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Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections. Nat Commun 2021; 12:264. [PMID: 33431876 PMCID: PMC7801428 DOI: 10.1038/s41467-020-20465-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/03/2020] [Indexed: 01/10/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neutralizing antibodies against SARS-CoV-2 are an option for drug development for treating COVID-19. Here, we report the identification and characterization of two groups of mouse neutralizing monoclonal antibodies (MAbs) targeting the receptor-binding domain (RBD) on the SARS-CoV-2 spike (S) protein. MAbs 2H2 and 3C1, representing the two antibody groups, respectively, bind distinct epitopes and are compatible in formulating a noncompeting antibody cocktail. A humanized version of the 2H2/3C1 cocktail is found to potently neutralize authentic SARS-CoV-2 infection in vitro with half inhibitory concentration (IC50) of 12 ng/mL and effectively treat SARS-CoV-2-infected mice even when administered at as late as 24 h post-infection. We determine an ensemble of cryo-EM structures of 2H2 or 3C1 Fab in complex with the S trimer up to 3.8 Å resolution, revealing the conformational space of the antigen–antibody complexes and MAb-triggered stepwise allosteric rearrangements of the S trimer, delineating a previously uncharacterized dynamic process of coordinated binding of neutralizing antibodies to the trimeric S protein. Our findings provide important information for the development of MAb-based drugs for preventing and treating SARS-CoV-2 infections. Here, the authors identify and characterize two mouse-derived monoclonal antibodies against SARS-CoV-2 spike protein that target different epitopes in RBD and block the interaction S/ACE2 and show that a formulated humanized version cocktail exhibits prophylaxis and therapeutic antiviral effects in an hACE2-adenovector expressed mouse model.
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752
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Khelashvili G, Plante A, Doktorova M, Weinstein H. Ca 2+ -dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33299996 DOI: 10.1101/2020.12.03.410472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cell penetration after recognition of the SARS-CoV-2 virus by the ACE2 receptor, and the fusion of its viral envelope membrane with cellular membranes, are the early steps of infectivity. A region of the Spike protein (S) of the virus, identified as the "fusion peptide" (FP), is liberated at its N-terminal site by a specific cleavage occurring in concert with the interaction of the receptor binding domain of the Spike. Studies have shown that penetration is enhanced by the required binding of Ca 2+ ions to the FPs of corona viruses, but the mechanisms of membrane insertion and destabilization remain unclear. We have predicted the preferred positions of Ca 2+ binding to the SARS-CoV-2-FP, the role of Ca 2+ ions in mediating peptide-membrane interactions, the preferred mode of insertion of the Ca 2+ -bound SARS-CoV-2-FP and consequent effects on the lipid bilayer from extensive atomistic molecular dynamics (MD) simulations and trajectory analyses. In a systematic sampling of the interactions of the Ca 2+ -bound peptide models with lipid membranes SARS-CoV-2-FP penetrated the bilayer and disrupted its organization only in two modes involving different structural domains. In one, the hydrophobic residues F833/I834 from the middle region of the peptide are inserted. In the other, more prevalent mode, the penetration involves residues L822/F823 from the LLF motif which is conserved in CoV-2-like viruses, and is achieved by the binding of Ca 2+ ions to the D830/D839 and E819/D820 residue pairs. FP penetration is shown to modify the molecular organization in specific areas of the bilayer, and the extent of membrane binding of the SARS-CoV-2 FP is significantly reduced in the absence of Ca 2+ ions. These findings provide novel mechanistic insights regarding the role of Ca 2+ in mediating SARS-CoV-2 fusion and provide a detailed structural platform to aid the ongoing efforts in rational design of compounds to inhibit SARS-CoV-2 cell entry. STATEMENT OF SIGNIFICANCE SARS-CoV-2, the cause of the COVID-19 pandemic, penetrates host cell membranes and uses viral-to-cellular membrane fusion to release its genetic material for replication. Experiments had identified a region termed "fusion peptide" (FP) in the Spike proteins of coronaviruses, as the spearhead in these initial processes, and suggested that Ca 2+ is needed to support both functions. Absent structure and dynamics-based mechanistic information these FP functions could not be targeted for therapeutic interventions. We describe the development and determination of the missing information from analysis of extensive MD simulation trajectories, and propose specific Ca 2+ -dependent mechanisms of SARS-CoV-2-FP membrane insertion and destabilization. These results offer a structure-specific platform to aid the ongoing efforts to use this target for the discovery and/or of inhibitors.
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753
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Song X, Shi Y, Ding W, Niu T, Sun L, Tan Y, Chen Y, Shi J, Xiong Q, Huang X, Xiao S, Zhu Y, Cheng C, Fu ZF, Liu ZJ, Peng G. Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Nat Commun 2021; 12:141. [PMID: 33420048 PMCID: PMC7794242 DOI: 10.1038/s41467-020-20401-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not been elucidated in Alphacoronavirus. Here, we report the cryo-EM structures of the HCoV-229E S trimer in prefusion state with two conformations. The activated conformation may pose the potential exposure of the S1-RBDs by decreasing of the interaction area between the S1-RBDs and the surrounding S1-NTDs and S1-RBDs compared to the closed conformation. Furthermore, structural comparison of our structures with the previously reported HCoV-229E S structure showed that the S trimers trended to open the S2 subunit from the closed conformation to open conformation, which could promote the transition from pre- to postfusion. Our results provide insights into the mechanisms involved in S glycoprotein-mediated Alphacoronavirus entry and have implications for vaccine and therapeutic antibody design.
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Affiliation(s)
- Xiyong Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Wei Ding
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, P.O.Box 603, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Limeng Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yubei Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qiqi Xiong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yanping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Zhi-Jie Liu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China. .,iHuman Institute, ShanghaiTech University, Shanghai, China.
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. .,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
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754
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Development and Validation of a Multiplex, Bead-based Assay to Detect Antibodies Directed Against SARS-CoV-2 Proteins. Transplantation 2021; 105:79-89. [PMID: 33273320 DOI: 10.1097/tp.0000000000003524] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Transplant recipients who develop COVID-19 may be at increased risk for morbidity and mortality. Determining the status of antibodies against SARS-CoV-2 in both candidates and recipients will be important to understand the epidemiology and clinical course of COVID-19 in this population. While there are multiple tests to detect antibodies to SARS-CoV-2, their performance is variable. Tests vary according to their platforms and the antigenic targets which make interpretation of the results challenging. Furthermore, for some assays, sensitivity and specificity are less than optimal. Additionally, currently available serological tests do not exclude the possibility that positive responses are due to cross reactive antibodies to community coronaviruses rather than SARS-CoV-2. METHODS This study describes the development and validation of a high-throughput multiplex antibody detection assay. RESULTS The multiplex assay has the capacity to identify, simultaneously, patient responses to 5 SARS-CoV-2 proteins, namely, the full spike protein, 3 individual domains of the spike protein (S1, S2, and receptor binding domain), and the nucleocapsid protein. The antibody response to the above proteins are SARS-CoV-2-specific, as antibodies against 4 common coronaviruses do not cross-react. CONCLUSIONS This new assay provides a novel tool to interrogate the spectrum of immune responses to SAR-CoV-2 and is uniquely suitable for use in the transplant setting. Test configuration is essentially identical to the single antigen bead assays used in the majority of histocompatibility laboratories around the world and could easily be implemented into routine screening of transplant candidates and recipients.
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755
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Cavasotto CN, Lamas MS, Maggini J. Functional and druggability analysis of the SARS-CoV-2 proteome. Eur J Pharmacol 2021; 890:173705. [PMID: 33137330 PMCID: PMC7604074 DOI: 10.1016/j.ejphar.2020.173705] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023]
Abstract
The infectious coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, appeared in December 2019 in Wuhan, China, and has spread worldwide. As of today, more than 46 million people have been infected and over 1.2 million fatalities. With the purpose of contributing to the development of effective therapeutics, we performed an in silico determination of binding hot-spots and an assessment of their druggability within the complete SARS-CoV-2 proteome. All structural, non-structural, and accessory proteins have been studied, and whenever experimental structural data of SARS-CoV-2 proteins were not available, homology models were built based on solved SARS-CoV structures. Several potential allosteric or protein-protein interaction druggable sites on different viral targets were identified, knowledge that could be used to expand current drug discovery endeavors beyond the currently explored cysteine proteases and the polymerase complex. It is our hope that this study will support the efforts of the scientific community both in understanding the molecular determinants of this disease and in widening the repertoire of viral targets in the quest for repurposed or novel drugs against COVID-19.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina; Facultad de Ciencias Biomédicas, Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina; Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina.
| | - Maximiliano Sánchez Lamas
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina; Meton AI, Inc., Wilmington, DE, 19801, USA
| | - Julián Maggini
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina; Technology Transfer Office, Universidad Austral, Pilar, Buenos Aires, Argentina
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756
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Abstract
PURPOSE OF REVIEW The spike glycoprotein plays a critical role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by recognizing the angiotensin converting enzyme 2 (ACE2) receptor and mediating fusion of the viral envelope with the cell membrane. It is also the major target for neutralizing antibodies and vaccines. This review summarizes recent studies on the structure and function of spike glycoprotein, which revealed the structural basis of SARS-CoV-2 infection. RECENT FINDINGS SARS-CoV-2 spike glycoprotein, similar to those of SARS-CoV and Middle East respiratory syndrome coronavirus, spontaneously samples different prefusion states with the receptor-binding domain (RBD) adopting 'up' or 'down' conformations, and the RBD 'down' to 'up' conformational change is required for ACE2 binding. Receptor binding and spike glycoprotein priming by host proteases such as furin and transmembrane protease serine 2 induce pre to postfusion conformational changes of the spike trimer that enable membrane fusion. Interactions between SARS-CoV-2 RBD and ACE2 were elucidated at atomic resolution using high-resolution crystal structures. These structures, together with adapted and remodeled SARS-CoV-2 strains, further revealed critical residues of the spike glycoprotein for SARS-CoV-2 infection and cross-species transmission. SUMMARY Recent studies on SARS-CoV-2 spike glycoprotein provide important structural knowledge for a better understanding of the molecular mechanisms of SARS-CoV-2 infection and cross-species transmission.
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757
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Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton O, Bowen J, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D. Structural basis for broad coronavirus neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.12.29.424482. [PMID: 33398277 PMCID: PMC7781312 DOI: 10.1101/2020.12.29.424482] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARS-CoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryo-electron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.
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Affiliation(s)
- Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - M. Alexandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur, Unité de Virologie Structurale, Paris, France; CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Leah Homad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Oliver Acton
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Chunyan Wang
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Xiaoli Xiong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin G. Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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758
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Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33442681 DOI: 10.1101/2020.12.31.424987] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. We performed sequence and structural analyses to explore how antibody features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer revealed its binding interactions and ability to disassemble spike. Despite heavy chain sequence similarity, biophysical analyses of IGHV3-53/3-66 antibodies highlighted the importance of native heavy:light pairings for ACE2 binding competition and for SARS-CoV-2 neutralization. We defined paired heavy:light sequence signatures and determined antibody precursor prevalence to be ~1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These data reveal key structural and functional neutralization features in the IGHV3-53/3-66 public antibody class to accelerate antibody-based medical interventions against SARS-CoV-2. Highlights A molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralizationCryo-EM analyses detail the structure of a novel public antibody class member, antibody 910-30, in complex with SARS-CoV-2 spike trimerCryo-EM data reveal that 910-30 can both bind assembled trimer and can disassemble the SARS-CoV-2 spikeSequence-structure-function signatures defined for IGHV3-53/3-66 class antibodies including both heavy and light chainsIGHV3-53/3-66 class precursors have a prevalence of 1:44,000 B cells in healthy human antibody repertoires.
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759
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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760
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Xu C, Wang Y, Liu C, Zhang C, Han W, Hong X, Wang Y, Hong Q, Wang S, Zhao Q, Wang Y, Yang Y, Chen K, Zheng W, Kong L, Wang F, Zuo Q, Huang Z, Cong Y. Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM. SCIENCE ADVANCES 2021; 7:eabe5575. [PMID: 33277323 PMCID: PMC7775788 DOI: 10.1126/sciadv.abe5575] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/04/2020] [Indexed: 05/21/2023]
Abstract
The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We report the cryo-EM structures of a tightly closed SARS-CoV-2 S trimer with packed fusion peptide and an ACE2-bound S trimer at 2.7- and 3.8-Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing motions. Notably, the SARS-CoV-2 S trimer appears much more sensitive to the ACE2 receptor than the SARS-CoV S trimer regarding receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer conformational transitions from the ground prefusion state toward the postfusion state, facilitating development of anti-SARS-CoV-2 vaccines and therapeutics.
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Affiliation(s)
- Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalei Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Yang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaijian Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zheng
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang Kong
- The National Facility for Protein Science in Shanghai (NFPS), Shanghai 201210, China
| | - Fangfang Wang
- The National Facility for Protein Science in Shanghai (NFPS), Shanghai 201210, China
| | - Qinyu Zuo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China
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761
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Yazhini A, Sidhanta DSP, Srinivasan N. D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Bioinformation 2021; 17:439-445. [PMID: 34092964 DOI: 10.1101/2020.11.02.364273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 05/21/2023] Open
Abstract
Mutations in the spike protein of SARS-CoV-2 are the major causes for the modulation of ongoing COVID-19 infection. Currently, the D614G substitution in the spike protein has become dominant worldwide. It is associated with higher infectivity than the ancestral (D614)variant. We demonstrate using Gaussian network model-based normal mode analysis that the D614G substitution occurs at the hinge region that facilitates domain-domain motions between receptor binding domain and S2 region of the spike protein. Computer-aided mutagenesis and inter-residue energy calculations reveal that contacts involving D614 are energetically frustrated. However, contacts involving G614 are energetically favourable, implying the substitution strengthens residue contacts that are formed within as well as between protomers. We also find that the free energy difference (ΔΔG) between two variants is -2.6 kcal/mol for closed and -2.0 kcal/mol for 1-RBD up conformation. Thus, the thermodynamic stability has increased upon D614G substitution. Whereas the reverse mutation in spike protein structures having G614 substitution has resulted in the free energy differences of 6.6 kcal/mol and 6.3 kcal/mol for closed and 1-RBD up conformations, respectively, indicating that the overall thermodynamic stability has decreased. These results suggest that the D614G substitution modulates the flexibility of spike protein and confers enhanced thermodynamic stability irrespective of conformational states. This data concurs with the known information demonstrating increased availability of the functional form of spikeprotein trimer upon D614G substitution.
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore, Karnataka, 560012, India
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762
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Kelleher AD. Acute treatment with monoclonal antibodies: their design and their use. MICROBIOLOGY AUSTRALIA 2021. [DOI: 10.1071/ma21011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Passive anti-viral immunotherapy, including monoclonal antibodies (mAb), was identified early as a promising therapeutic avenue for COVID-19 with a rapid development pathway. This has been driven by the lack of existing effective direct acting antivirals for coronaviruses, the marginal clinical impact of remdesivir and the relative lack of efficacy of antivirals against other respiratory pathogens, combined with the failure of repurposed drugs. This review explores the potential utility of mAb targeting SARS-CoV-2, to prevent or treat COVID-19 infection. The use of mAb against host factors (e.g. tocilizumab targeting IL-6 receptor and canakinumab targeting IL1-β) to mitigate the inflammatory response seen in progressive disease will not be considered. This review will primarily consider mAb that have direct neutralising activity via their targeting of the SARS-CoV-2 Spike (S) protein focussing on: the targets of mAb; how they mediate viral neutralisation; their propensity to generate escape mutants; their clinical use so far, and their likely place in the therapeutic play book.
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763
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Yang H, Rao Z. Structural biology of SARS-CoV-2 and implications for therapeutic development. Nat Rev Microbiol 2021; 19:685-700. [PMID: 34535791 PMCID: PMC8447893 DOI: 10.1038/s41579-021-00630-8] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an unprecedented global health crisis. However, therapeutic options for treatment are still very limited. The development of drugs that target vital proteins in the viral life cycle is a feasible approach for treating COVID-19. Belonging to the subfamily Orthocoronavirinae with the largest RNA genome, SARS-CoV-2 encodes a total of 29 proteins. These non-structural, structural and accessory proteins participate in entry into host cells, genome replication and transcription, and viral assembly and release. SARS-CoV-2 proteins can individually perform essential physiological roles, be components of the viral replication machinery or interact with numerous host cellular factors. In this Review, we delineate the structural features of SARS-CoV-2 from the whole viral particle to the individual viral proteins and discuss their functions as well as their potential as targets for therapeutic interventions.
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Affiliation(s)
- Haitao Yang
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.12527.330000 0001 0662 3178Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China ,grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China ,grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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764
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Thakur S, Mayank, Sarkar B, Ansari AJ, Khandelwal A, Arya A, Poduri R, Joshi G. Exploring the magic bullets to identify Achilles' heel in SARS-CoV-2: Delving deeper into the sea of possible therapeutic options in Covid-19 disease: An update. Food Chem Toxicol 2021; 147:111887. [PMID: 33253764 PMCID: PMC7694479 DOI: 10.1016/j.fct.2020.111887] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
The symptoms associated with Covid-19 caused by SARS-CoV-2 in severe conditions can cause multiple organ failure and fatality via a plethora of mechanisms, and it is essential to discover the efficacious and safe drug. For this, a successful strategy is to inhibit in different stages of the SARS-CoV-2 life cycle and host cell reactions. The current review briefly put forth the summary of the SARS-CoV-2 pandemic and highlight the critical areas of understanding in genomics, proteomics, medicinal chemistry, and natural products derived drug discovery. The review further extends to briefly put forth the updates in the drug testing system, biologics, biophysics, and their advances concerning SARS-CoV-2. The salient features include information on SARS-CoV-2 morphology, genomic characterization, and pathophysiology along with important protein targets and how they influence the drug design and development against SARS-CoV-2 and a concerted and integrated approach to target these stages. The review also gives the status of drug design and discovery to identify the drugs acting on critical targets in SARS-CoV-2 and host reactions to treat Covid-19.
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Affiliation(s)
- Shikha Thakur
- Department of Pharmaceutical Sciences and Natural Products, School of Health Science, Central University of Punjab, Bathinda 151 001, India
| | - Mayank
- Shobhaben Pratapbhai Patel - School of Pharmacy & Technology Management, SVKM's NMIMS University, Vile Parle, Mumbai 400056, India
| | - Bibekananda Sarkar
- B.S.S. College, Supaul. B.N Mandal University, Madhepura, Bihar 852131, India
| | - Arshad J Ansari
- School of Chemical Sciences and Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer 305817, Rajasthan, India
| | - Akanksha Khandelwal
- Department of Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Anil Arya
- Department of Physics, Central University of Punjab, Bathinda 151 001, India.
| | - Ramarao Poduri
- Department of Pharmaceutical Sciences and Natural Products, School of Health Science, Central University of Punjab, Bathinda 151 001, India.
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences and Natural Products, School of Health Science, Central University of Punjab, Bathinda 151 001, India.
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765
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Barlas SB, Adalier N, Dasdag O, Dasdag S. Evaluation of SARS-CoV-2 with a biophysical perspective. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1885997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Sait Berk Barlas
- Pre-Graduate Internship Department, Medical School, Koc University, Istanbul, Turkey
| | - Nur Adalier
- Pre-Graduate Internship Department, Medical School, Koc University, Istanbul, Turkey
| | - Omer Dasdag
- Pre-Graduate Internship Department, Medical School, Biruni University, Istanbul, Turkey
| | - Suleyman Dasdag
- Biophysics Department, Medical School, Istanbul Medeniyet University, Istanbul, Turkey
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766
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Abstract
In this issue of Cell Host & Microbe, Lu et al. utilize single-molecule FRET to reveal the conformation dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, showing transitions from a closed ground state to the open receptor-accessible conformation via an on-path intermediate. These insights into spike conformations will facilitate rational immunogen design.
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Affiliation(s)
- Vitor Hugo B Serrão
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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767
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Sicard T, Kassardjian A, Julien JP. B cell targeting by molecular adjuvants for enhanced immunogenicity. Expert Rev Vaccines 2020; 19:1023-1039. [PMID: 33252273 DOI: 10.1080/14760584.2020.1857736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Adjuvants are critical components of vaccines to improve the quality and durability of immune responses. Molecular adjuvants are a specific subclass of adjuvants where ligands of known immune-modulatory receptors are directly fused to an antigen. Co-stimulation of the B cell receptor (BCR) and immune-modulatory receptors through this strategy can augment downstream signaling to improve antibody titers and/or potency, and survival in challenge models. AREAS COVERED C3d has been the most extensively studied molecular adjuvant and shown to improve immune responses to a number of antigens. Similarly, tumor necrosis superfamily ligands, such as BAFF and APRIL, as well as CD40, CD180, and immune complex ligands can also improve humoral immunity as molecular adjuvants. EXPERT OPINION However, no single strategy has emerged that improves immune outcomes in all contexts. Thus, systematic exploration of molecular adjuvants that target B cell receptors will be required to realize their full potential as next-generation vaccine technologies.
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Affiliation(s)
- Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute , Toronto, ON, Canada.,Department of Biochemistry, University of Toronto , ON, Canada
| | - Audrey Kassardjian
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute , Toronto, ON, Canada.,Department of Immunology, University of Toronto , ON, Canada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute , Toronto, ON, Canada.,Department of Biochemistry, University of Toronto , ON, Canada.,Department of Immunology, University of Toronto , ON, Canada
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768
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Garvin MR, T Prates E, Pavicic M, Jones P, Amos BK, Geiger A, Shah MB, Streich J, Felipe Machado Gazolla JG, Kainer D, Cliff A, Romero J, Keith N, Brown JB, Jacobson D. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol 2020; 21:304. [PMID: 33357233 PMCID: PMC7756312 DOI: 10.1186/s13059-020-02191-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. RESULTS Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp614Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro323Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. CONCLUSIONS These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
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Affiliation(s)
- Michael R Garvin
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Erica T Prates
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Piet Jones
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - B Kirtley Amos
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY, USA
| | - Armin Geiger
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Manesh B Shah
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Jared Streich
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | | | - David Kainer
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Ashley Cliff
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Jonathon Romero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Nathan Keith
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - James B Brown
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
- Department of Psychology, University of Tennessee Knoxville, Knoxville, TN, USA.
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769
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Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.18.344622. [PMID: 33398275 PMCID: PMC7781310 DOI: 10.1101/2020.10.18.344622] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE2 2 .v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign IL 61821
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
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770
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Littler DR, MacLachlan BJ, Watson GM, Vivian JP, Gully BS. A pocket guide on how to structure SARS-CoV-2 drugs and therapies. Biochem Soc Trans 2020; 48:2625-2641. [PMID: 33258925 PMCID: PMC7752054 DOI: 10.1042/bst20200396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/18/2023]
Abstract
The race to identify a successful treatment for COVID19 will be defined by fundamental research into the replication cycle of the SARS-CoV-2 virus. This has identified five distinct stages from which numerous vaccination and clinical trials have emerged alongside an innumerable number of drug discovery studies currently in development for disease intervention. Informing every step of the viral replication cycle has been an unprecedented 'call-to-arms' by the global structural biology community. Of the 20 main SARS-CoV-2 proteins, 13 have been resolved structurally for SARS-CoV-2 with most having a related SARS-CoV and MERS-CoV structural homologue totalling some 300 structures currently available in public repositories. Herein, we review the contribution of structural studies to our understanding of the virus and their role in structure-based development of therapeutics.
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Affiliation(s)
- Dene R. Littler
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Bruce J. MacLachlan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Gabrielle M. Watson
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Julian P. Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Benjamin S. Gully
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
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771
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Xiang Y, Nambulli S, Xiao Z, Liu H, Sang Z, Duprex WP, Schneidman-Duhovny D, Zhang C, Shi Y. Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science 2020; 370:1479-1484. [PMID: 33154108 PMCID: PMC7857400 DOI: 10.1126/science.abe4747] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
Cost-effective, efficacious therapeutics are urgently needed to combat the COVID-19 pandemic. In this study, we used camelid immunization and proteomics to identify a large repertoire of highly potent neutralizing nanobodies (Nbs) to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor binding domain (RBD). We discovered Nbs with picomolar to femtomolar affinities that inhibit viral infection at concentrations below the nanograms-per-milliliter level, and we determined a structure of one of the most potent Nbs in complex with the RBD. Structural proteomics and integrative modeling revealed multiple distinct and nonoverlapping epitopes and indicated an array of potential neutralization mechanisms. We bioengineered multivalent Nb constructs that achieved ultrahigh neutralization potency (half-maximal inhibitory concentration as low as 0.058 ng/ml) and may prevent mutational escape. These thermostable Nbs can be rapidly produced in bulk from microbes and resist lyophilization and aerosolization.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/therapy
- Camelids, New World
- Escherichia coli
- Humans
- Neutralization Tests
- Protein Binding
- Protein Domains
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- SARS-CoV-2/immunology
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhengyun Xiao
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
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772
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Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science 2020; 370:1473-1479. [PMID: 33154106 PMCID: PMC7857409 DOI: 10.1126/science.abe3255] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/30/2020] [Indexed: 01/12/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.
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Affiliation(s)
- Michael Schoof
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Corresponding author. (M.S.); (P.W.); (A.M.)
| | - Bryan Faust
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Reuben A. Saunders
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Smriti Sangwan
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Veronica Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Nick Hoppe
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Morgane Boone
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Christian B. Billesbølle
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Cristina Puchades
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Caleigh M. Azumaya
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Huong T. Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Marcell Zimanyi
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Jiahao Liang
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Sasha Dickinson
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Henry C. Nguyen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Cynthia M. Chio
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Gregory E. Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Michael C. Thompson
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Devan Diwanji
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Kaitlin Schaefer
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Aditya A. Anand
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Niv Dobzinski
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Camille R. Simoneau
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kristoffer Leon
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Un Seng Chio
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Meghna Gupta
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Mingliang Jin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Fei Li
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Yanxin Liu
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Kaihua Zhang
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - David Bulkley
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Ming Sun
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Amber M. Smith
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Alexandrea N. Rizo
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Frank Moss
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Axel F. Brilot
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Sergei Pourmal
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Raphael Trenker
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Thomas Pospiech
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin Barsi-Rhyne
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Vladislav Belyy
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | | | - Silke Nock
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Yuwei Liu
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA
| | - Corie Y. Ralston
- Molecular Biophysics and Integrated Bioimaging and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melanie Ott
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | | | - Peter Walter
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Corresponding author. (M.S.); (P.W.); (A.M.)
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Anesthesia and Perioperative Care, University of California at San Francisco, San Francisco, CA, USA.,Corresponding author. (M.S.); (P.W.); (A.M.)
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773
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Silva de Souza A, Rivera JD, Almeida VM, Ge P, de Souza RF, Farah CS, Ulrich H, Marana SR, Salinas RK, Guzzo CR. Molecular Dynamics Reveals Complex Compensatory Effects of Ionic Strength on the Severe Acute Respiratory Syndrome Coronavirus 2 Spike/Human Angiotensin-Converting Enzyme 2 Interaction. J Phys Chem Lett 2020; 11:10446-10453. [PMID: 33269932 PMCID: PMC7737395 DOI: 10.1021/acs.jpclett.0c02602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/30/2020] [Indexed: 05/13/2023]
Abstract
The SARS-CoV-2 pandemic has already killed more than one million people worldwide. To gain entry, the virus uses its Spike protein to bind to host hACE-2 receptors on the host cell surface and mediate fusion between viral and cell membranes. As initial steps leading to virus entry involve significant changes in protein conformation as well as in the electrostatic environment in the vicinity of the Spike/hACE-2 complex, we explored the sensitivity of the interaction to changes in ionic strength through computational simulations and surface plasmon resonance. We identified two regions in the receptor-binding domain (RBD), E1 and E2, which interact differently with hACE-2. At high salt concentration, E2-mediated interactions are weakened but are compensated by strengthening E1-mediated hydrophobic interactions. These results provide a detailed molecular understanding of Spike RBD/hACE-2 complex formation and stability under a wide range of ionic strengths.
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Affiliation(s)
- Anacleto Silva de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 5508-900 São Paulo, Brazil
| | - Jose David Rivera
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Vitor Medeiros Almeida
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Pingju Ge
- Acrobiosystems
Inc., Beijing 100176, China
| | - Robson Francisco de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 5508-900 São Paulo, Brazil
| | - Chuck Shaker Farah
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Henning Ulrich
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Sandro Roberto Marana
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Roberto Kopke Salinas
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 5508-900 São Paulo, Brazil
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774
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Mariano G, Farthing RJ, Lale-Farjat SLM, Bergeron JRC. Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be. Front Mol Biosci 2020; 7:605236. [PMID: 33392262 PMCID: PMC7773825 DOI: 10.3389/fmolb.2020.605236] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread in humans in almost every country, causing the disease COVID-19. Since the start of the COVID-19 pandemic, research efforts have been strongly directed towards obtaining a full understanding of the biology of the viral infection, in order to develop a vaccine and therapeutic approaches. In particular, structural studies have allowed to comprehend the molecular basis underlying the role of many of the SARS-CoV-2 proteins, and to make rapid progress towards treatment and preventive therapeutics. Despite the great advances that have been provided by these studies, many knowledge gaps on the biology and molecular basis of SARS-CoV-2 infection still remain. Filling these gaps will be the key to tackle this pandemic, through development of effective treatments and specific vaccination strategies.
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Affiliation(s)
- Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rebecca J. Farthing
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | | | - Julien R. C. Bergeron
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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775
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Onishchenko GG, Sizikova TE, Lebedev VN, Borisevich SV. Analysis of Promising Approaches to COVID-19 Vaccine Development. ACTA ACUST UNITED AC 2020. [DOI: 10.30895/2221-996x-2020-20-4-216-227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The number of confirmed COVID-19 cases worldwide amounted to 50 million at the beginning of November 2020. This is clearly not enough for the formation of herd immunity, which will prevent repeated outbreaks of the disease. Quarantine measures can only curb the spread of the disease to some extent, therefore specific preventive measures are needed to create collective immunity to COVID-19.The underlying principle of collective immunity is indirect protection of the whole of the population by immunising a certain part of it. Vaccination is the most effective approach to prevention of epidemic outbreaks. The aim of the study was to analyse promising approaches to the development of vaccines against novel coronavirus COVID-19 infection. The paper summarises data on development studies and clinical trials of COVID-19 vaccines conducted in different countries. It analyses the pros and cons of different platforms for vaccine development (attenuated vaccines, inactivated vaccines, subunit vaccines, DNA and RNA vaccines, recombinant vector vaccines). The paper presents a potential design of novel vaccines. It was concluded that COVID-19 vaccines might be developed both for immunising high-risk groups and for mass immunisation. An optimal solution for the second task would be to develop human or monkey adenovirus vector-based vaccines whose mass production has already been unveiled.
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776
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Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 DOI: 10.1101/2020.05.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 05/20/2023]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
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777
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Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 PMCID: PMC7857411 DOI: 10.1126/science.abe1107] [Citation(s) in RCA: 598] [Impact Index Per Article: 149.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
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778
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Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe 2020; 28:867-879.e5. [PMID: 33271067 PMCID: PMC7670890 DOI: 10.1016/j.chom.2020.11.004] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phinikoula S Katsamba
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jared M Sampson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jonathan Stuckey
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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779
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Tarke A, Sidney J, Kidd CK, Dan JM, Ramirez SI, Yu ED, Mateus J, da Silva Antunes R, Moore E, Rubiro P, Methot N, Phillips E, Mallal S, Frazier A, Rawlings SA, Greenbaum JA, Peters B, Smith DM, Crotty S, Weiskopf D, Grifoni A, Sette A. Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33330869 DOI: 10.1101/2020.12.08.416750] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens, and precisely measure virus-specific CD4 + and CD8 + T cells, we studied epitope-specific T cell responses of approximately 100 convalescent COVID-19 cases. The SARS-CoV-2 proteome was probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of HLA alleles for class II responses. For HLA class I, we studied an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identified several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance were observed, which differed for CD4 + T cells, CD8 + T cells, and antibodies. The class I and class II epitopes were combined into new epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4 + and CD8 + T cells.
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780
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Lu M, Uchil PD, Li W, Zheng D, Terry DS, Gorman J, Shi W, Zhang B, Zhou T, Ding S, Gasser R, Prévost J, Beaudoin-Bussières G, Anand SP, Laumaea A, Grover JR, Liu L, Ho DD, Mascola JR, Finzi A, Kwong PD, Blanchard SC, Mothes W. Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles. Cell Host Microbe 2020; 28:880-891.e8. [PMID: 33242391 PMCID: PMC7664471 DOI: 10.1016/j.chom.2020.11.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 12/15/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) mediates viral entry into cells and is critical for vaccine development against coronavirus disease 2019 (COVID-19). Structural studies have revealed distinct conformations of S, but real-time information that connects these structures is lacking. Here we apply single-molecule fluorescence (Förster) resonance energy transfer (smFRET) imaging to observe conformational dynamics of S on virus particles. Virus-associated S dynamically samples at least four distinct conformational states. In response to human receptor angiotensin-converting enzyme 2 (hACE2), S opens sequentially into the hACE2-bound S conformation through at least one on-path intermediate. Conformational preferences observed upon exposure to convalescent plasma or antibodies suggest mechanisms of neutralization involving either competition with hACE2 for binding to the receptor-binding domain (RBD) or allosteric interference with conformational changes required for entry. Our findings inform on mechanisms of S recognition and conformations for immunogen design.
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Affiliation(s)
- Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Desheng Zheng
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Annemarie Laumaea
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
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781
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A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. PLoS Pathog 2020; 16:e1009089. [PMID: 33275640 PMCID: PMC7744049 DOI: 10.1371/journal.ppat.1009089] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/16/2020] [Accepted: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that is able to cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential cross-neutralizing epitopes on SARS-like viruses. The ongoing COVID-19 pandemic is caused by SARS-CoV-2. Due to the genetic similarity of SARS-CoV-2 and SARS-CoV, which caused an epidemic in 2003, a few of the SARS-CoV antibodies have now been found to also cross-react with SARS-CoV-2. One such antibody is CR3022, which was isolated from a convalescent SARS patient 14 years ago. However, the 100-fold lower binding to SARS-CoV-2 does not enable neutralization of SARS-CoV-2 compared to SARS-CoV. This study shows that one (P384A) of the four mutational differences in the CR3022 epitope between SARS-CoV and SARS-COV-2 fully accounts for the differences in CR3022 binding affinity and neutralization. These findings advance our understanding of antibody cross-reactivity among SARS-like CoVs with implications for vaccine and therapeutic design.
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782
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Di Natale C, La Manna S, De Benedictis I, Brandi P, Marasco D. Perspectives in Peptide-Based Vaccination Strategies for Syndrome Coronavirus 2 Pandemic. Front Pharmacol 2020; 11:578382. [PMID: 33343349 PMCID: PMC7744882 DOI: 10.3389/fphar.2020.578382] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023] Open
Abstract
At the end of December 2019, an epidemic form of respiratory tract infection now named COVID-19 emerged in Wuhan, China. It is caused by a newly identified viral pathogen, the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which can cause severe pneumonia and acute respiratory distress syndrome. On January 30, 2020, due to the rapid spread of infection, COVID-19 was declared as a global health emergency by the World Health Organization. Coronaviruses are enveloped RNA viruses belonging to the family of Coronaviridae, which are able to infect birds, humans and other mammals. The majority of human coronavirus infections are mild although already in 2003 and in 2012, the epidemics of SARS-CoV and Middle East Respiratory Syndrome coronavirus (MERS-CoV), respectively, were characterized by a high mortality rate. In this regard, many efforts have been made to develop therapeutic strategies against human CoV infections but, unfortunately, drug candidates have shown efficacy only into in vitro studies, limiting their use against COVID-19 infection. Actually, no treatment has been approved in humans against SARS-CoV-2, and therefore there is an urgent need of a suitable vaccine to tackle this health issue. However, the puzzled scenario of biological features of the virus and its interaction with human immune response, represent a challenge for vaccine development. As expected, in hundreds of research laboratories there is a running out of breath to explore different strategies to obtain a safe and quickly spreadable vaccine; and among others, the peptide-based approach represents a turning point as peptides have demonstrated unique features of selectivity and specificity toward specific targets. Peptide-based vaccines imply the identification of different epitopes both on human cells and virus capsid and the design of peptide/peptidomimetics able to counteract the primary host-pathogen interaction, in order to induce a specific host immune response. SARS-CoV-2 immunogenic regions are mainly distributed, as well as for other coronaviruses, across structural areas such as spike, envelope, membrane or nucleocapsid proteins. Herein, we aim to highlight the molecular basis of the infection and recent peptide-based vaccines strategies to fight the COVID-19 pandemic including their delivery systems.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano Di Tecnologia, Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB) and Dipartimento di Ingegneria Chimica, Dei Materiali e Della Produzione Industriale, University of Naples Federico II, Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | - Paola Brandi
- Centro Nacional De Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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783
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Abstract
Many research teams all over the world focus their research on the SARS-CoV-2, the new coronavirus that causes the so-called COVID-19 disease. Most of the studies identify the main protease or 3C-like protease (Mpro/3CLpro) as a valid target for large-spectrum inhibitors. Also, the interaction of the human receptor angiotensin-converting enzyme 2 (ACE2) with the viral surface glycoprotein (S) is studied in depth. Structural studies tried to identify the residues responsible for enhancement/weaken virus-ACE2 interactions or the cross-reactivity of the neutralizing antibodies. Although the understanding of the immune system and the hyper-inflammatory process in COVID-19 are crucial for managing the immediate and the long-term consequences of the disease, not many X-ray/NMR/cryo-EM crystals are available. In addition to 3CLpro, the crystal structures of other nonstructural proteins offer valuable information for elucidating some aspects of the SARS-CoV-2 infection. Thus, the structural analysis of the SARS-CoV-2 is currently mainly focused on three directions-finding Mpro/3CLpro inhibitors, the virus-host cell invasion, and the virus-neutralizing antibody interaction.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 6 Louis Pasteur, 400349, Cluj-Napoca, Romania.
- Department of Microbiology, County Emergency Clinical Hospital, 400006, Cluj-Napoca, Romania.
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784
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Ke Z, Oton J, Qu K, Cortese M, Zila V, McKeane L, Nakane T, Zivanov J, Neufeldt CJ, Cerikan B, Lu JM, Peukes J, Xiong X, Kräusslich HG, Scheres SHW, Bartenschlager R, Briggs JAG. Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature 2020; 588:498-502. [PMID: 32805734 PMCID: PMC7116492 DOI: 10.1038/s41586-020-2665-2] [Citation(s) in RCA: 766] [Impact Index Per Article: 191.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude1. Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor and mediate entry of virions into target cells2-6. S exhibits extensive conformational flexibility: it modulates exposure of its receptor-binding site and subsequently undergoes complete structural rearrangement to drive fusion of viral and cellular membranes2,7,8. The structures and conformations of soluble, overexpressed, purified S proteins have been studied in detail using cryo-electron microscopy2,7,9-12, but the structure and distribution of S on the virion surface remain unknown. Here we applied cryo-electron microscopy and tomography to image intact SARS-CoV-2 virions and determine the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. These results reveal the conformations of S on the virion, and provide a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.
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Affiliation(s)
- Zunlong Ke
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joaquin Oton
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kun Qu
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Lesley McKeane
- Visual Aids Department, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Takanori Nakane
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jasenko Zivanov
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - John M Lu
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julia Peukes
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Xiaoli Xiong
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
| | - Sjors H W Scheres
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John A G Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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785
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Benton DJ, Wrobel AG, Xu P, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ. Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature 2020; 588:327-330. [PMID: 32942285 PMCID: PMC7116727 DOI: 10.1038/s41586-020-2772-0] [Citation(s) in RCA: 543] [Impact Index Per Article: 135.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/11/2020] [Indexed: 11/09/2022]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors1-4, followed by fusion of the virus and cell membranes to release the virus genome into the cell. Both receptor binding and membrane fusion activities are mediated by the virus spike glycoprotein5-7. As with other class-I membrane-fusion proteins, the spike protein is post-translationally cleaved, in this case by furin, into the S1 and S2 components that remain associated after cleavage8-10. Fusion activation after receptor binding is proposed to involve the exposure of a second proteolytic site (S2'), cleavage of which is required for the release of the fusion peptide11,12. Here we analyse the binding of ACE2 to the furin-cleaved form of the SARS-CoV-2 spike protein using cryo-electron microscopy. We classify ten different molecular species, including the unbound, closed spike trimer, the fully open ACE2-bound trimer and dissociated monomeric S1 bound to ACE2. The ten structures describe ACE2-binding events that destabilize the spike trimer, progressively opening up, and out, the individual S1 components. The opening process reduces S1 contacts and unshields the trimeric S2 core, priming the protein for fusion activation and dissociation of ACE2-bound S1 monomers. The structures also reveal refolding of an S1 subdomain after ACE2 binding that disrupts interactions with S2, which involves Asp61413-15 and leads to the destabilization of the structure of S2 proximal to the secondary (S2') cleavage site.
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Affiliation(s)
- Donald J Benton
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Antoni G Wrobel
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Pengqi Xu
- Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Francis Crick Institute, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Stephen R Martin
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, UK
| | - John J Skehel
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
| | - Steven J Gamblin
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
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786
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Affiliation(s)
- Imre Berger
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol, BS8 1TS, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.
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787
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Borges V, Isidro J, Cortes-Martins H, Duarte S, Vieira L, Leite R, Gordo I, Caetano CP, Nunes B, Sá R, Oliveira A, Guiomar R, Gomes JP. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerg Microbes Infect 2020; 9:2488-2496. [PMID: 33131453 PMCID: PMC7717510 DOI: 10.1080/22221751.2020.1844552] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 01/02/2023]
Abstract
Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Helena Cortes-Martins
- Reference and Surveillance Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ricardo Leite
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Constantino P. Caetano
- Department of Epidemiology, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Baltazar Nunes
- Department of Epidemiology, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Centro de Investigação em Saúde Pública, Escola Nacional de Saúde Pública, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Regina Sá
- Public Health Unit, Primary Care Cluster of Baixo Vouga, Central Regional Health Administration, Aveiro, Portugal
| | - Ana Oliveira
- Public Health Unit, Primary Care Cluster of Baixo Vouga, Central Regional Health Administration, Aveiro, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | | | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
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788
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Bangaru S, Ozorowski G, Turner HL, Antanasijevic A, Huang D, Wang X, Torres JL, Diedrich JK, Tian JH, Portnoff AD, Patel N, Massare MJ, Yates JR, Nemazee D, Paulson JC, Glenn G, Smith G, Ward AB. Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Science 2020; 370:1089-1094. [PMID: 33082295 PMCID: PMC7857404 DOI: 10.1126/science.abe1502] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022]
Abstract
Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.
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Affiliation(s)
- Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Greg Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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789
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Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G, Arumugaswami V, Fries BC, Arditi M, Bahar I. A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33269352 PMCID: PMC7709177 DOI: 10.1101/2020.11.24.395079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We recently discovered a superantigen-like motif, similar to Staphylococcal enterotoxin B (SEB), near the S1/S2 cleavage site of SARS-CoV-2 Spike protein, which might explain the multisystem-inflammatory syndrome (MIS-C) observed in children and cytokine storm in severe COVID-19 patients. We show here that an anti-SEB monoclonal antibody (mAb), 6D3, can bind this viral motif, and in particular its PRRA insert, to inhibit infection by blocking the access of host cell proteases, TMPRSS2 or furin, to the cleavage site. The high affinity of 6D3 for the furin-cleavage site originates from a poly-acidic segment at its heavy chain CDR2, a feature shared with SARS-CoV-2-neutralizing mAb 4A8. The affinity of 6D3 and 4A8 for this site points to their potential utility as therapeutics for treating COVID-19, MIS-C, or common cold caused by human coronaviruses (HCoVs) that possess a furin-like cleavage site.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rebecca A Porritt
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Magali Noval Rivas
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - James M Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Asli Beyza Ozdemir
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA90095, USA
| | - Bettina C Fries
- Department of Medicine, Stony Brook University Hospital, Stony Brook, New York, 11794, USA
| | - Moshe Arditi
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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790
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Wang L, Xiang Y. Spike Glycoprotein-Mediated Entry of SARS Coronaviruses. Viruses 2020; 12:E1289. [PMID: 33187074 PMCID: PMC7696831 DOI: 10.3390/v12111289] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/07/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 are enveloped, positive-sense, single-stranded RNA viruses and causes of epidemic diseases that have resulted in public health emergencies worldwide. Angiotensin-converting enzyme 2 (ACE2) is the receptor that allows the entry of these two viruses into host cells, a key step in the life cycle of the pathogens. The characterization of the interactions of ACE2 with the viral spike glycoproteins and structural studies of the ACE2-binding-induced conformational changes in the viral spike glycoproteins have furthered our understanding of the entry processes of these two viruses, and these studies provide useful information that will facilitate the development of antiviral agents and vaccines to control the diseases.
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Affiliation(s)
| | - Ye Xiang
- Center for Infectious Disease Research, Beijing Frontier Research Center for Biological Structure & Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China;
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791
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Peters MH, Bastidas O, Kokron DS, Henze CE. Static all-atom energetic mappings of the SARS-Cov-2 spike protein and dynamic stability analysis of "Up" versus "Down" protomer states. PLoS One 2020; 15:e0241168. [PMID: 33170884 PMCID: PMC7654774 DOI: 10.1371/journal.pone.0241168] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/10/2020] [Indexed: 11/23/2022] Open
Abstract
The SARS-CoV-2 virion responsible for the current world-wide pandemic COVID-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD) within its distal, prefusion S1 domain. The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-CoV-2 Spike protein in its static prefusion state based on two recent and independent experimental structure publications. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called “glue” points) between residues in the Up and Down state protomers. The S2 proximal, fusion domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer’s intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. This included, for example, a key RBD residue ARG357 in the Up-Down interaction and a three residue sequence ALA520-PRO521-ALA522, associated with a turn structure in the RBD of the Up state protomer, acting as a stabilizing interaction with the NTD of its neighbor protomer. Additionally, our intra chain dominant energy mappings within each protomer, identified a significant “glue” point or possible “latch” for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the amino acid R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-CoV-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. We conducted preliminary molecular dynamics simulations across 0.1 μ seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. Full trimeric Spike protein studies of the same mutation across all protomers, however, did not exhibit latch release demonstrating the critical importance of interchain interactions across the S1 domain, including RBD-NTD neighboring chain interactions. Therapies aimed at disrupting these noncovalent interactions could be a viable route for the physico-chemical mitigation of this deadly virion.
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Affiliation(s)
- Michael H. Peters
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| | - Oscar Bastidas
- College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Daniel S. Kokron
- NASA Ames Research Center, Moffett Field, California, United Sates of America
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792
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Verkhivker GM. Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. J Proteome Res 2020; 19:4587-4608. [PMID: 33006900 PMCID: PMC7640983 DOI: 10.1021/acs.jproteome.0c00654] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Indexed: 12/13/2022]
Abstract
The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have recently characterized the conformational landscapes of the SARS-CoV-2 spike glycoproteins in the prefusion form, revealing a spectrum of stable and more dynamic states. By employing molecular simulations and network modeling approaches, this study systematically examined functional dynamics and identified the regulatory centers of allosteric interactions for distinct functional states of the wild-type and mutant variants of the SARS-CoV-2 prefusion spike trimer. This study presents evidence that the SARS-CoV-2 spike protein can function as an allosteric regulatory engine that fluctuates between dynamically distinct functional states. Perturbation-based modeling of the interaction networks revealed a key role of the cross-talk between the effector hotspots in the receptor binding domain and the fusion peptide proximal region of the SARS-CoV-2 spike protein. The results have shown that the allosteric hotspots of the interaction networks in the SARS-CoV-2 spike protein can control the dynamic switching between functional conformational states that are associated with virus entry to the host receptor. This study offers a useful and novel perspective on the underlying mechanisms of the SARS-CoV-2 spike protein through the lens of allosteric signaling as a regulatory apparatus of virus transmission that could open up opportunities for targeted allosteric drug discovery against SARS-CoV-2 proteins and contribute to the rapid response to the current and potential future pandemic scenarios.
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Affiliation(s)
- Gennady M. Verkhivker
- Graduate
Program in Computational and Data Sciences, Keck Center for Science
and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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793
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Wijesundara DK, Avumegah MS, Lackenby J, Modhiran N, Isaacs A, Young PR, Watterson D, Chappell KJ. Rapid Response Subunit Vaccine Design in the Absence of Structural Information. Front Immunol 2020; 11:592370. [PMID: 33250897 PMCID: PMC7672035 DOI: 10.3389/fimmu.2020.592370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/06/2020] [Indexed: 11/23/2022] Open
Abstract
Prior to 2020, the threat of a novel viral pandemic was omnipresent but largely ignored. Just 12 months prior to the Coronavirus disease 2019 (COVID-19) pandemic our team received funding from the Coalition for Epidemic Preparedness Innovations (CEPI) to establish and validate a rapid response pipeline for subunit vaccine development based on our proprietary Molecular Clamp platform. Throughout the course of 2019 we conducted two mock tests of our system for rapid antigen production against two potential, emerging viral pathogens, Achimota paramyxovirus and Wenzhou mammarenavirus. For each virus we expressed a small panel of recombinant variants of the membrane fusion protein and screened for expression level, product homogeneity, and the presence of the expected trimeric pre-fusion conformation. Lessons learned from this exercise paved the way for our response to COVID-19, for which our candidate antigen is currently in phase I clinical trial.
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Affiliation(s)
- Danushka K Wijesundara
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Michael S Avumegah
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Julia Lackenby
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD, Australia
| | - Ariel Isaacs
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Paul R Young
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD, Australia
| | - Keith J Chappell
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.,The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD, Australia
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794
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Zhang Q, Chen CZ, Swaroop M, Xu M, Wang L, Lee J, Wang AQ, Pradhan M, Hagen N, Chen L, Shen M, Luo Z, Xu X, Xu Y, Huang W, Zheng W, Ye Y. Heparan sulfate assists SARS-CoV-2 in cell entry and can be targeted by approved drugs in vitro. Cell Discov 2020; 6:80. [PMID: 33298900 PMCID: PMC7610239 DOI: 10.1038/s41421-020-00222-5] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
The cell entry of SARS-CoV-2 has emerged as an attractive drug repurposing target for COVID-19. Here we combine genetics and chemical perturbation to demonstrate that ACE2-mediated entry of SARS-Cov and CoV-2 requires the cell surface heparan sulfate (HS) as an assisting cofactor: ablation of genes involved in HS biosynthesis or incubating cells with a HS mimetic both inhibit Spike-mediated viral entry. We show that heparin/HS binds to Spike directly, and facilitates the attachment of Spike-bearing viral particles to the cell surface to promote viral entry. We screened approved drugs and identified two classes of inhibitors that act via distinct mechanisms to target this entry pathway. Among the drugs characterized, Mitoxantrone is a potent HS inhibitor, while Sunitinib and BNTX disrupt the actin network to indirectly abrogate HS-assisted viral entry. We further show that drugs of the two classes can be combined to generate a synergized activity against SARS-CoV-2-induced cytopathic effect. Altogether, our study establishes HS as an attachment factor that assists SARS coronavirus cell entry and reveals drugs capable of targeting this important step in the viral life cycle.
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Affiliation(s)
- Qi Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Catherine Zhengzheng Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Manju Swaroop
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Juhyung Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy Qiu Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Natalie Hagen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Zhiji Luo
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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795
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Adhikari N, Amin SA, Jha T. Dissecting the Drug Development Strategies Against SARS-CoV-2 Through Diverse Computational Modeling Techniques. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/7653_2020_46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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796
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He J, Huang F, Zhang J, Chen Q, Zheng Z, Zhou Q, Chen D, Li J, Chen J. Vaccine design based on 16 epitopes of SARS-CoV-2 spike protein. J Med Virol 2020; 93:2115-2131. [PMID: 33091154 PMCID: PMC7675516 DOI: 10.1002/jmv.26596] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/18/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022]
Abstract
The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) urgently requires an effective vaccine for prevention. In this study, 66 epitopes containing pentapeptides of SARS‐CoV‐2 spike protein in the IEDB database were compared with the amino acid sequence of SARS‐CoV‐2 spike protein, and 66 potentially immune‐related peptides of SARS‐CoV‐2 spike protein were obtained. Based on the single‐nucleotide polymorphisms analysis of spike protein of 1218 SARS‐CoV‐2 isolates, 52 easily mutated sites were identified and used for vaccine epitope screening. The best vaccine candidate epitopes in the 66 peptides of SARS‐CoV‐2 spike protein were screened out through mutation and immunoinformatics analysis. The best candidate epitopes were connected by different linkers in silico to obtain vaccine candidate sequences. The results showed that 16 epitopes were relatively conservative, immunological, nontoxic, and nonallergenic, could induce the secretion of cytokines, and were more likely to be exposed on the surface of the spike protein. They were both B‐ and T‐cell epitopes, and could recognize a certain number of HLA molecules and had high coverage rates in different populations. Moreover, epitopes 897‐913 were predicted to have possible cross‐immunoprotection for SARS‐CoV and SARS‐CoV‐2. The results of vaccine candidate sequences screening suggested that sequences (without linker, with linker GGGSGGG, EAAAK, GPGPG, and KK, respectively) were the best. The proteins translated by these sequences were relatively stable, with a high antigenic index and good biological activity. Our study provided vaccine candidate epitopes and sequences for the research of the SARS‐CoV‐2 vaccine.
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Affiliation(s)
- Jinlei He
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Fan Huang
- Department of First Surgical, Chengdu Shuangliu Hospital of Traditional Chinese Medicine, Chengdu, China
| | - Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiwei Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qi Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
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797
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020; 11:e02707-20. [PMID: 33127862 PMCID: PMC7642679 DOI: 10.1128/mbio.02707-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antibodies, Neutralizing/immunology
- Base Sequence
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus RNA-Dependent RNA Polymerase
- Genome, Viral
- Genotype
- Humans
- Machine Learning
- Models, Molecular
- Molecular Diagnostic Techniques
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Texas/epidemiology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - David W Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hoang A T Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - J Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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798
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Yao H, Song Y, Chen Y, Wu N, Xu J, Sun C, Zhang J, Weng T, Zhang Z, Wu Z, Cheng L, Shi D, Lu X, Lei J, Crispin M, Shi Y, Li L, Li S. Molecular Architecture of the SARS-CoV-2 Virus. Cell 2020; 183:730-738.e13. [PMID: 32979942 PMCID: PMC7474903 DOI: 10.1016/j.cell.2020.09.018] [Citation(s) in RCA: 673] [Impact Index Per Article: 168.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/10/2020] [Accepted: 09/03/2020] [Indexed: 01/16/2023]
Abstract
SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were determined to average resolutions of 8.7-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diameter lumen.
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Affiliation(s)
- Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Yutong Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Yong Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Jialu Xu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chujie Sun
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jiaxing Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Tianhao Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Zheyuan Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Zhigang Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Jianlin Lei
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yigong Shi
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China.
| | - Sai Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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799
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Zhang J, Cai Y, Xiao T, Lu J, Peng H, Sterling SM, Walsh RM, Rits-Volloch S, Sliz P, Chen B. Structural impact on SARS-CoV-2 spike protein by D614G substitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33083806 DOI: 10.1101/2020.10.13.337980] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Substitution for aspartic acid by glycine at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing pandemic, appears to facilitate rapid viral spread. The G614 variant has now replaced the D614-carrying virus as the dominant circulating strain. We report here cryo-EM structures of a full-length S trimer carrying G614, which adopts three distinct prefusion conformations differing primarily by the position of one receptor-binding domain (RBD). A loop disordered in the D614 S trimer wedges between domains within a protomer in the G614 spike. This added interaction appears to prevent premature dissociation of the G614 trimer, effectively increasing the number of functional spikes and enhancing infectivity. The loop transition may also modulate structural rearrangements of S protein required for membrane fusion. These findings extend our understanding of viral entry and suggest an improved immunogen for vaccine development.
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800
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Monette A, Mouland AJ. Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates. Viruses 2020; 12:E1179. [PMID: 33081049 PMCID: PMC7589941 DOI: 10.3390/v12101179] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative diseases. Treatment of BMC-related diseases will greatly benefit from identification of therapeutics preventing pathological aggregates while sparing BMCs required for cellular functions. Numerous viruses that block SG assembly also utilize or engineer BMCs for their replication. While BMC formation first depends on prion-like disordered protein domains (PrLDs), metal ion-controlled RNA-binding domains (RBDs) also orchestrate their formation. Virus replication and viral genomic RNA (vRNA) packaging dynamics involving nucleocapsid (NC) proteins and their orthologs rely on Zinc (Zn) availability, while virus morphology and infectivity are negatively influenced by excess Copper (Cu). While virus infections modify physiological metal homeostasis towards an increased copper to zinc ratio (Cu/Zn), how and why they do this remains elusive. Following our recent finding that pan-retroviruses employ Zn for NC-mediated LLPS for virus assembly, we present a pan-virus bioinformatics and literature meta-analysis study identifying metal-based mechanisms linking virus-induced BMCs to neurodegenerative disease processes. We discover that conserved degree and placement of PrLDs juxtaposing metal-regulated RBDs are associated with disease-causing prion-like proteins and are common features of viral proteins responsible for virus capsid assembly and structure. Virus infections both modulate gene expression of metalloproteins and interfere with metal homeostasis, representing an additional virus strategy impeding physiological and cellular antiviral responses. Our analyses reveal that metal-coordinated virus NC protein PrLDs initiate LLPS that nucleate pan-virus assembly and contribute to their persistence as cell-free infectious aerosol droplets. Virus aerosol droplets and insoluble neurological disease aggregates should be eliminated by physiological or environmental metals that outcompete PrLD-bound metals. While environmental metals can control virus spreading via aerosol droplets, therapeutic interference with metals or metalloproteins represent additional attractive avenues against pan-virus infection and virus-exacerbated neurological diseases.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
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