, the adoption of E. coli expression systems for the preparation of vaccines will also result in cost savings. This study offers logical guidelines for the development of a secure and efficacious subunit vaccine against TGEV, in addition to providing a novel theoretical foundation and strategy to prevent associated CoV infections.
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Affiliation(s)
- Yihan Bai
- College of Biology, Hunan University, Changsha 410082, China;
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Mingxia Zhou
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Naidong Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Yi Yang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
| | - Dongliang Wang
- College of Biology, Hunan University, Changsha 410082, China;
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (M.Z.); (N.W.); (Y.Y.)
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11
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McCallum M, Park YJ, Stewart C, Sprouse KR, Addetia A, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. Cell 2024; 187:4231-4245.e13. [PMID: 38964328 DOI: 10.1016/j.cell.2024.06.006] [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: 01/02/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. We designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2, providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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12
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Hills RA, Tan TK, Cohen AA, Keeffe JR, Keeble AH, Gnanapragasam PNP, Storm KN, Rorick AV, West AP, Hill ML, Liu S, Gilbert-Jaramillo J, Afzal M, Napier A, Admans G, James WS, Bjorkman PJ, Townsend AR, Howarth MR. Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses. NATURE NANOTECHNOLOGY 2024; 19:1216-1223. [PMID: 38710880 PMCID: PMC11329374 DOI: 10.1038/s41565-024-01655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 05/08/2024]
Abstract
Defending against future pandemics requires vaccine platforms that protect across a range of related pathogens. Nanoscale patterning can be used to address this issue. Here, we produce quartets of linked receptor-binding domains (RBDs) from a panel of SARS-like betacoronaviruses, coupled to a computationally designed nanocage through SpyTag/SpyCatcher links. These Quartet Nanocages, possessing a branched morphology, induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented in the vaccine. Equivalent antibody responses are raised to RBDs close to the nanocage or at the tips of the nanoparticle's branches. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increase the strength and breadth of an otherwise narrow immune response. A Quartet Nanocage including the Omicron XBB.1.5 'Kraken' RBD induced antibodies with binding to a broad range of sarbecoviruses, as well as neutralizing activity against this variant of concern. Quartet nanocages are a nanomedicine approach with potential to confer heterotypic protection against emergent zoonotic pathogens and facilitate proactive pandemic protection.
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Affiliation(s)
- Rory A Hills
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Kaya N Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Annie V Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michelle L Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Javier Gilbert-Jaramillo
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Madeeha Afzal
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Amy Napier
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gabrielle Admans
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - William S James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
| | - Mark R Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
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13
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Díaz-Salinas MA, Jain A, Durham ND, Munro JB. Single-molecule imaging reveals allosteric stimulation of SARS-CoV-2 spike receptor binding domain by host sialic acid. SCIENCE ADVANCES 2024; 10:eadk4920. [PMID: 39018397 PMCID: PMC466946 DOI: 10.1126/sciadv.adk4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
Conformational dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S) mediate exposure of the binding site for the cellular receptor, angiotensin-converting enzyme 2 (ACE2). The N-terminal domain (NTD) of S binds terminal sialic acid (SA) moieties on the cell surface, but the functional role of this interaction in virus entry is unknown. Here, we report that NTD-SA interaction enhances both S-mediated virus attachment and ACE2 binding. Through single-molecule Förster resonance energy transfer imaging of individual S trimers, we demonstrate that SA binding to the NTD allosterically shifts the S conformational equilibrium, favoring enhanced exposure of the ACE2-binding site. Antibodies that target the NTD block SA binding, which contributes to their mechanism of neutralization. These findings inform on mechanisms of S activation at the cell surface.
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Affiliation(s)
- Marco A. Díaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Natasha D. Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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14
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Figgins MD, Asarnow D, Stewart C, Lee J, Logue J, Bedford T, Murrell B, Chu HY, Veesler D, Bloom JD. Spike deep mutational scanning helps predict success of SARS-CoV-2 clades. Nature 2024; 631:617-626. [PMID: 38961298 PMCID: PMC11254757 DOI: 10.1038/s41586-024-07636-1] [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: 11/13/2023] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion1 and affect other properties that contribute to viral fitness, such as ACE2 receptor binding and cell entry2,3. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning4 to measure how more than 9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully affected ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456 and 473; however, the antigenic effects of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however, many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Teagan E McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marlin D Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jenni Logue
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helen Y Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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15
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Lee J, Stewart C, Schäfer A, Leaf EM, Park YJ, Asarnow D, Powers JM, Treichel C, Sprouse KR, Corti D, Baric R, King NP, Veesler D. A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines. Nat Commun 2024; 15:5496. [PMID: 38944664 PMCID: PMC11214633 DOI: 10.1038/s41467-024-49656-5] [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: 01/04/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
Evolution of SARS-CoV-2 alters the antigenicity of the immunodominant spike (S) receptor-binding domain and N-terminal domain, undermining the efficacy of vaccines and antibody therapies. To overcome this challenge, we set out to develop a vaccine focusing antibody responses on the highly conserved but metastable S2 subunit, which folds as a spring-loaded fusion machinery. We describe a strategy for prefusion-stabilization and high yield recombinant production of SARS-CoV-2 S2 trimers with native structure and antigenicity. We demonstrate that our design strategy is broadly generalizable to sarbecoviruses, as exemplified with the SARS-CoV-1 (clade 1a) and PRD-0038 (clade 3) S2 subunits. Immunization of mice with a prefusion-stabilized SARS-CoV-2 S2 trimer elicits broadly reactive sarbecovirus antibodies and neutralizing antibody titers of comparable magnitude against Wuhan-Hu-1 and the immune evasive XBB.1.5 variant. Vaccinated mice were protected from weight loss and disease upon challenge with XBB.1.5, providing proof-of-principle for fusion machinery sarbecovirus vaccines.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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16
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Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X. An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep 2024; 43:114265. [PMID: 38805396 DOI: 10.1016/j.celrep.2024.114265] [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: 06/22/2023] [Revised: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 antibody isolated from a patient infected with the SARS-CoV-2 ancestral strain, effectively neutralizes most Omicron variants tested, including XBB.1.5. We identify that D1F6 in the immunoglobulin G (IgG) form is able to overcome the effect of most Omicron mutations through its avidity-enhanced multivalent S-trimer binding. Cryo-electron microscopy (cryo-EM) and biochemical analyses show that three simultaneous epitope mutations are generally needed to substantially disrupt the multivalent S-trimer binding by D1F6 IgG. Antigenic mutations at spike positions 346, 444, and 445, which appeared in the latest variants, have little effect on D1F6 binding individually. However, these mutations are able to act synergistically with earlier Omicron mutations to impair neutralization by affecting the interaction between D1F6 IgG and the S-trimer. These results provide insight into the mechanism by which accumulated antigenic mutations facilitate evasion of affinity-matured antibodies.
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Affiliation(s)
- Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yijun Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qian Wang
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China
| | - Yuanyi Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Shuangshuang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingxian Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengzhen Su
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Xiancheng Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Yinglin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenyi Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Ling Chen
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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17
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Adair A, Tan LL, Feng J, Girkin J, Bryant N, Wang M, Mordant F, Chan LJ, Bartlett NW, Subbarao K, Pymm P, Tham WH. Human coronavirus OC43 nanobody neutralizes virus and protects mice from infection. J Virol 2024; 98:e0053124. [PMID: 38709106 PMCID: PMC11237593 DOI: 10.1128/jvi.00531-24] [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: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Human coronavirus (hCoV) OC43 is endemic to global populations and usually causes asymptomatic or mild upper respiratory tract illness. Here, we demonstrate the neutralization efficacy of isolated nanobodies from alpacas immunized with the S1B and S1C domain of the hCoV-OC43 spike glycoprotein. A total of 40 nanobodies bound to recombinant OC43 protein with affinities ranging from 1 to 149 nM. Two nanobodies WNb 293 and WNb 294 neutralized virus at 0.21 and 1.79 nM, respectively. Intranasal and intraperitoneal delivery of WNb 293 fused to an Fc domain significantly reduced nasal viral load in a mouse model of hCoV-OC43 infection. Using X-ray crystallography, we observed that WNb 293 bound to an epitope on the OC43 S1B domain, distal from the sialoglycan-binding site involved in host cell entry. This result suggests that neutralization mechanism of this nanobody does not involve disruption of glycan binding. Our work provides characterization of nanobodies against hCoV-OC43 that blocks virus entry and reduces viral loads in vivo and may contribute to future nanobody-based therapies for hCoV-OC43 infections. IMPORTANCE The pandemic potential presented by coronaviruses has been demonstrated by the ongoing COVID-19 pandemic and previous epidemics caused by severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Outside of these major pathogenic coronaviruses, there are four endemic coronaviruses that infect humans: hCoV-OC43, hCoV-229E, hCoV-HKU1, and hCoV-NL63. We identified a collection of nanobodies against human coronavirus OC43 (hCoV-OC43) and found that two high-affinity nanobodies potently neutralized hCoV-OC43 at low nanomolar concentrations. Prophylactic administration of one neutralizing nanobody reduced viral loads in mice infected with hCoV-OC43, showing the potential for nanobody-based therapies for hCoV-OC43 infections.
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Affiliation(s)
- Amy Adair
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jackson Feng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Girkin
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Nathan Bryant
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mingyang Wang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nathan W. Bartlett
- />College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
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18
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Nagahawatta DP, Liyanage NM, Jayawardena TU, Jayawardhana HHACK, Jeong SH, Kwon HJ, Jeon YJ. Role of marine natural products in the development of antiviral agents against SARS-CoV-2: potential and prospects. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:280-297. [PMID: 38827130 PMCID: PMC11136918 DOI: 10.1007/s42995-023-00215-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/17/2023] [Indexed: 06/04/2024]
Abstract
A novel coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has surfaced and caused global concern owing to its ferocity. SARS-CoV-2 is the causative agent of coronavirus disease 2019; however, it was only discovered at the end of the year and was considered a pandemic by the World Health Organization. Therefore, the development of novel potent inhibitors against SARS-CoV-2 and future outbreaks is urgently required. Numerous naturally occurring bioactive substances have been studied in the clinical setting for diverse disorders. The intricate infection and replication mechanism of SARS-CoV-2 offers diverse therapeutic drug targets for developing antiviral medicines by employing natural products that are safer than synthetic compounds. Marine natural products (MNPs) have received increased attention in the development of novel drugs owing to their high diversity and availability. Therefore, this review article investigates the infection and replication mechanisms, including the function of the SARS-CoV-2 genome and structure. Furthermore, we highlighted anti-SARS-CoV-2 therapeutic intervention efforts utilizing MNPs and predicted SARS-CoV-2 inhibitor design. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00215-9.
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Affiliation(s)
- D. P. Nagahawatta
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
| | - N. M. Liyanage
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
| | - Thilina U. Jayawardena
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3 Canada
| | | | - Seong-Hun Jeong
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - You-Jin Jeon
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
- Marine Science Institute, Jeju National University, Jeju, 63333 Republic of Korea
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19
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Wang Z, McCallum M, Yan L, Gibson CA, Sharkey W, Park YJ, Dang HV, Amaya M, Person A, Broder CC, Veesler D. Structure and design of Langya virus glycoprotein antigens. Proc Natl Acad Sci U S A 2024; 121:e2314990121. [PMID: 38593070 PMCID: PMC11032465 DOI: 10.1073/pnas.2314990121] [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: 08/31/2023] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse, and hamster target cells using a different, yet unknown, receptor than Nipah virus (NiV) and Hendra virus (HeV) and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryoelectron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing their conformational landscape and distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
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Affiliation(s)
- Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD20814
| | - Cecily A. Gibson
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - William Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA98195
- HHMI, Seattle, WA98195
| | - Ha V. Dang
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD20814
| | - Ashley Person
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD20814
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- HHMI, Seattle, WA98195
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20
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Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi A, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.586409. [PMID: 38617298 PMCID: PMC11014493 DOI: 10.1101/2024.03.31.586409] [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
Middle-East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Most vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts, however, are limited by a poor understanding of antibody responses elicited by infection along with their durability, fine specificity and contribution of distinct S antigenic sites to neutralization. To address this knowledge gap, we analyzed S-directed binding and neutralizing antibody titers in plasma collected from individuals infected with MERS-CoV in 2017-2019 (prior to the COVID-19 pandemic). We observed that binding and neutralizing antibodies peak 1 to 6 weeks after symptom onset/hospitalization, persist for at least 6 months, and broadly neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the RBD, account for most plasma neutralizing activity. Antigenic site mapping revealed that polyclonal plasma antibodies frequently target RBD epitopes, particularly a site exposed irrespective of the S trimer conformation, whereas targeting of S2 subunit epitopes is rare, similar to SARS-CoV-2. Our data reveal in unprecedented details the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Kyung Hee University, Seoul, South Korea
| | - Abeer Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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21
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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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22
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Cyril AC, Ali NM, Nelliyulla Parambath A, Vazhappilly CG, Jan RK, Karuvantevida N, Aburamadan H, Lozon Y, Radhakrishnan R. Nigella sativa and its chemical constituents: pre-clinical and clinical evidence for their potential anti-SARS-CoV-2 effects. Inflammopharmacology 2024; 32:273-285. [PMID: 37966624 DOI: 10.1007/s10787-023-01385-9] [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: 05/01/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 500 million reported cases of COVID-19 worldwide with relatively high morbidity and mortality. Although global vaccination drive has helped control the pandemic, the newer variant of the virus still holds the world in ransom. Several medicinal herbs with antiviral properties have been reported, and one such promising herb is Nigella sativa (NS). Recent molecular docking, pre-clinical, and clinical studies have shown that NS extracts may have the potential to prevent the entry of coronaviruses into the host cell as well as to treat and manage COVID-19 symptoms. Several active compounds from NS, such as nigelledine, α-hederin, dithymoquinone (DTQ), and thymoquinone (TQ), have been proposed as excellent ligands to target angiotensin-converting enzyme 2 (ACE2 receptors) and other targets on host cells as well as the spike protein (S protein) on SARS-CoV-2. By binding to these target proteins, these ligands could potentially prevent the binding between ACE2 and S protein. Though several articles have been published on the promising therapeutic role of NS and its constituents against SARS-CoV-2 infection, in this review, we consolidate the published information on NS and SARS-CoV-2, focusing on pre-clinical in silico studies as well as clinical trials reported between 2012 and 2023.
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Affiliation(s)
- Asha Caroline Cyril
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Najma Mohamed Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Anagha Nelliyulla Parambath
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Cijo George Vazhappilly
- Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
| | - Reem Kais Jan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Haneen Aburamadan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Yosra Lozon
- Dubai Pharmacy College for Girls, Dubai, United Arab Emirates
| | - Rajan Radhakrishnan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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23
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Sankhala RS, Dussupt V, Chen WH, Bai H, Martinez EJ, Jensen JL, Rees PA, Hajduczki A, Chang WC, Choe M, Yan L, Sterling SL, Swafford I, Kuklis C, Soman S, King J, Corbitt C, Zemil M, Peterson CE, Mendez-Rivera L, Townsley SM, Donofrio GC, Lal KG, Tran U, Green EC, Smith C, de Val N, Laing ED, Broder CC, Currier JR, Gromowski GD, Wieczorek L, Rolland M, Paquin-Proulx D, van Dyk D, Britton Z, Rajan S, Loo YM, McTamney PM, Esser MT, Polonis VR, Michael NL, Krebs SJ, Modjarrad K, Joyce MG. Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain. Structure 2024; 32:131-147.e7. [PMID: 38157856 PMCID: PMC11145656 DOI: 10.1016/j.str.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/14/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
Given the continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs), immunotherapeutics that target conserved epitopes on the spike (S) glycoprotein have therapeutic advantages. Here, we report the crystal structure of the SARS-CoV-2 S receptor-binding domain (RBD) at 1.95 Å and describe flexibility and distinct conformations of the angiotensin-converting enzyme 2 (ACE2)-binding site. We identify a set of SARS-CoV-2-reactive monoclonal antibodies (mAbs) with broad RBD cross-reactivity including SARS-CoV-2 Omicron subvariants, SARS-CoV-1, and other sarbecoviruses and determine the crystal structures of mAb-RBD complexes with Ab246 and CR3022 mAbs targeting the class IV site, WRAIR-2134, which binds the recently designated class V epitope, and WRAIR-2123, the class I ACE2-binding site. The broad reactivity of class IV and V mAbs to conserved regions of SARS-CoV-2 VoCs and other sarbecovirus provides a framework for long-term immunotherapeutic development strategies.
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Affiliation(s)
- Rajeshwer S Sankhala
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Vincent Dussupt
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hongjun Bai
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth J Martinez
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jaime L Jensen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Phyllis A Rees
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - William C Chang
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Misook Choe
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Spencer L Sterling
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Isabella Swafford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caitlin Kuklis
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sandrine Soman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jocelyn King
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Courtney Corbitt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caroline E Peterson
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Samantha M Townsley
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gina C Donofrio
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kerri G Lal
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ursula Tran
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ethan C Green
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Clayton Smith
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Morgane Rolland
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dewald van Dyk
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Zachary Britton
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Saravanan Rajan
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Yueh Ming Loo
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Patrick M McTamney
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Shelly J Krebs
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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24
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McCallum M, Park YJ, Stewart C, Sprouse KR, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574565. [PMID: 38260518 PMCID: PMC10802434 DOI: 10.1101/2024.01.09.574565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- 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
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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25
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Stiving AQ, Foreman DJ, VanAernum ZL, Durr E, Wang S, Vlasak J, Galli J, Kafader JO, Tsukidate T, Li X, Schuessler HA, Richardson DD. Dissecting the Heterogeneous Glycan Profiles of Recombinant Coronavirus Spike Proteins with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:62-73. [PMID: 38032172 DOI: 10.1021/jasms.3c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Surface-embedded glycoproteins, such as the spike protein trimers of coronaviruses MERS, SARS-CoV, and SARS-CoV-2, play a key role in viral function and are the target antigen for many vaccines. However, their significant glycan heterogeneity poses an analytical challenge. Here, we utilized individual ion mass spectrometry (I2MS), a multiplexed charge detection measurement with similarities to charge detection mass spectrometry (CDMS), in which a commercially available Orbitrap analyzer is used to directly produce mass profiles of these heterogeneous coronavirus spike protein trimers under native-like conditions. Analysis by I2MS shows that glycosylation contributes to the molecular mass of each protein trimer more significantly than expected by bottom-up techniques, highlighting the importance of obtaining complementary intact mass information when characterizing glycosylation of such heterogeneous proteins. Enzymatic dissection to remove sialic acid or N-linked glycans demonstrates that I2MS can be used to better understand the glycan profile from a native viewpoint. Deglycosylation of N-glycans followed by I2MS analysis indicates that the SARS-CoV-2 spike protein trimer contains glycans that are more difficult to remove than its MERS and SARS-CoV counterparts, and these differences are correlated with solvent accessibility. I2MS technology enables characterization of protein mass and intact glycan profile and is orthogonal to traditional mass analysis methods such as size exclusion chromatography-multiangle light scattering (SEC-MALS) and field flow fractionation-multiangle light scattering (FFF-MALS). An added advantage of I2MS is low sample use, requiring 100-fold less than other methodologies. This work highlights how I2MS technology can enable efficient development of vaccines and therapeutics for pharmaceutical development.
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Affiliation(s)
- Alyssa Q Stiving
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - David J Foreman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary L VanAernum
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eberhard Durr
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shiyi Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Josef Vlasak
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer Galli
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Taku Tsukidate
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Hillary A Schuessler
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Douglas D Richardson
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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26
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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27
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Firdaus ARR, Baroroh U, Ramdani Tohari T, Hardianto A, Subroto T, Yusuf M. Computational design of scFv anti-receptor binding domain of SARS-CoV-2 spike protein based on antibody S230 anti-SARS-CoV-1. J Biomol Struct Dyn 2024; 42:22-33. [PMID: 37880854 DOI: 10.1080/07391102.2023.2265485] [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: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 10/27/2023]
Abstract
Developing therapeutics such as neutralizing antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is essential to halt the Covid-19 infection. However, antibody production is expensive and relatively inaccessible to many low-income countries. Therefore, a more efficient and smaller antibody fragment, such as a single-chain variable fragment (scFv), derived from a known neutralizing antibody structure, is of interest due to the lower cost of recombinant protein production and the ability to tailor scFvs against circulating viruses. In this study, we used computational design to create an scFv based on the structure of a known neutralizing antibody, S230, for SARS-CoV-1. By analyzing the interaction of S230 with the RBD of both SARS-CoV-1 and SARS-CoV-2, five mutations were introduced to improve the binding of the scFv to the RBD of SARS-CoV-2. These mutations were Ser32Thr, Trp99Val, Asn57Val, Lys65Glu, and Tyr106Ile. Molecular dynamics simulations were used to evaluate the stability and affinity of the designed scFv. Our results showed that the designed scFv improved binding to the RBD of SARS-CoV-2 compared to the original S230, as indicated by principal component analysis, distance analysis, and MM/GBSA interaction energy. Furthermore, a positive result in a spot test lateral flow assay of the expressed scFv against the RBD indicated that the mutations did not alter the protein's structure. The designed scFv showed a negative result when tested against human serum albumin as a negative control, indicating reasonable specificity. We hope that this study will be useful in designing a specific and low-cost therapeutic agent, particularly during early outbreaks when information on neutralizing antibodies is limited.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ade R R Firdaus
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Biotechnology Master Program, Postgraduate School, Universitas Padjadjaran, Bandung, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Pharmacy, Sekolah Tinggi Farmasi Indonesia, Bandung, Indonesia
| | - Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Ari Hardianto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Toto Subroto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Muhammad Yusuf
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
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28
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Lee J, Stewart C, Schaefer A, Leaf EM, Park YJ, Asarnow D, Powers JM, Treichel C, Corti D, Baric R, King NP, Veesler D. A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571160. [PMID: 38168207 PMCID: PMC10760017 DOI: 10.1101/2023.12.12.571160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Continuous evolution of SARS-CoV-2 alters the antigenicity of the immunodominant spike (S) receptor-binding domain and N-terminal domain, undermining the efficacy of vaccines and monoclonal antibody therapies. To overcome this challenge, we set out to develop a vaccine focusing antibody responses on the highly conserved but metastable S2 subunit, which folds as a spring-loaded fusion machinery. Here, we describe a protein design strategy enabling prefusion-stabilization of the SARS-CoV-2 S2 subunit and high yield recombinant expression of trimers with native structure and antigenicity. We demonstrate that our design strategy is broadly generalizable to all sarbecoviruses, as exemplified with the SARS-CoV-1 (clade 1a) and PRD-0038 (clade 3) S2 fusion machineries. Immunization of mice with a prefusion-stabilized SARS-CoV-2 S2 trimer vaccine elicits broadly reactive sarbecovirus antibody responses and neutralizing antibody titers of comparable magnitude against Wuhan-Hu-1 and the immune evasive XBB.1.5 variant. Vaccinated mice were protected from weight loss and disease upon challenge with SARS-CoV-2 XBB.1.5, providing proof-of-principle for fusion machinery sarbecovirus vaccines motivating future development.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Alexandra Schaefer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elizabeth M. Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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29
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Rani M, Sharma AK, Chouhan R, Sur S, Mansuri R, Singh RK. Natural flavonoid pectolinarin computationally targeted as a promising drug candidate against SARS-CoV-2. Curr Res Struct Biol 2023; 7:100120. [PMID: 38205118 PMCID: PMC10776443 DOI: 10.1016/j.crstbi.2023.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Coronavirus disease-2019 (COVID-19) has become a global pandemic, necessitating the development of new medicines. In this investigation, we identified potential natural flavonoids and compared their inhibitory activity against spike glycoprotein, which is a target of SARS-CoV-2 and SARS-CoV. The target site for the interaction of new inhibitors for the treatment of SARS-CoV-2 has 82% sequence identity and the remaining 18% dissimilarities in RBD S1-subunit, S2-subunit, and 2.5% others. Molecular docking was employed to analyse the various binding processes used by each ligand in a library of 85 natural flavonoids that act as anti-viral medications and FDA authorised treatments for COVID-19. In the binding pocket of the target active site, remdesivir has less binding interaction than pectolinarin, according to the docking analysis. Pectolinarin is a natural flavonoid isolated from Cirsiumsetidensas that has anti-cancer, vasorelaxant, anti-inflammatory, hepatoprotective, anti-diabetic, anti-microbial, and anti-oxidant properties. The S-glycoprotein RBD region (330-583) is inhibited by kaempferol, rhoifolin, and herbacetin, but the S2 subunit (686-1270) is inhibited by pectolinarin, morin, and remdesivir. MD simulation analysis of S-glycoprotein of SARS-CoV-2 with pectolinarin complex at 100ns based on high dock-score. Finally, ADMET analysis was used to validate the proposed compounds with the highest binding energy.
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Affiliation(s)
- Mukta Rani
- National Institute for Plant Biotechnology, Indian Council of Agricultural Research, Pusa Campus, New Delhi, 110012, India
| | - Amit Kumar Sharma
- Department of Physics, Faculty of Engineering, Teerthanker Mahaveer University, Moradabad, 244001, U.P, India
| | - R.S. Chouhan
- Department of Environmental Sciences, Jozef Stefan Institute, Jamova Cesta-39, Ljubljana, Slovenia
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Moradabad, 244001, U.P, India
| | - Rani Mansuri
- School of Pharmaceutical Sciences, Apeejay Stya University, Gurugram, Haryana, 122103, India
| | - Rajesh K. Singh
- Department of Pharmaceutical Chemistry, Shivalik College of Pharmacy, Nangal, District Ropar, Punjab, 140126, India
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30
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. Cell Host Microbe 2023; 31:1961-1973.e11. [PMID: 37989312 PMCID: PMC10913562 DOI: 10.1016/j.chom.2023.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rhinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad angiotensin-converting enzyme 2 (ACE2) usage and that receptor-binding domain (RBD) mutations further expand receptor promiscuity and enable human ACE2 utilization. We determine a cryo-EM structure of the PRD-0038 RBD bound to Rhinolophus alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryo-EM and monoclonal antibody reactivity reveals its distinct antigenicity relative to SARS-CoV-2 and identifies PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicits greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared with SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 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
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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31
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Pronker MF, Creutznacher R, Drulyte I, Hulswit RJG, Li Z, van Kuppeveld FJM, Snijder J, Lang Y, Bosch BJ, Boons GJ, Frank M, de Groot RJ, Hurdiss DL. Sialoglycan binding triggers spike opening in a human coronavirus. Nature 2023; 624:201-206. [PMID: 37794193 DOI: 10.1038/s41586-023-06599-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Coronavirus spike proteins mediate receptor binding and membrane fusion, making them prime targets for neutralizing antibodies. In the cases of severe acute respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus, spike proteins transition freely between open and closed conformations to balance host cell attachment and immune evasion1-5. Spike opening exposes domain S1B, allowing it to bind to proteinaceous receptors6,7, and is also thought to enable protein refolding during membrane fusion4,5. However, with a single exception, the pre-fusion spike proteins of all other coronaviruses studied so far have been observed exclusively in the closed state. This raises the possibility of regulation, with spike proteins more commonly transitioning to open states in response to specific cues, rather than spontaneously. Here, using cryogenic electron microscopy and molecular dynamics simulations, we show that the spike protein of the common cold human coronavirus HKU1 undergoes local and long-range conformational changes after binding a sialoglycan-based primary receptor to domain S1A. This binding triggers the transition of S1B domains to the open state through allosteric interdomain crosstalk. Our findings provide detailed insight into coronavirus attachment, with possibilities of dual receptor usage and priming of entry as a means of immune escape.
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Affiliation(s)
- Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Robert Creutznacher
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Ruben J G Hulswit
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Zeshi Li
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Yifei Lang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Raoul J de Groot
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Shamabadi NS, Bagasra AB, Pawar S, Bagasra O. Potential use of endemic human coronaviruses to stimulate immunity against pathogenic SARS-CoV-2 and its variants. Libyan J Med 2023; 18:2209949. [PMID: 37186902 DOI: 10.1080/19932820.2023.2209949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes significant morbidity and mortality in humans, there is a wide range of disease outcomes following virus exposures. Some individuals are asymptomatic while others develop complications within a few days after infection that can lead to fatalities in a smaller portion of the population. In the present study, we have analyzed the factors that may influence the outcome of post-SARS-CoV-2 infection. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to endemic coronaviruses (eCOVIDs) which cause the common cold in humans and generally, most children are exposed to one of the four eCOVIDs before 2 years of age. Here, we have carried out protein sequence analyses to show the amino acid homologies between the four eCOVIDs (i.e. OC43, HKU1, 229E, and NL63) as well as examining the cross-reactive immune responses between SARS-CoV-2 and eCOVIDs by epidemiologic analyses. Our results show that the nations where continuous exposures to eCOVIDs are very high due to religious and traditional causes showed significantly lower cases and low mortality rates per 100,000. We hypothesize that in the areas of the globe where Muslims are in majority and due to religious practices are regularly exposed to eCOVIDs they show a significantly lower infection, as well as mortality rate, and that is due to pre-existing cross-immunity against SARS-CoV-2. This is due to cross-reactive antibodies and T-cells that recognize SARS-CoV-2 antigens. We also have reviewed the current literature that has also proposed that human infections with eCOVIDs impart protection against disease caused by subsequent exposure to SARS-CoV-2. We propose that a nasal spray vaccine consisting of selected genes of eCOVIDs would be beneficial against SARS-CoV-2 and other pathogenic coronaviruses.
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Affiliation(s)
| | - Anisah B Bagasra
- Department of Psychology, Kennesaw State University, Kennesaw, GA, USA
| | - Shrikant Pawar
- Department of Computer Science and Biology, Claflin University, SC, USA
| | - Omar Bagasra
- South Carolina Center for Biotechnology, Claflin University, Orangeburg, SC, USA
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Zaman N, Parvaiz N, Gul F, Yousaf R, Gul K, Azam SS. Dynamics of water-mediated interaction effects on the stability and transmission of Omicron. Sci Rep 2023; 13:20894. [PMID: 38017052 PMCID: PMC10684572 DOI: 10.1038/s41598-023-48186-2] [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: 11/24/2022] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fouzia Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rimsha Yousaf
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Kainat Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Asarnow D, Stewart C, Logue J, Murrell B, Chu HY, Veesler D, Bloom JD. Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566961. [PMID: 38014024 PMCID: PMC10680755 DOI: 10.1101/2023.11.13.566961] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SARS-CoV-2 variants acquire mutations in spike that promote immune evasion and impact other properties that contribute to viral fitness such as ACE2 receptor binding and cell entry. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning to measure how >9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry, or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully impacted ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456, and 473-however, the antigenic impacts of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Teagan E McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jenni Logue
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helen Y. Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98195, USA
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35
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Wang R, Han Y, Zhang R, Zhu J, Nan X, Liu Y, Yang Z, Zhou B, Yu J, Lin Z, Li J, Chen P, Wang Y, Li Y, Liu D, Shi X, Wang X, Zhang Q, Yang YR, Li T, Zhang L. Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Immunity 2023; 56:2635-2649.e6. [PMID: 37924813 DOI: 10.1016/j.immuni.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
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Affiliation(s)
- Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China
| | - Rui Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yaping Liu
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziqing Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zichun Lin
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinqian Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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36
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Shang Z, Deng Z, Yi X, Yang M, Nong X, Lin M, Xia F. Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5564-5576. [PMID: 37861233 DOI: 10.1039/d3ay01618h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.
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Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Zixuan Deng
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
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37
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Yu S, Zheng X, Zhou Y, Gao Y, Zhou B, Zhao Y, Li T, Li Y, Mou J, Cui X, Yang Y, Li D, Chen M, Lavillette D, Meng G. Antibody-mediated spike activation promotes cell-cell transmission of SARS-CoV-2. PLoS Pathog 2023; 19:e1011789. [PMID: 37948454 PMCID: PMC10664894 DOI: 10.1371/journal.ppat.1011789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/22/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
The COVID pandemic fueled by emerging SARS-CoV-2 new variants of concern remains a major global health concern, and the constantly emerging mutations present challenges to current therapeutics. The spike glycoprotein is not only essential for the initial viral entry, but is also responsible for the transmission of SARS-CoV-2 components via syncytia formation. Spike-mediated cell-cell transmission is strongly resistant to extracellular therapeutic and convalescent antibodies via an unknown mechanism. Here, we describe the antibody-mediated spike activation and syncytia formation on cells displaying the viral spike. We found that soluble antibodies against receptor binding motif (RBM) are capable of inducing the proteolytic processing of spike at both the S1/S2 and S2' cleavage sites, hence triggering ACE2-independent cell-cell fusion. Mechanistically, antibody-induced cell-cell fusion requires the shedding of S1 and exposure of the fusion peptide at the cell surface. By inhibiting S1/S2 proteolysis, we demonstrated that cell-cell fusion mediated by spike can be re-sensitized towards antibody neutralization in vitro. Lastly, we showed that cytopathic effect mediated by authentic SARS-CoV-2 infection remain unaffected by the addition of extracellular neutralization antibodies. Hence, these results unveil a novel mode of antibody evasion and provide insights for antibody selection and drug design strategies targeting the SARS-CoV-2 infected cells.
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Affiliation(s)
- Shi Yu
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Xu Zheng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Yanqiu Zhou
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yuhui Gao
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Bingjie Zhou
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Yapei Zhao
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Tingting Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yunyi Li
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jiabin Mou
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoxian Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yuying Yang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Min Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Dimitri Lavillette
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
- Pasteurien College, Soochow University, Suzhou, Jiangsu, China
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Guangxun Meng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
- Pasteurien College, Soochow University, Suzhou, Jiangsu, China
- Nanjing Advanced Academy of Life and Health, Nanjing, Jiangsu, China
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38
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Abstract
Neutralizing antibodies (nAbs) are being increasingly used as passive antiviral reagents in prophylactic and therapeutic modalities and to guide viral vaccine design. In vivo, nAbs can mediate antiviral functions through several mechanisms, including neutralization, which is defined by in vitro assays in which nAbs block viral entry to target cells, and antibody effector functions, which are defined by in vitro assays that evaluate nAbs against viruses and infected cells in the presence of effector systems. Interpreting in vivo results in terms of these in vitro assays is challenging but important in choosing optimal passive antibody and vaccine strategies. Here, I review findings from many different viruses and conclude that, although some generalizations are possible, deciphering the relative contributions of different antiviral mechanisms to the in vivo efficacy of antibodies currently requires consideration of individual antibody-virus interactions.
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Affiliation(s)
- Dennis R Burton
- Department of Immunology and Microbiology, Consortium for HIV/AIDS Vaccine Development, International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
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39
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Hsiao YW, Bray DJ, Taddese T, Jiménez-Serratos G, Crain J. Structure adaptation in Omicron SARS-CoV-2/hACE2: Biophysical origins of evolutionary driving forces. Biophys J 2023; 122:4057-4067. [PMID: 37717145 PMCID: PMC10624932 DOI: 10.1016/j.bpj.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/20/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Since its emergence, the COVID-19 threat has been sustained by a series of transmission waves initiated by new variants of the SARS-CoV-2 virus. Some of these arise with higher transmissivity and/or increased disease severity. Here, we use molecular dynamics simulations to examine the modulation of the fundamental interactions between the receptor binding domain (RBD) of the spike glycoprotein and the host cell receptor (human angiotensin-converting enzyme 2 [hACE2]) arising from Omicron variant mutations (BA.1 and BA.2) relative to the original wild-type strain. Our key findings are that glycans play a vital role at the RBD···hACE2 interface for the Omicrons, and the interplay between glycans and sequence mutations leads to enhanced binding. We find significant structural differences in the complexes, which overall bring the spike protein and its receptor into closer proximity. These are consistent with and attributed to the higher positive charge on the RBD conferred by BA.1 and BA.2 mutations relative to the wild-type. However, further differences between subvariants BA.1 and BA.2 (which have equivalent RBD charges) are also evident: mutations reduce interdomain interactions between the up chain and its clockwise neighbor chain in particular for the latter, resulting in enhanced flexibility for BA.2. Consequently, we see occurrence of additional close contacts in one replica of BA.2, which include binding to hACE2 by a second RBD in addition to the up chain. Although this motif is not seen in BA.1, we find that the Omicrons can directly/indirectly bind a down-RBD to hACE2 through glycans: the role of the glycan on N90 of hACE2 switches from inhibiting to facilitating the binding to Omicron spike protein via glycan-protein lateral interactions. These structural and electrostatic differences offer further insight into the mechanisms by which viral mutations modulate host cell binding and provide a biophysical basis for evolutionary driving forces.
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Affiliation(s)
- Ya-Wen Hsiao
- The Hartree Centre, STFC Daresbury Laboratory, Warrington, United Kingdom; Scientific Computing Department, STFC Daresbury Laboratory, Warrington, United Kingdom.
| | - David J Bray
- The Hartree Centre, STFC Daresbury Laboratory, Warrington, United Kingdom
| | - Tseden Taddese
- The Hartree Centre, STFC Daresbury Laboratory, Warrington, United Kingdom
| | | | - Jason Crain
- IBM Research Europe, Hartree Centre, Warrington, United Kingdom; Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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Viollet S, Enouf E, Picot J, Noël L, Huet S, Le Pennec D, Sécher T, Heuzé-Vourc'h N, Kitten O, Cinier M. Inhalable Nanofitin demonstrates high neutralization of SARS-CoV-2 virus via direct application in respiratory tract. Mol Ther 2023; 31:2861-2871. [PMID: 37652011 PMCID: PMC10556219 DOI: 10.1016/j.ymthe.2023.08.010] [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: 04/12/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Nanofitins are small and hyperthermostable alternative protein scaffolds that display physicochemical properties making them suitable for the development of topical therapeutics, notably for the treatment of pulmonary infectious diseases. Local administration of biologics to the lungs involves a particularly stressful step of nebulization that is poorly tolerated by most antibodies, which limits their application by this delivery route. During the COVID-19 pandemic, we generated anti-SARS-CoV-2 monomeric Nanofitins of high specificity for the spike protein. Hit Nanofitin candidates were identified based on their binding properties with punctual spike mutants and assembled into a linear multimeric construction constituting of four different Nanofitins, allowing the generation of a highly potent anti-SARS-CoV-2 molecule. The therapeutic efficacy of the multimeric assembly was demonstrated both in in vitro and in vivo models. Interestingly, the neutralization mechanism of the multimeric construction seems to involve a particular conformation switch of the spike trimer. In addition, we reported the stability and the conserved activity of the tetrameric construction after nebulization. This advantageous developability feature for pulmonary administration associated with the ease of assembly, as well as the fast generation process position the Nanofitin technology as a potential therapeutic solution for emerging infectious diseases.
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Affiliation(s)
| | | | | | | | | | - Déborah Le Pennec
- INSERM, Research Center for Respiratory Diseases, U1100, F-37032 Tours, France; University of Tours, F-37032 Tours, France
| | - Thomas Sécher
- INSERM, Research Center for Respiratory Diseases, U1100, F-37032 Tours, France; University of Tours, F-37032 Tours, France
| | - Nathalie Heuzé-Vourc'h
- INSERM, Research Center for Respiratory Diseases, U1100, F-37032 Tours, France; University of Tours, F-37032 Tours, France
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Khatri R, Lohiya B, Kaur G, Maithil V, Goswami A, Sarmadhikari D, Asthana S, Samal S. Understanding the role of conserved proline and serine residues in the SARS-CoV-2 spike cleavage sites in the virus entry, fusion, and infectivity. 3 Biotech 2023; 13:323. [PMID: 37663753 PMCID: PMC10469153 DOI: 10.1007/s13205-023-03749-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
The spike (S) glycoprotein of the SARS-CoV-2 virus binds to the host cell receptor and promotes the virus's entry into the target host cell. This interaction is primed by host cell proteases like furin and TMPRSS2, which act at the S1/S2 and S2´ cleavage sites, respectively. Both cleavage sites have serine or proline residues flanking either the single or polybasic region and were found to be conserved in coronaviruses. Unravelling the effects of these conserved residues on the virus entry and infectivity might facilitate the development of novel therapeutics. Here, we have investigated the role of the conserved serine and proline residues in the SARS-CoV-2 spike mediated entry, fusogenicity, and viral infectivity by using the HIV-1/spike-based pseudovirus system. A conserved serine residue mutation to alanine (S2´S-A) at the S2´ cleavage site resulted in the complete loss of spike cleavage. Exogenous treatment with trypsin or overexpression of TMPRSS2 protease could not rescue the loss of spike cleavage and biological activity. The S2´S-A mutant showed no significant responses against E-64d, TMPRSS2 or other relevant inhibitors. Taken together, serine at the S2´ site in the spike protein was indispensable for spike protein cleavage and virus infectivity. Thus, novel interventions targeting the conserved serine at the S2´ cleavage site should be explored to reduce severe disease caused by SARS-CoV-2-and novel emerging variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03749-y.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Bharat Lohiya
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Gurleen Kaur
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Vikas Maithil
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Abhishek Goswami
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Debapriyo Sarmadhikari
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Shailendra Asthana
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Sweety Samal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557371. [PMID: 37745523 PMCID: PMC10515872 DOI: 10.1101/2023.09.12.557371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad ACE2 usage and that RBD mutations further expand receptor promiscuity and enable human ACE2 utilization. We determined a cryoEM structure of the PRD-0038 RBD bound to R. alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryoEM and monoclonal antibody reactivity revealed its distinct antigenicity relative to SARS-CoV-2 and identified PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicited greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared to SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Samantha K. Zepeda
- 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
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Elizabeth M. Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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Grosche VR, Souza LPF, Ferreira GM, Guevara-Vega M, Carvalho T, Silva RRDS, Batista KLR, Abuna RPF, Silva JS, Calmon MDF, Rahal P, da Silva LCN, Andrade BS, Teixeira CS, Sabino-Silva R, Jardim ACG. Mannose-Binding Lectins as Potent Antivirals against SARS-CoV-2. Viruses 2023; 15:1886. [PMID: 37766292 PMCID: PMC10536204 DOI: 10.3390/v15091886] [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: 05/23/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 entry into host cells is mainly mediated by the interactions between the viral spike protein (S) and the ACE-2 cell receptor, which are highly glycosylated. Therefore, carbohydrate binding agents may represent potential candidates to abrogate virus infection. Here, we evaluated the in vitro anti-SARS-CoV-2 activity of two mannose-binding lectins isolated from the Brazilian plants Canavalia brasiliensis and Dioclea violacea (ConBR and DVL). These lectins inhibited SARS-CoV-2 Wuhan-Hu-1 strain and variants Gamma and Omicron infections, with selectivity indexes (SI) of 7, 1.7, and 6.5, respectively for ConBR; and 25, 16.8, and 22.3, for DVL. ConBR and DVL inhibited over 95% of the early stages of the viral infection, with strong virucidal effect, and also protected cells from infection and presented post-entry inhibition. The presence of mannose resulted in the complete lack of anti-SARS-CoV-2 activity by ConBR and DVL, recovering virus titers. ATR-FTIR, molecular docking, and dynamic simulation between SARS-CoV-2 S and either lectins indicated molecular interactions with predicted binding energies of -85.4 and -72.0 Kcal/Mol, respectively. Our findings show that ConBR and DVL lectins possess strong activities against SARS-CoV-2, potentially by interacting with glycans and blocking virus entry into cells, representing potential candidates for the development of novel antiviral drugs.
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Affiliation(s)
- Victória Riquena Grosche
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | - Leandro Peixoto Ferreira Souza
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Giulia Magalhães Ferreira
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Tamara Carvalho
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | | | | | - Rodrigo Paolo Flores Abuna
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (R.P.F.A.); (J.S.S.)
- Oswaldo Cruz Foundation (Fiocruz), Bi-Institutional Platform for Translational Medicine, Ribeirão Preto 14049-900, Brazil
| | - João Santana Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (R.P.F.A.); (J.S.S.)
- Oswaldo Cruz Foundation (Fiocruz), Bi-Institutional Platform for Translational Medicine, Ribeirão Preto 14049-900, Brazil
| | - Marília de Freitas Calmon
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | - Paula Rahal
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | | | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Jequié 45205-490, Brazil;
| | - Claudener Souza Teixeira
- Center of Agrarian Science and Biodiversity, Federal University of Cariri (UFCA), Crato 63130-025, Brazil; (R.R.d.S.S.); (C.S.T.)
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
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Liu M, Liang Z, Cheng ZJ, Liu L, Liu Q, Mai Y, Chen H, Lei B, Yu S, Chen H, Zheng P, Sun B. SARS-CoV-2 neutralising antibody therapies: Recent advances and future challenges. Rev Med Virol 2023; 33:e2464. [PMID: 37322826 DOI: 10.1002/rmv.2464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic represents an unparalleled global public health crisis. Despite concerted research endeavours, the repertoire of effective treatment options remains limited. However, neutralising-antibody-based therapies hold promise across an array of practices, encompassing the prophylaxis and management of acute infectious diseases. Presently, numerous investigations into COVID-19-neutralising antibodies are underway around the world, with some studies reaching clinical application stages. The advent of COVID-19-neutralising antibodies signifies the dawn of an innovative and promising strategy for treatment against SARS-CoV-2 variants. Comprehensively, our objective is to amalgamate contemporary understanding concerning antibodies targeting various regions, including receptor-binding domain (RBD), non-RBD, host cell targets, and cross-neutralising antibodies. Furthermore, we critically examine the prevailing scientific literature supporting neutralising antibody-based interventions, and also delve into the functional evaluation of antibodies, with a particular focus on in vitro (vivo) assays. Lastly, we identify and consider several pertinent challenges inherent to the realm of COVID-19-neutralising antibody-based treatments, offering insights into potential future directions for research and development.
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Affiliation(s)
- Mingtao Liu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiman Liang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhangkai J Cheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Liu
- Guangzhou Medical University, Guangzhou, China
| | - Qiwen Liu
- Guangzhou Medical University, Guangzhou, China
| | - Yiyin Mai
- Guangzhou Medical University, Guangzhou, China
| | | | - Baoying Lei
- Guangzhou Medical University, Guangzhou, China
| | - Shangwei Yu
- Guangzhou Medical University, Guangzhou, China
| | - Huihui Chen
- Guangzhou Medical University, Guangzhou, China
| | - Peiyan Zheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X. Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Life Sci Alliance 2023; 6:e202201796. [PMID: 37402591 PMCID: PMC10320017 DOI: 10.26508/lsa.202201796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions.
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Affiliation(s)
- Xixi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yutong Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qian Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lutang Fu
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Peiyi Wang
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Xiaolin Zhong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Liang Jin
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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Qing E, Gallagher T. Adaptive variations in SARS-CoV-2 spike proteins: effects on distinct virus-cell entry stages. mBio 2023; 14:e0017123. [PMID: 37382441 PMCID: PMC10470846 DOI: 10.1128/mbio.00171-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/14/2023] [Indexed: 06/30/2023] Open
Abstract
Evolved SARS-CoV-2 variants of concern (VOCs) spread through human populations in succession. Major virus variations are in the entry-facilitating viral spike (S) proteins; Omicron VOCs have 29-40 S mutations relative to ancestral D614G viruses. The impacts of this Omicron divergence on S protein structure, antigenicity, cell entry pathways, and pathogenicity have been extensively evaluated, yet gaps remain in correlating specific alterations with S protein functions. In this study, we compared the functions of ancestral D614G and Omicron VOCs using cell-free assays that can reveal differences in several distinct steps of the S-directed virus entry process. Relative to ancestral D614G, Omicron BA.1 S proteins were hypersensitized to receptor activation, to conversion into intermediate conformational states, and to membrane fusion-activating proteases. We identified mutations conferring these changes in S protein character by evaluating domain-exchanged D614G/Omicron recombinants in the cell-free assays. Each of the three functional alterations was mapped to specific S protein domains, with the recombinants providing insights on inter-domain interactions that fine-tune S-directed virus entry. Our results provide a structure-function atlas of the S protein variations that may promote the transmissibility and infectivity of current and future SARS-CoV-2 VOCs. IMPORTANCE Continuous SARS-CoV-2 adaptations generate increasingly transmissible variants. These succeeding variants show ever-increasing evasion of suppressive antibodies and host factors, as well as increasing invasion of susceptible host cells. Here, we evaluated the adaptations enhancing invasion. We used reductionist cell-free assays to compare the entry steps of ancestral (D614G) and Omicron (BA.1) variants. Relative to D614G, Omicron entry was distinguished by heightened responsiveness to entry-facilitating receptors and proteases and by enhanced formation of intermediate states that execute virus-cell membrane fusion. We found that these Omicron-specific characteristics arose from mutations in specific S protein domains and subdomains. The results reveal the inter-domain networks controlling S protein dynamics and efficiencies of entry steps, and they offer insights on the evolution of SARS-CoV-2 variants that arise and ultimately dominate infections worldwide.
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Affiliation(s)
- Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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Wang Z, McCallum M, Yan L, Sharkey W, Park YJ, Dang HV, Amaya M, Person A, Broder CC, Veesler D. Structure and design of Langya virus glycoprotein antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.554025. [PMID: 37645760 PMCID: PMC10462157 DOI: 10.1101/2023.08.20.554025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse and hamster target cells using a different, yet unknown, receptor than NiV and HeV and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryo-electron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing previously unknown conformational landscapes and their distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
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Affiliation(s)
- Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - William Sharkey
- 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
| | - Ha V. Dang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Ashley Person
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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Modhiran N, Lauer SM, Amarilla AA, Hewins P, Lopes van den Broek SI, Low YS, Thakur N, Liang B, Nieto GV, Jung J, Paramitha D, Isaacs A, Sng JD, Song D, Jørgensen JT, Cheuquemilla Y, Bürger J, Andersen IV, Himelreichs J, Jara R, MacLoughlin R, Miranda-Chacon Z, Chana-Cuevas P, Kramer V, Spahn C, Mielke T, Khromykh AA, Munro T, Jones ML, Young PR, Chappell K, Bailey D, Kjaer A, Herth MM, Jurado KA, Schwefel D, Rojas-Fernandez A, Watterson D. A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants. iScience 2023; 26:107085. [PMID: 37361875 PMCID: PMC10251734 DOI: 10.1016/j.isci.2023.107085] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/12/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) Omicron variant sub-lineages spread rapidly worldwide, mostly due to their immune-evasive properties. This has put a significant part of the population at risk for severe disease and underscores the need for effective anti-SARS-CoV-2 agents against emergent strains in vulnerable patients. Camelid nanobodies are attractive therapeutic candidates due to their high stability, ease of large-scale production, and potential for delivery via inhalation. Here, we characterize the receptor binding domain (RBD)-specific nanobody W25 and show superior neutralization activity toward Omicron sub-lineages in comparison to all other SARS-CoV2 variants. Structure analysis of W25 in complex with the SARS-CoV2 spike glycoprotein shows that W25 engages an RBD epitope not covered by any of the antibodies previously approved for emergency use. In vivo evaluation of W25 prophylactic and therapeutic treatments across multiple SARS-CoV-2 variant infection models, together with W25 biodistribution analysis in mice, demonstrates favorable pre-clinical properties. Together, these data endorse W25 for further clinical development.
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Affiliation(s)
- Naphak Modhiran
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Simon Malte Lauer
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Peter Hewins
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Irene Lopes van den Broek
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
| | - Yu Shang Low
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Nazia Thakur
- The Pirbright Institute, Ash Road, Guildford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin Liang
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Guillermo Valenzuela Nieto
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - James Jung
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Devina Paramitha
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Ariel Isaacs
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Julian D.J. Sng
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - David Song
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesper Tranekjær Jørgensen
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Yorka Cheuquemilla
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ida Vang Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Johanna Himelreichs
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Ronald Jara
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Ronan MacLoughlin
- Research and Development, Science and Emerging Technologies, Aerogen Limited, Galway Business Park, H91 HE94 Galway, Ireland
| | | | - Pedro Chana-Cuevas
- CETRAM & Faculty of Medical Science Universidad de Santiago de Chile, Chile
| | - Vasko Kramer
- PositronPharma SA, Rancagua 878, 7500921 Providencia, Santiago, Chile
| | - Christian Spahn
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Trent Munro
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Paul R. Young
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Keith Chappell
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Dalan Bailey
- The Pirbright Institute, Ash Road, Guildford, UK
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Matthias Manfred Herth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Schwefel
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alejandro Rojas-Fernandez
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Berking Biotechnology, Valdivia, Chile
| | - Daniel Watterson
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
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49
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McConnell SA, Sachithanandham J, Mudrak NJ, Zhu X, Farhang PA, Cordero RJB, Wear MP, Shapiro JR, Park HS, Klein SL, Tobian AAR, Bloch EM, Sullivan DJ, Pekosz A, Casadevall A. Spike-protein proteolytic antibodies in COVID-19 convalescent plasma contribute to SARS-CoV-2 neutralization. Cell Chem Biol 2023; 30:726-738.e4. [PMID: 37354908 PMCID: PMC10288624 DOI: 10.1016/j.chembiol.2023.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/23/2023] [Accepted: 05/26/2023] [Indexed: 06/26/2023]
Abstract
Understanding the mechanisms of antibody-mediated neutralization of SARS-CoV-2 is critical in combating the COVID-19 pandemic. Based on previous reports of antibody catalysis, we investigated the proteolysis of spike (S) by antibodies in COVID-19 convalescent plasma (CCP) and its contribution to viral neutralization. Quenched fluorescent peptides were designed based on S epitopes to sensitively detect antibody-mediated proteolysis. We observed epitope cleavage by CCP from different donors which persisted when plasma was heat-treated or when IgG was isolated from plasma. Further, purified CCP antibodies proteolyzed recombinant S domains, as well as authentic viral S. Cleavage of S variants suggests CCP antibody-mediated proteolysis is a durable phenomenon despite antigenic drift. We differentiated viral neutralization occurring via direct interference with receptor binding from that occurring by antibody-mediated proteolysis, demonstrating that antibody catalysis enhanced neutralization. These results suggest that antibody-catalyzed damage of S is an immunologically relevant function of neutralizing antibodies against SARS-CoV-2.
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Affiliation(s)
- Scott A McConnell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nathan J Mudrak
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Parsa Alba Farhang
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Radames J B Cordero
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Maggie P Wear
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Janna R Shapiro
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
| | - Han-Sol Park
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - David J Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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50
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Chen K, Gao Y, Li J. New-onset and relapsed Graves' disease following COVID-19 vaccination: a comprehensive review of reported cases. Eur J Med Res 2023; 28:232. [PMID: 37443067 DOI: 10.1186/s40001-023-01210-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Global Coronavir us disease 2019 (COVID-19) vaccination efforts are being intensified to combat the pandemic. As the frequency of immunization against COVID-19 has increased, some adverse effects related to vaccination have emerged. Within this context, this article reviewed 62 Graves' disease (GD) cases following COVID-19 vaccination, to probe the potential association between the vaccination and the onset of GD. A comprehensive search of the PubMed, Web of Science, and Scopus databases was conducted to collect GD cases following COVID-19 vaccination up to June 7, 2023. Among the 62 GD cases included in this review, there were 33 (53.2%) new-onset GD and 10 (16.1%) relapsed GD patients following mRNA vaccination, 14 (22.6%) new-onset GD and 4 (6.5%) relapsed GD patients following viral vector vaccination, and 1 (1.6%) relapsed GD patients following inactivated vaccination. Median durations to symptoms onset for new-onset and relapsed GD were 12 (range: 1-60) and 21 (range: 5-30) days following mRNA vaccination, while 7 (range: 1-28) and 14 (range: 10-14) days following viral vector vaccination, respectively. While the definitive pathogenesis of GD following COVID-19 vaccination remains unclear, it might be associated with cross-immune responses triggered by molecular mimicry, and an adjuvant-induced autoimmune/inflammatory syndrome. However, due to the limited number of observed GD cases following COVID-19 vaccination and the lack of systematic experimental studies, a causal relationship between COVID-19 vaccination and the onset of GD has not been definitively confirmed. It should be highlighted that most of GD patients following COVID-19 vaccination experienced positive outcomes after treatment. In the broader context of ending the COVID-19 pandemic and reducing mortality rates, the benefits of COVID-19 vaccination significantly outweigh mild risks such as treatable GD. Adherence to the COVID-19 vaccination schedule is therefore imperative in effectively managing the pandemic.
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Affiliation(s)
- Kan Chen
- Department of Endocrinology and Metabolism, The Institute of Endocrinology, NHC Key Laboratory of Diagnosis and Treatment of Thyroid Disease, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiyang Gao
- Department of Endocrinology and Metabolism, The Institute of Endocrinology, NHC Key Laboratory of Diagnosis and Treatment of Thyroid Disease, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jing Li
- Department of Endocrinology and Metabolism, The Institute of Endocrinology, NHC Key Laboratory of Diagnosis and Treatment of Thyroid Disease, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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