1
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Dutta M, Su Y, Plescia CB, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. J Biol Chem 2024:107456. [PMID: 38866325 DOI: 10.1016/j.jbc.2024.107456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA.
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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2
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Yan R, Liu J, Chen Z, Wan P, Liang T, Li K, Liu D, Ma M, Chen X, Li A, He Y, Li H, Mao Y. Rapid production of COVID-19 subunit vaccine candidates and their immunogenicity evaluation in pigs. Int J Biol Macromol 2024; 272:132798. [PMID: 38838896 DOI: 10.1016/j.ijbiomac.2024.132798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 04/11/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
The emergence of various variants of concern (VOCs) necessitates the development of more efficient vaccines for COVID-19. In this study, we established a rapid and robust production platform for a novel subunit vaccine candidate based on eukaryotic HEK-293 T cells. The immunogenicity of the vaccine candidate was evaluated in pigs. The results demonstrated that the pseudovirus neutralizing antibody (pNAb) titers reached 7751 and 306 for the SARS-CoV-2 Delta and Omicron variants, respectively, after the first boost. Subsequently, pNAb titers further increased to 10,201 and 1350, respectively, after the second boost. Additionally, ELISPOT analysis revealed a robust T-cell response characterized by IFN-γ (171 SFCs/106 cells) and IL-2 (101 SFCs/106 cells) production. Our study demonstrates that a vaccine candidate based on the Delta variant spike protein may provide strong and broad protection against the prototype SARS-CoV-2 and VOCs. Moreover, the strategy for the efficient and stable expression of recombinant proteins utilizing HEK-293 T cells can be employed as a universal platform for future vaccine development.
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Affiliation(s)
- Renhe Yan
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China
| | - Jun Liu
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Zedian Chen
- The First Affiliated Hospital, Guangzhou University of Traditional Chinese Medicine, Guangzhou 510000, China
| | - Pengfei Wan
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China
| | - Tiekun Liang
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China
| | - Kanhe Li
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China
| | - Dandan Liu
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China
| | - Manxin Ma
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China
| | - Xueji Chen
- South China Institute of Biomedicine, Guangzhou 510000, China
| | - Andrew Li
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Yuezhong He
- South China Institute of Biomedicine, Guangzhou 510000, China
| | - Hongwei Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Yingying Mao
- Guangzhou Bioneeds Biotechnology CO., Ltd, Guangzhou, 510000, China; South China Institute of Biomedicine, Guangzhou 510000, China.
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3
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Wang R, Lu S, Deng F, Wu L, Yang G, Chong S, Liu Y. Enhancing the understanding of SARS-CoV-2 protein with structure and detection methods: An integrative review. Int J Biol Macromol 2024; 270:132237. [PMID: 38734351 DOI: 10.1016/j.ijbiomac.2024.132237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
As the rapid and accurate screening of infectious diseases can provide meaningful information for outbreak prevention and control, as well as owing to the existing limitations of the polymerase chain reaction (PCR), it is imperative to have new and validated detection techniques for SARS-CoV-2. Therefore, the rationale for outlining the techniques used to detect SARS-CoV-2 proteins and performing a comprehensive comparison to serve as a practical benchmark for future identification of similar viral proteins is clear. This review highlights the urgent need to strengthen pandemic preparedness by emphasizing the importance of integrated measures. These include improved tools for pathogen characterization, optimized societal precautions, the establishment of early warning systems, and the deployment of highly sensitive diagnostics for effective surveillance, triage, and resource management. Additionally, with an improved understanding of the virus' protein structure, considerable advances in targeted detection, treatment, and prevention strategies are expected to greatly improve our ability to respond to future outbreaks.
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Affiliation(s)
- Ruiqi Wang
- Shenyang University of Chemical Technology, Shenyang 110142, China; National Institute of Metrology, Beijing 100029, China
| | - Song Lu
- National Institute of Metrology, Beijing 100029, China
| | - Fanyu Deng
- National Institute of Metrology, Beijing 100029, China; North University of China, Taiyuan 030051, China
| | - Liqing Wu
- National Institute of Metrology, Beijing 100029, China
| | - Guowu Yang
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen 518055, China
| | - Siying Chong
- Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Yahui Liu
- National Institute of Metrology, Beijing 100029, China.
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4
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Deinhardt-Emmer S, Deshpande S, Kitazawa K, Herman AB, Bons J, Rose JP, Kumar PA, Anerillas C, Neri F, Ciotlos S, Perez K, Köse-Vogel N, Häder A, Abdelmohsen K, Löffler B, Gorospe M, Desprez PY, Melov S, Furman D, Schilling B, Campisi J. Role of the Senescence-Associated Factor Dipeptidyl Peptidase 4 in the Pathogenesis of SARS-CoV-2 Infection. Aging Dis 2024; 15:1398-1415. [PMID: 37728586 PMCID: PMC11081172 DOI: 10.14336/ad.2023.0812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/12/2023] [Indexed: 09/21/2023] Open
Abstract
During cellular senescence, persistent growth arrest and changes in protein expression programs are accompanied by a senescence-associated secretory phenotype (SASP). In this study, we detected the upregulation of the SASP-related protein dipeptidyl peptidase 4 (DDP4) in human primary lung cells rendered senescent by exposure to ionizing radiation. DPP4 is an exopeptidase that plays a crucial role in the cleavage of various proteins, resulting in the loss of N-terminal dipeptides and proinflammatory effects. Interestingly, our data revealed an association between severe coronavirus disease 2019 (COVID-19) and DDP4, namely that DPP4 levels increased in the plasma of patients with COVID-19 and were correlated with age and disease progression. Although we could not determine the direct effect of DDP4 on viral replication, mechanistic studies in cell culture revealed a negative impact on the expression of the tight junction protein zonula occludens-1 (ZO-1), which contributes to epithelial barrier function. Mass spectrometry analysis indicated that DPP4 overexpressing cells exhibited a decrease in ZO-1 and increased expression of pro-inflammatory cytokines and chemokines. By investigating the effect of DPP4 on the barrier function of human primary cells, we detected an increase in ZO-1 using DPP4 inhibitors. These results provide an important contribution to our understanding of DPP4 in the context of senescence, suggesting that DPP4 plays a major role as part of the SASP. Our results provide evidence that cellular senescence, a hallmark of aging, has an important impact on respiratory infections.
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Affiliation(s)
- Stefanie Deinhardt-Emmer
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | | | - Koji Kitazawa
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Allison B. Herman
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | | | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Francesco Neri
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Serban Ciotlos
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Kevin Perez
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Nilay Köse-Vogel
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Antje Häder
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - David Furman
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Buck Artificial Intelligence Platform, Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | | | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
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5
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Jones-Nosacek C. Vaccine Mandates: Weighing the Common Good vs Personal Conscience and Autonomy. LINACRE QUARTERLY 2024; 91:147-167. [PMID: 38726310 PMCID: PMC11078137 DOI: 10.1177/00243639231213515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
COVID-19 is a serious illness with significant morbidity and mortality. Vaccines to immunize against it were developed in record time. Mandates followed. The question to be considered is when mandates are ethical. Mandates can be used to prevent spread of an infection, prevent overwhelming the healthcare system, or protect public safety, thereby protecting the vulnerable and allowing for full flourishing of the common good. At the same time, one must be careful about respecting autonomy by allowing those who consciences do not allow them to be vaccinated to refuse. Because COVID-19 knowledge is rapidly changing as more information is known and the virus mutates, the conditions under which mandates are ethical change as well. At present, since vaccines prevent severe infection and death in high-risk individuals with added benefit for those who are vaccinated and have a history of infection, mandates can be imposed on those individuals. With an estimated 95% of the US population believed to have been infected and prior history of infection shown to be as effective as vaccination, with immunity lasting at least 500 days, and ability to prevent spread unknown at present but limited at best in the past, the vaccines therefore cannot be ethically mandated for those who are low risk for the versions released September 2023 based on information as of October 2023.
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6
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Gupta G, Verkhivker G. Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking. Int J Mol Sci 2024; 25:4955. [PMID: 38732174 PMCID: PMC11084335 DOI: 10.3390/ijms25094955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and machine-learning-based binding pocket detection with the ensemble-based ligand docking and binding free energy analysis to characterize the potential allosteric binding sites and determine structural and energetic determinants of allosteric inhibition for a series of experimentally validated allosteric molecules. The results demonstrate a good agreement between computational and experimental binding affinities, providing support to the predicted binding modes and suggesting key interactions formed by the allosteric ligands to elicit the experimentally observed inhibition. We establish structural and energetic determinants of allosteric binding for the experimentally known allosteric molecules, indicating a potential mechanism of allosteric modulation by targeting the hinges of the inter-protomer movements and blocking conformational changes between the closed and open spike trimer forms. The results of this study demonstrate that combining ensemble-based ligand docking with conformational states of spike protein and rigorous binding energy analysis enables robust characterization of the ligand binding modes, the identification of allosteric binding hotspots, and the prediction of binding affinities for validated allosteric modulators, which is consistent with the experimental data. This study suggested that the conformational adaptability of the protein allosteric sites and the diversity of ligand bound conformations are both in play to enable efficient targeting of allosteric binding sites and interfere with the conformational changes.
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Affiliation(s)
- Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA;
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA;
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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7
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Lv X, Martin J, Hoover H, Joshi B, Wilkens M, Ullisch DA, Leibold T, Juchum JS, Revadkar S, Kalinovska B, Keith J, Truby A, Liu G, Sun E, Haserick J, DeGnore J, Conolly J, Hill AV, Baldoni J, Kensil C, Levey D, Spencer AJ, Gorr G, Findeis M, Tanne A. Chemical and biological characterization of vaccine adjuvant QS-21 produced via plant cell culture. iScience 2024; 27:109006. [PMID: 38361610 PMCID: PMC10867646 DOI: 10.1016/j.isci.2024.109006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Many vaccines, including those using recombinant antigen subunits, rely on adjuvant(s) to enhance the efficacy of the host immune responses. Among the few adjuvants clinically approved, QS-21, a saponin-based immunomodulatory molecule isolated from the tree bark of Quillaja saponaria (QS) is used in complex formulations in approved effective vaccines. High demand of the QS raw material as well as manufacturing scalability limitation has been barriers here. We report for the first-time successful plant cell culture production of QS-21 having structural, chemical, and biologic, properties similar to the bark extracted product. These data ensure QS-21 and related saponins are broadly available and accessible to drug developers.
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Affiliation(s)
| | | | | | | | | | | | | | - John S. Juchum
- Phyton Biotech LLC, 1503 Cliveden Avenue, Delta, BC V3M 6P7, Canada
| | | | | | | | - Adam Truby
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Adrian V.S. Hill
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | - Alexandra J. Spencer
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Hunter Medical Research Institute, School of Biomedical Sciences and Pharmacy, College of Health, Medicine & Wellbeing; Immune Health Program, New Lambton Heights, NSW, Australia
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8
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Chao CW, Sprouse KR, Miranda MC, Catanzaro NJ, Hubbard ML, Addetia A, Stewart C, Brown JT, Dosey A, Valdez A, Ravichandran R, Hendricks GG, Ahlrichs M, Dobbins C, Hand A, Treichel C, Willoughby I, Walls AC, McGuire AT, Leaf EM, Baric RS, Schäfer A, Veesler D, King NP. Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584735. [PMID: 38558973 PMCID: PMC10979991 DOI: 10.1101/2024.03.13.584735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and has therefore been the focus of vaccine design efforts. Currently there are no licensed vaccines against MERS-CoV and only a few candidates have advanced to Phase I clinical trials. Here we developed MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for SARS-CoV-2. Two-component protein nanoparticles displaying MERS-CoV S-derived antigens induced robust neutralizing antibody responses and protected mice against challenge with mouse-adapted MERS-CoV. Electron microscopy polyclonal epitope mapping and serum competition assays revealed the specificities of the dominant antibody responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle vaccine elicited antibodies targeting multiple non-overlapping epitopes in the RBD, whereas anti-NTD antibodies elicited by the S-2P- and NTD-based immunogens converged on a single antigenic site. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
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Affiliation(s)
- Cara W Chao
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adian Valdez
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Grace G Hendricks
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Isabelle Willoughby
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Leaf
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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9
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Rutten L, Swart M, Koornneef A, Bouchier P, Blokland S, Sadi A, Juraszek J, Vijayan A, Schmit-Tillemans S, Verspuij J, Choi Y, Daal CE, Perkasa A, Torres Morales S, Myeni SK, Kikkert M, Tolboom J, van Manen D, Kuipers H, Schuitemaker H, Zahn R, Langedijk JPM. Impact of SARS-CoV-2 spike stability and RBD exposure on antigenicity and immunogenicity. Sci Rep 2024; 14:5735. [PMID: 38459086 PMCID: PMC10923862 DOI: 10.1038/s41598-024-56293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
The spike protein (S) of SARS-CoV-2 induces neutralizing antibodies and is the key component of current COVID-19 vaccines. The most efficacious COVID-19 vaccines are genetically-encoded spikes with a double proline substitution in the hinge region to stabilize S in the prefusion conformation (S-2P). A subunit vaccine can be a valuable addition to mRNA and viral vector-based vaccines but requires high stability of spike. In addition, further stabilization of the prefusion conformation of spike might improve immunogenicity. To test this, five spike proteins were designed and characterized, ranging from low to high stability. The immunogenicity of these proteins was assessed in mice, demonstrating that a spike (S-closed-2) with a high melting temperature, which still allowed ACE2 binding, induced the highest neutralization titers against homologous and heterologous strains (up to 16-fold higher than the least stabilized spike). In contrast, the most stable spike variant (S-locked), in which the receptor binding domains (RBDs) were locked in a closed conformation and thus not able to breathe, induced relatively low neutralizing antibody titers against heterologous strains. These data demonstrate that S protein stabilization with RBDs exposing highly conserved epitopes may be needed to increase the immunogenicity of spike proteins for future COVID-19 vaccines.
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Affiliation(s)
- Lucy Rutten
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Maarten Swart
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Annemart Koornneef
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Pascale Bouchier
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Sven Blokland
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Ava Sadi
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Jarek Juraszek
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Aneesh Vijayan
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | | | - Johan Verspuij
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Ying Choi
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Chenandly E Daal
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Aditya Perkasa
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Shessy Torres Morales
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sebenzile K Myeni
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Tolboom
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Daniëlle van Manen
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Harmjan Kuipers
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Hanneke Schuitemaker
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Roland Zahn
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Johannes P M Langedijk
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands.
- ForgeBio, Amsterdam, The Netherlands.
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10
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Magazine N, Zhang T, Bungwon AD, McGee MC, Wu Y, Veggiani G, Huang W. Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development. Immunohorizons 2024; 8:214-226. [PMID: 38427047 PMCID: PMC10985062 DOI: 10.4049/immunohorizons.2400003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and virus immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination in humans. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the TLRs, B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.
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Affiliation(s)
- Nicholas Magazine
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Anang D. Bungwon
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Michael C. McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Yingying Wu
- Department of Mathematics, University of Houston, Houston, TX
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
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11
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Manfrini N, Notarbartolo S, Grifantini R, Pesce E. SARS-CoV-2: A Glance at the Innate Immune Response Elicited by Infection and Vaccination. Antibodies (Basel) 2024; 13:13. [PMID: 38390874 PMCID: PMC10885122 DOI: 10.3390/antib13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to almost seven million deaths worldwide. SARS-CoV-2 causes infection through respiratory transmission and can occur either without any symptoms or with clinical manifestations which can be mild, severe or, in some cases, even fatal. Innate immunity provides the initial defense against the virus by sensing pathogen-associated molecular patterns and triggering signaling pathways that activate the antiviral and inflammatory responses, which limit viral replication and help the identification and removal of infected cells. However, temporally dysregulated and excessive activation of the innate immune response is deleterious for the host and associates with severe COVID-19. In addition to its defensive role, innate immunity is pivotal in priming the adaptive immune response and polarizing its effector function. This capacity is relevant in the context of both SARS-CoV-2 natural infection and COVID-19 vaccination. Here, we provide an overview of the current knowledge of the innate immune responses to SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Samuele Notarbartolo
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- CheckmAb Srl, 20122 Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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12
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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13
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Wang N, Wang T. Innovative translational platforms for rapid developing clinical vaccines against COVID-19 and other infectious disease. Biotechnol J 2024; 19:e2300658. [PMID: 38403469 DOI: 10.1002/biot.202300658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
A vaccine is a biological preparation that contains the antigen capable of stimulating the immune system to form the defense against pathogens. Vaccine development often confronts big challenges, including time/energy-consuming, low efficacy, lag to pathogen emergence and mutation, and even safety concern. However, these seem now mostly conquerable through constructing the advanced translational platforms that can make innovative vaccines, sometimes, potentiated with a distinct multifunctional VADS (vaccine adjuvant delivery system), as evidenced by the development of various vaccines against the covid-19 pandemic at warp speed. Particularly, several covid-19 vaccines, such as the viral-vectored vaccines, mRNA vaccines and DNA vaccines, regarded as the innovative ones that are rapidly made via the high technology-based translational platforms. These products have manifested powerful efficacy while showing no unacceptable safety profile in clinics, allowing them to be approved for massive vaccination at also warp speed. Now, the proprietary translational platforms integrated with the state-of-the-art biotechnologies, and even the artificial intelligence (AI), represent an efficient mode for rapid making innovative clinical vaccines against infections, thus increasingly attracting interests of vaccine research and development. Herein, the advanced translational platforms for making innovative vaccines, together with their design principles and immunostimulatory efficacies, are comprehensively elaborated.
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Affiliation(s)
- Ning Wang
- School of Food and Biological engineering, Hefei University of Technology, Hefei, Anhui Province, China
| | - Ting Wang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China
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14
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Samsudin F, Zuzic L, Marzinek JK, Bond PJ. Mechanisms of allostery at the viral surface through the eyes of molecular simulation. Curr Opin Struct Biol 2024; 84:102761. [PMID: 38142635 DOI: 10.1016/j.sbi.2023.102761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
Abstract
The outermost surface layer of any virus is formed by either a capsid shell or envelope. Such layers have traditionally been thought of as immovable structures, but it is becoming apparent that they cannot be viewed exclusively as static architectures protecting the viral genome. A limited number of proteins on the virion surface must perform a multitude of functions in order to orchestrate the viral life cycle, and allostery can regulate their structures at multiple levels of organization, spanning individual molecules, protomers, large oligomeric assemblies, or entire viral surfaces. Here, we review recent contributions from the molecular simulation field to viral surface allostery, with a particular focus on the trimeric spike glycoprotein emerging from the coronavirus surface, and the icosahedral flaviviral envelope complex. As emerging viral pathogens continue to pose a global threat, an improved understanding of viral dynamics and allosteric regulation will prove crucial in developing novel therapeutic strategies.
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Affiliation(s)
- Firdaus Samsudin
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, 07-01 Matrix, 138671, Singapore
| | - Lorena Zuzic
- Department of Chemistry, Langelandsgade 140, Aarhus University, Aarhus 8000, Denmark
| | - Jan K Marzinek
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, 07-01 Matrix, 138671, Singapore
| | - Peter J Bond
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, 07-01 Matrix, 138671, Singapore; Department of Biological Sciences, 16 Science Drive 4, National University of Singapore, 117558, Singapore.
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15
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Bruch EM, Zhu S, Szymkowicz L, Blake T, Kiss T, James DA, Rak A, Narayan K, Balmer MT, Chicz RM. Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Sci Rep 2024; 14:2038. [PMID: 38263191 PMCID: PMC10805794 DOI: 10.1038/s41598-024-52499-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, uses a surface expressed trimeric spike glycoprotein for cell entry. This trimer is the primary target for neutralizing antibodies making it a key candidate for vaccine development. During the global pandemic circulating variants of concern (VOC) caused several waves of infection, severe disease, and death. The reduced efficacy of the ancestral trimer-based vaccines against emerging VOC led to the need for booster vaccines. Here we present a detailed characterization of the Sanofi Beta trimer, utilizing cryo-EM for structural elucidation. We investigate the conformational dynamics and stabilizing features using orthogonal SPR, SEC, nanoDSF, and HDX-MS techniques to better understand how this antigen elicits superior broad neutralizing antibodies as a variant booster vaccine. This structural analysis confirms the Beta trimer preference for canonical quaternary structure with two RBD in the up position and the reversible equilibrium between the canonical spike and open trimer conformations. Moreover, this report provides a better understanding of structural differences between spike antigens contributing to differential vaccine efficacy.
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16
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Lenart K, Arcoverde Cerveira R, Hellgren F, Ols S, Sheward DJ, Kim C, Cagigi A, Gagne M, Davis B, Germosen D, Roy V, Alter G, Letscher H, Van Wassenhove J, Gros W, Gallouët AS, Le Grand R, Kleanthous H, Guebre-Xabier M, Murrell B, Patel N, Glenn G, Smith G, Loré K. Three immunizations with Novavax's protein vaccines increase antibody breadth and provide durable protection from SARS-CoV-2. NPJ Vaccines 2024; 9:17. [PMID: 38245545 PMCID: PMC10799869 DOI: 10.1038/s41541-024-00806-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024] Open
Abstract
The immune responses to Novavax's licensed NVX-CoV2373 nanoparticle Spike protein vaccine against SARS-CoV-2 remain incompletely understood. Here, we show in rhesus macaques that immunization with Matrix-MTM adjuvanted vaccines predominantly elicits immune events in local tissues with little spillover to the periphery. A third dose of an updated vaccine based on the Gamma (P.1) variant 7 months after two immunizations with licensed NVX-CoV2373 resulted in significant enhancement of anti-spike antibody titers and antibody breadth including neutralization of forward drift Omicron variants. The third immunization expanded the Spike-specific memory B cell pool, induced significant somatic hypermutation, and increased serum antibody avidity, indicating considerable affinity maturation. Seven months after immunization, vaccinated animals controlled infection by either WA-1 or P.1 strain, mediated by rapid anamnestic antibody and T cell responses in the lungs. In conclusion, a third immunization with an adjuvanted, low-dose recombinant protein vaccine significantly improved the quality of B cell responses, enhanced antibody breadth, and provided durable protection against SARS-CoV-2 challenge.
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Affiliation(s)
- Klara Lenart
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rodrigo Arcoverde Cerveira
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Fredrika Hellgren
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Ols
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alberto Cagigi
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brandon Davis
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Hélène Letscher
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Jérôme Van Wassenhove
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Wesley Gros
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Anne-Sophie Gallouët
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Harry Kleanthous
- Bill & Melinda Gates Foundation, Seattle, WA, USA
- SK Biosciences, Boston, MA, USA
| | | | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Karin Loré
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden.
- Karolinska University Hospital, Stockholm, Sweden.
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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17
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Zaidi AK, Dawoodi S. Structural biology of SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:31-43. [PMID: 38237989 DOI: 10.1016/bs.pmbts.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a comprehensive overview of the techniques employed to unravel the structural biology of SARS-CoV-2, facilitating a deeper understanding of the virus for developing future therapeutic strategies. Various techniques such as Electron microscopy (EM) for capturing high-resolution images of the virus and X-ray crystallography used for determining atomic-level structures of viral proteins are discussed. Cryo-electron microscopy (cryo-EM) imaging is also examined as a powerful tool for visualizing the virus's structure in its native state. Intracellular detection and tracking of SARS-CoV-2 are discussed, highlighting the techniques employed to study the virus's behavior within host cells. The chapter further explores how cryo-EM has been instrumental in delivering high-quality structural information on SARS-CoV-2, enabling researchers to better understand its mechanisms of infection and replication. The structural visualization of SARS-CoV-2 is then presented, focusing on key components such as the spike protein structure, RNA polymerase structure, and the visualization of intact and in-situ virions using cryo-electron tomography (cryo-ET). Lastly, the chapter touches upon the application of nuclear magnetic resonance (NMR) spectroscopy for studying the dynamics and interactions of viral proteins.
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Affiliation(s)
| | - Sunny Dawoodi
- Anaesthesiologist, University Hospitals Birmingham and NHS Foundation Trust, United Kingdom.
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18
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Sun P, Cheng B, Ru J, Li X, Fang G, Xie Y, Shi G, Hou J, Zhao L, Gan L, Ma L, Liang C, Chen Y, Li Z. Nano-carrier DMSN for effective multi-antigen vaccination against SARS-CoV-2. J Nanobiotechnology 2024; 22:11. [PMID: 38167103 PMCID: PMC10763455 DOI: 10.1186/s12951-023-02271-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has had a profound impact on the global health and economy. While mass vaccination for herd immunity is effective, emerging SARS-CoV-2 variants can evade spike protein-based COVID-19 vaccines. In this study, we develop a new immunization strategy by utilizing a nanocarrier, dendritic mesoporous silica nanoparticle (DMSN), to deliver the receptor-binding domain (RBD) and conserved T-cell epitope peptides (DMSN-P-R), aiming to activate both humoral and cellular immune responses in the host. The synthesized DMSN had good uniformity and dispersion and showed a strong ability to load the RBD and peptide antigens, enhancing their uptake by antigen-presenting cells (APCs) and promoting antigen delivery to lymph nodes. The DMSN-P-R vaccine elicited potent humoral immunity, characterized by highly specific RBD antibodies. Neutralization tests demonstrated significant antibody-mediated neutralizing activity against live SARS-CoV-2. Crucially, the DMSN-P-R vaccine also induced robust T-cell responses that were specifically stimulated by the RBD and conserved T-cell epitope peptides of SARS-CoV-2. The DMSN demonstrated excellent biocompatibility and biosafety in vitro and in vivo, along with degradability. Our study introduces a promising vaccine strategy that utilizes nanocarriers to deliver a range of antigens, effectively enhancing both humoral and cellular immune responses to prevent virus transmission.
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Affiliation(s)
- Peng Sun
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Bingsheng Cheng
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Jiaxi Ru
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Xiaoyan Li
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China
| | - Guicun Fang
- Microscopy Core Facility, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Yinli Xie
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Guangjiang Shi
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Jichao Hou
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Longwei Zhao
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Lipeng Gan
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Lina Ma
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Chao Liang
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| | - Yin Chen
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China.
| | - Zhiyong Li
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China.
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China.
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19
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Stiving AQ, Foreman DJ, VanAernum ZL, Durr E, Wang S, Vlasak J, Galli J, Kafader JO, Tsukidate T, Li X, Schuessler HA, Richardson DD. Dissecting the Heterogeneous Glycan Profiles of Recombinant Coronavirus Spike Proteins with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:62-73. [PMID: 38032172 DOI: 10.1021/jasms.3c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Surface-embedded glycoproteins, such as the spike protein trimers of coronaviruses MERS, SARS-CoV, and SARS-CoV-2, play a key role in viral function and are the target antigen for many vaccines. However, their significant glycan heterogeneity poses an analytical challenge. Here, we utilized individual ion mass spectrometry (I2MS), a multiplexed charge detection measurement with similarities to charge detection mass spectrometry (CDMS), in which a commercially available Orbitrap analyzer is used to directly produce mass profiles of these heterogeneous coronavirus spike protein trimers under native-like conditions. Analysis by I2MS shows that glycosylation contributes to the molecular mass of each protein trimer more significantly than expected by bottom-up techniques, highlighting the importance of obtaining complementary intact mass information when characterizing glycosylation of such heterogeneous proteins. Enzymatic dissection to remove sialic acid or N-linked glycans demonstrates that I2MS can be used to better understand the glycan profile from a native viewpoint. Deglycosylation of N-glycans followed by I2MS analysis indicates that the SARS-CoV-2 spike protein trimer contains glycans that are more difficult to remove than its MERS and SARS-CoV counterparts, and these differences are correlated with solvent accessibility. I2MS technology enables characterization of protein mass and intact glycan profile and is orthogonal to traditional mass analysis methods such as size exclusion chromatography-multiangle light scattering (SEC-MALS) and field flow fractionation-multiangle light scattering (FFF-MALS). An added advantage of I2MS is low sample use, requiring 100-fold less than other methodologies. This work highlights how I2MS technology can enable efficient development of vaccines and therapeutics for pharmaceutical development.
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Affiliation(s)
- Alyssa Q Stiving
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - David J Foreman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary L VanAernum
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eberhard Durr
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shiyi Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Josef Vlasak
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer Galli
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Taku Tsukidate
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Hillary A Schuessler
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Douglas D Richardson
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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20
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Chen K, Jiang M, Liu J, Huang D, Yang YR. DNA nanostructures as biomolecular scaffolds for antigen display. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1921. [PMID: 37562787 DOI: 10.1002/wnan.1921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Nanoparticle-based vaccines offer a multivalent approach for antigen display, efficiently activating T and B cells in the lymph nodes. Among various nanoparticle design strategies, DNA nanotechnology offers an innovative alternative platform, featuring high modularity, spatial addressing, nanoscale regulation, high functional group density, and lower self-antigenicity. This review delves into the potential of DNA nanostructures as biomolecular scaffolds for antigen display, addressing: (1) immunological mechanisms behind nanovaccines and commonly used nanoparticles in their design, (2) techniques for characterizing protein NP-antigen complexes, (3) advancements in DNA nanotechnology and DNA-protein assembly approach, (4) strategies for precise antigen presentation on DNA scaffolds, and (5) current applications and future possibilities of DNA scaffolds in antigen display. This analysis aims to highlight the transformative potential of DNA nanoscaffolds in immunology and vaccinology. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Ming Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
| | - Jin Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Deli Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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21
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Liu S, Hu M, Liu X, Liu X, Chen T, Zhu Y, Liang T, Xiao S, Li P, Ma X. Nanoparticles and Antiviral Vaccines. Vaccines (Basel) 2023; 12:30. [PMID: 38250843 PMCID: PMC10819235 DOI: 10.3390/vaccines12010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Viruses have threatened human lives for decades, causing both chronic and acute infections accompanied by mild to severe symptoms. During the long journey of confrontation, humans have developed intricate immune systems to combat viral infections. In parallel, vaccines are invented and administrated to induce strong protective immunity while generating few adverse effects. With advancements in biochemistry and biophysics, different kinds of vaccines in versatile forms have been utilized to prevent virus infections, although the safety and effectiveness of these vaccines are diverse from each other. In this review, we first listed and described major pathogenic viruses and their pandemics that emerged in the past two centuries. Furthermore, we summarized the distinctive characteristics of different antiviral vaccines and adjuvants. Subsequently, in the main body, we reviewed recent advances of nanoparticles in the development of next-generation vaccines against influenza viruses, coronaviruses, HIV, hepatitis viruses, and many others. Specifically, we described applications of self-assembling protein polymers, virus-like particles, nano-carriers, and nano-adjuvants in antiviral vaccines. We also discussed the therapeutic potential of nanoparticles in developing safe and effective mucosal vaccines. Nanoparticle techniques could be promising platforms for developing broad-spectrum, preventive, or therapeutic antiviral vaccines.
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Affiliation(s)
- Sen Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Meilin Hu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Xiaoqing Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xingyu Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Tao Chen
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Yiqiang Zhu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Taizhen Liang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Shiqi Xiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Peiwen Li
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Xiancai Ma
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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22
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Baboo S, Diedrich JK, Torres JL, Copps J, Singh B, Garrett PT, Ward AB, Paulson JC, Yates JR. Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539897. [PMID: 37214937 PMCID: PMC10197516 DOI: 10.1101/2023.05.08.539897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bhavya Singh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Patrick T. Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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23
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Lusiany T, Terada T, Kishikawa JI, Hirose M, Chen DV, Sugihara F, Ismanto HS, van Eerden FJ, Li S, Kato T, Arase H, Yoshiharu M, Okada M, Standley DM. Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies. Viruses 2023; 15:2421. [PMID: 38140662 PMCID: PMC10747171 DOI: 10.3390/v15122421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding surface, have been found to augment ACE2 binding and enhance SARS-CoV-2 infection. Notably, these antibodies exert their effect independently of the antibody fragment crystallizable (Fc) region, distinguishing their mode of action from previously described antibody-dependent infection-enhancing (ADE) mechanisms. Building upon previous hypotheses and experimental evidence, we propose that these NTD-targeting infection-enhancing antibodies (NIEAs) achieve their effect through the crosslinking of neighboring spike proteins. In this study, we present refined structural models of NIEA fragment antigen-binding region (Fab)-NTD complexes, supported by molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Furthermore, we provide direct evidence confirming the crosslinking of spike NTDs by NIEAs. Collectively, our findings advance our understanding of the molecular mechanisms underlying NIEAs and their impact on SARS-CoV-2 infection.
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Affiliation(s)
- Tina Lusiany
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan;
| | - Jun-ichi Kishikawa
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Mika Hirose
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - David Virya Chen
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Fuminori Sugihara
- Core Facility, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka 565-0871, Japan;
| | - Hendra Saputra Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Floris J. van Eerden
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Takayuki Kato
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan;
- Department of Immunochemistry, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Matsuura Yoshiharu
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Masato Okada
- Center for Advanced Modalities and DDS, Osaka University, 2-8 Yamadaoka, Suita 565-0871, Japan;
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
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24
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Lee IJ, Lan YH, Wu PY, Wu YW, Chen YH, Tseng SC, Kuo TJ, Sun CP, Jan JT, Ma HH, Liao CC, Liang JJ, Ko HY, Chang CS, Liu WC, Ko YA, Chen YH, Sie ZL, Tsung SI, Lin YL, Wang IH, Tao MH. A receptor-binding domain-based nanoparticle vaccine elicits durable neutralizing antibody responses against SARS-CoV-2 and variants of concern. Emerg Microbes Infect 2023; 12:2149353. [PMID: 36395071 PMCID: PMC9793938 DOI: 10.1080/22221751.2022.2149353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Numerous vaccines have been developed to address the current COVID-19 pandemic, but safety, cross-neutralizing efficacy, and long-term protectivity of currently approved vaccines are still important issues. In this study, we developed a subunit vaccine, ASD254, by using a nanoparticle vaccine platform to encapsulate the SARS-CoV-2 spike receptor-binding domain (RBD) protein. As compared with the aluminum-adjuvant RBD vaccine, ASD254 induced higher titers of RBD-specific antibodies and generated 10- to 30-fold more neutralizing antibodies. Mice vaccinated with ASD254 showed protective immune responses against SARS-CoV-2 challenge, with undetectable infectious viral loads and reduced typical lesions in lung. Besides, neutralizing antibodies in vaccinated mice lasted for at least one year and were effective against various SARS-CoV-2 variants of concern, including B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Furthermore, particle size, polydispersity index, and zeta-potential of ASD254 remained stable after 8-month storage at 4°C. Thus, ASD254 is a promising nanoparticle vaccine with good immunogenicity and stability to be developed as an effective vaccine option in controlling upcoming waves of COVID-19.
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Affiliation(s)
- I-Jung Lee
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Hua Lan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ping-Yi Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yan-Wei Wu
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Hung Chen
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Che Tseng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tzu-Jiun Kuo
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Cheng-Pu Sun
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Hua Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hui-Ying Ko
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chih-Shin Chang
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Chun Liu
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-An Ko
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Yen-Hui Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Zong-Lin Sie
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Szu-I Tsung
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan,Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - I-Hsuan Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Mi-Hua Tao
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan,Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan, Mi-Hua Tao Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; Biomedical Translation Research Center, Academia Sinica, Taipei115, Taiwan
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25
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Chen F, Zhang M, Yang F, Wang L, Liu J, Liu J, Pang Y. Dual-Antigen-Displaying Nanovaccines Elicit Synergistic Immunoactivation for Treating Cancer and Preventing Infectious Complications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2307748. [PMID: 38037689 DOI: 10.1002/smll.202307748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/30/2023] [Indexed: 12/02/2023]
Abstract
As one of the most common complications, infection causes the majority of mortality in cancer patients. However, therapeutic strategies that can simultaneously suppress tumors and protect patients from infection have been rarely reported. Here, the use of dual-antigen-displaying nanovaccines (DADNs) is described to elicit synergistic immunoactivation for treating cancer and preventing infectious complications. DADNs are prepared by wrapping immunoadjuvant-loaded nanoparticles with a hybrid coating, which is fused from cell membranes that are separately genetically engineered to express tumor and infectious pathogenic antigens. Due to the presence of a dual-antigen combination, DADNs are able to promote the maturation of dendritic cells and more importantly to trigger cross-presentation of both combined antigens. During in vivo investigations, we find that DADNs can reverse immunosuppression by stimulating tumor-associated antigen-specific T-cell responses, resulting in significantly delayed tumor growth in mice. These nanovaccines also elicit effective protective immunity against tumor challenges and induce robust production of pathogenic antigen-specific immunoglobulin G antibody in a prophylactic study. This work offers a unique approach to develop dual-mode vaccines, which are promising for synchronously treating cancer and preventing infection.
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Affiliation(s)
- Fangjie Chen
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer Renji Hospital School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Lung Cancer Institute, Jinan, Shandong, 250117, China
| | - Mengmeng Zhang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer Renji Hospital School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fengmin Yang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer Renji Hospital School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lu Wang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer Renji Hospital School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jinyao Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer Renji Hospital School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Yan Pang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China
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26
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Bamberger C, Pankow S, Martínez-Bartolomé S, Diedrich JK, Park RSK, Yates JR. Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein. J Proteome Res 2023; 22:3742-3753. [PMID: 37939376 DOI: 10.1021/acs.jproteome.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The β-coronavirus SARS-CoV-2 causes severe acute respiratory syndrome (COVID-19) in humans. It enters and infects epithelial airway cells upon binding of the receptor binding domain (RBD) of the virus entry protein spike to the host receptor protein Angiotensin Converting Enzyme 2 (ACE2). Here, we used coimmunoprecipitation coupled with bottom-up mass spectrometry to identify host proteins that engaged with the spike protein in human bronchial epithelial cells (16HBEo-). We found that the spike protein bound to extracellular laminin and thrombospondin and endoplasmatic reticulum (ER)-resident DJB11 and FBX2 proteins. The ER-resident proteins UGGT1, CALX, HSP7A, and GRP78/BiP bound preferentially to the original Wuhan D614 over the mutated G614 spike protein in the more rapidly spreading Alpha SARS-CoV-2 strain. The increase in protein binding to the D614 spike might be explained by higher accessibility of cryptic sites in "RDB open" and "S2 only" D614 spike protein conformations and may enable SARS-CoV-2 to infect additional, ACE2-negative cell types. Moreover, a novel proteome-based cell type set enrichment analysis (pCtSEA) found that host factors like laminin might render additional cell types such as macrophages and epithelial cells in the nephron permissive to SARS-CoV-2 infection.
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Affiliation(s)
- Casimir Bamberger
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Salvador Martínez-Bartolomé
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Robin S K Park
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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27
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Sun C, Kang YF, Fang XY, Liu YN, Bu GL, Wang AJ, Li Y, Zhu QY, Zhang H, Xie C, Kong XW, Peng YJ, Lin WJ, Zhou L, Chen XC, Lu ZZ, Xu HQ, Hong DC, Zhang X, Zhong L, Feng GK, Zeng YX, Xu M, Zhong Q, Liu Z, Zeng MS. A gB nanoparticle vaccine elicits a protective neutralizing antibody response against EBV. Cell Host Microbe 2023; 31:1882-1897.e10. [PMID: 37848029 DOI: 10.1016/j.chom.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 08/17/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Epstein-Barr virus (EBV) is a global public health concern, as it is known to cause multiple diseases while also being etiologically associated with a wide range of epithelial and lymphoid malignancies. Currently, there is no available prophylactic vaccine against EBV. gB is the EBV fusion protein that mediates viral membrane fusion and participates in host recognition, making it critical for EBV infection in both B cells and epithelial cells. Here, we present a gB nanoparticle, gB-I53-50 NP, that displays multiple copies of gB. Compared with the gB trimer, gB-I53-50 NP shows improved structural integrity and stability, as well as enhanced immunogenicity in mice and non-human primate (NHP) preclinical models. Immunization and passive transfer demonstrate a robust and durable protective antibody response that protects humanized mice against lethal EBV challenge. This vaccine candidate demonstrates significant potential in preventing EBV infection, providing a possible platform for developing prophylactic vaccines for EBV.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Yin-Feng Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Xin-Yan Fang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yi-Na Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Ao-Jie Wang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Qian-Ying Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Hua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China; MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Xiang-Wei Kong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Yong-Jian Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Wen-Jie Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Ling Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Xin-Chun Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Zheng-Zhou Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Hui-Qin Xu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Dong-Chun Hong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Xiao Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Ling Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Guo-Kai Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Miao Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China.
| | - Zheng Liu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China.
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Patel N, Trost JF, Guebre-Xabier M, Zhou H, Norton J, Jiang D, Cai Z, Zhu M, Marchese AM, Greene AM, Mallory RM, Kalkeri R, Dubovsky F, Smith G. XBB.1.5 spike protein COVID-19 vaccine induces broadly neutralizing and cellular immune responses against EG.5.1 and emerging XBB variants. Sci Rep 2023; 13:19176. [PMID: 37932354 PMCID: PMC10628164 DOI: 10.1038/s41598-023-46025-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023] Open
Abstract
Monovalent SARS-CoV-2 Prototype (Wuhan-Hu-1) and bivalent (Prototype + BA.4/5) COVID-19 vaccines have demonstrated a waning of vaccine-mediated immunity highlighted by lower neutralizing antibody responses against SARS-CoV-2 Omicron XBB sub-variants. The reduction of humoral immunity due to the rapid evolution of SARS-CoV-2 has signaled the need for an update to vaccine composition. A strain change for all authorized/approved vaccines to a monovalent composition with Omicron subvariant XBB.1.5 has been supported by the WHO, EMA, and FDA. Here, we demonstrate that immunization with a monovalent recombinant spike protein COVID-19 vaccine (Novavax, Inc.) based on the subvariant XBB.1.5 induces neutralizing antibodies against XBB.1.5, XBB.1.16, XBB.2.3, EG.5.1, and XBB.1.16.6 subvariants, promotes higher pseudovirus neutralizing antibody titers than bivalent (Prototype + XBB.1.5) vaccine, induces SARS-CoV-2 spike-specific Th1-biased CD4 + T-cell responses against XBB subvariants, and robustly boosts antibody responses in mice and nonhuman primates primed with a variety of monovalent and bivalent vaccines. Together, these data support updating the Novavax vaccine to a monovalent XBB.1.5 formulation for the 2023-2024 COVID-19 vaccination campaign.
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29
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Mo C, Li X, Wu Q, Fan Y, Liu D, Zhu Y, Yang Y, Liao X, Zhou Z, Zhou L, Li Q, Zhang Q, Liu W, Zhou R, Tian X. SARS-CoV-2 mRNA vaccine requires signal peptide to induce antibody responses. Vaccine 2023; 41:6863-6869. [PMID: 37821314 DOI: 10.1016/j.vaccine.2023.09.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
New SARS-CoV-2 variants continue to prevail worldwide, and effective vaccines are needed to prevent an epidemic. mRNA vaccines are gradually being applied to the prevention and control of infectious diseases with significant safety and effectiveness. The spike (S) protein of SARS-CoV-2 is the main target of mRNA vaccine design, but the impact of the signal peptide (SP), transmembrane region (TM), and cytoplasmic tail (CT) on mRNA vaccine remains unclear. In this study, we constructed three forms of mRNA vaccines related to the S protein: full-length, deletion of the TM and CT, and simultaneous deletion of the SP, TM and CT, and compared their immunogenicity. Our experimental data show that full-length S protein and deletion of the TM and CT could effectively induce neutralizing antibody production in mice, while S protein without the SP and TM could not. This indicates that the S protein SP is necessary for the design of mRNA vaccine.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Mice
- COVID-19 Vaccines/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Protein Sorting Signals/genetics
- mRNA Vaccines/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- COVID-19/prevention & control
- COVID-19/immunology
- Mice, Inbred BALB C
- Female
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/administration & dosage
- Humans
- Immunogenicity, Vaccine
- Antibody Formation/immunology
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Affiliation(s)
- Chuncong Mo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Xiao Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Qianying Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ye Fan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yuhui Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yujie Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xiaohong Liao
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Liling Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Qiuru Li
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Qiong Zhang
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China.
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
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30
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Magazine N, Zhang T, Bungwon AD, McGee MC, Wu Y, Veggiani G, Huang W. Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564184. [PMID: 37961687 PMCID: PMC10634854 DOI: 10.1101/2023.10.26.564184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the toll-like receptors (TLRs), B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.
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Affiliation(s)
- Nicholas Magazine
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Anang D. Bungwon
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michael C. McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yingying Wu
- Department of Mathematics, University of Houston, Houston, TX 77204, USA
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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31
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Wilkinson B, Patel KS, Smith K, Walker R, Wang C, Greene AM, Smith G, Smith ER, Gurwith M, Chen RT. A Brighton Collaboration standardized template with key considerations for a benefit/risk assessment for the Novavax COVID-19 Vaccine (NVX-CoV2373), a recombinant spike protein vaccine with Matrix-M adjuvant to prevent disease caused by SARS-CoV-2 viruses. Vaccine 2023; 41:6762-6773. [PMID: 37739888 DOI: 10.1016/j.vaccine.2023.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 09/24/2023]
Abstract
Novavax, a global vaccine company, began evaluating NVX-CoV2373 in human studies in May 2020 and the pivotal placebo-controlled phase 3 studies started in November 2020; five clinical studies provided adult and adolescent clinical data for over 31,000 participants who were administered NVX-CoV2373. This extensive data has demonstrated a well-tolerated response to NVX-CoV2373 and high vaccine efficacy against mild, moderate, or severe COVID-19 using a two-dose series (Dunkle et al., 2022) [1], (Heath et al., 2021) [2], (Keech et al., 2020) [3], (Mallory et al., 2022) [4]. The most common adverse events seen after administration with NVX-CoV2373 were injection site tenderness, injection site pain, fatigue, myalgia, headache, malaise, arthralgia, nausea, or vomiting. In addition, immunogenicity against variants of interest (VOI) and variants of concern (VOC) was established with high titers of ACE2 receptor-inhibiting and neutralizing antibodies in these studies (EMA, 2022) [5], (FDA, 2023) [6]. Further studies on correlates of protection determined that titers of anti-Spike IgG and neutralizing antibodies correlated with efficacy against symptomatic COVID-19 established in clinical trials (p < 0.001 for recombinant protein vaccine and p = 0.005 for mRNA vaccines for IgG levels) (Fong et al., 2022) [7]. Administration of a booster dose of the recombinant protein vaccine approximately 6 months following the primary two-dose series resulted in substantial increases in humoral antibodies against both the prototype strain and all evaluated variants, similar to or higher than the antibody levels observed in phase 3 studies that were associated with high vaccine efficacy (Dunkle et al., 2022) [1], (Mallory et al., 2022) [4]. These findings, together with the well tolerated safety profile, support use of the recombinant protein vaccine as primary series and booster regimens.
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Affiliation(s)
| | | | | | | | | | | | | | - Emily R Smith
- Brighton Collaboration, a program of the Task Force for Global Health, Decatur, GA, USA.
| | - Marc Gurwith
- Brighton Collaboration, a program of the Task Force for Global Health, Decatur, GA, USA
| | - Robert T Chen
- Brighton Collaboration, a program of the Task Force for Global Health, Decatur, GA, USA
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32
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Ni T, Mendonça L, Zhu Y, Howe A, Radecke J, Shah PM, Sheng Y, Krebs AS, Duyvesteyn HM, Allen E, Lambe T, Bisset C, Spencer A, Morris S, Stuart DI, Gilbert S, Zhang P. ChAdOx1 COVID vaccines express RBD open prefusion SARS-CoV-2 spikes on the cell surface. iScience 2023; 26:107882. [PMID: 37766989 PMCID: PMC10520439 DOI: 10.1016/j.isci.2023.107882] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/18/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proven to be an effective means of decreasing COVID-19 mortality, hospitalization rates, and transmission. One of the vaccines deployed worldwide is ChAdOx1 nCoV-19, which uses an adenovirus vector to drive the expression of the original SARS-CoV-2 spike on the surface of transduced cells. Using cryo-electron tomography and subtomogram averaging, we determined the native structures of the vaccine product expressed on cell surfaces in situ. We show that ChAdOx1-vectored vaccines expressing the Beta SARS-CoV-2 variant produce abundant native prefusion spikes predominantly in one-RBD-up conformation. Furthermore, the ChAdOx1-vectored HexaPro-stabilized spike yields higher cell surface expression, enhanced RBD exposure, and reduced shedding of S1 compared to the wild type. We demonstrate in situ structure determination as a powerful means for studying antigen design options in future vaccine development against emerging novel SARS-CoV-2 variants and broadly against other infectious viruses.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Luiza Mendonça
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Yanan Zhu
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Andrew Howe
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Julika Radecke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Pranav M. Shah
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Yuewen Sheng
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Anna-Sophia Krebs
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Helen M.E. Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Elizabeth Allen
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Cameron Bisset
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Alexandra Spencer
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Susan Morris
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, OX3 7TY, UK
| | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, OX3 7TY, UK
| | - Sarah Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford OX3 7BN, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, OX3 7TY, UK
| | - Peijun Zhang
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
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33
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites. Viruses 2023; 15:2073. [PMID: 37896850 PMCID: PMC10612107 DOI: 10.3390/v15102073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full-length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results are significant for understanding the functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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Affiliation(s)
- Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75275, USA; (S.X.); (P.T.)
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75275, USA; (S.X.); (P.T.)
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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Katarzyna Lesiów M, Witwicki M, Tan NK, Graziotto ME, New EJ. Unravelling the Mystery of COVID-19 Pathogenesis: Spike Protein and Cu Can Synergize to Trigger ROS Production. Chemistry 2023; 29:e202301530. [PMID: 37414735 DOI: 10.1002/chem.202301530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The COVID-19 pandemic has had a devastating impact on global health, highlighting the need to understand how the SARS-CoV-2 virus damages the lungs in order to develop effective treatments. Recent research has shown that patients with COVID-19 experience severe oxidative damage to various biomolecules. We propose that the overproduction of reactive oxygen species (ROS) in SARS-CoV-2 infection involves an interaction between copper ions and the virus's spike protein. We tested two peptide fragments, Ac-ELDKYFKNH-NH2 (L1) and Ac-WSHPQFEK-NH2 (L2), derived from the spike protein of the Wuhan strain and the β variant, respectively, and found that they bind Cu(II) ions and form a three-nitrogen complexes at lung pH. Our research demonstrates that these complexes trigger the overproduction of ROS, which can break both DNA strands and transform DNA into its linear form. Using A549 cells, we demonstrated that ROS overproduction occurs in the mitochondria, not in the cytoplasm. Our findings highlight the importance of the interaction between copper ions and the virus's spike protein in the development of lung damage and may aid in the development of therapeutic procedures.
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Affiliation(s)
| | - Maciej Witwicki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Nian Kee Tan
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for, Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Elizabeth Joy New
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for, Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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Wang J, Zhang Y, Liu C, Zha W, Dong S, Wang Y, Jiang Y, Xing H, Li X. Trivalent mRNA Vaccine against SARS-CoV-2 and Variants with Effective Immunization. Mol Pharm 2023; 20:4971-4983. [PMID: 37699256 DOI: 10.1021/acs.molpharmaceut.2c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
mRNA vaccines encoding a single spike protein effectively prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the emergence of SARS-CoV-2 variants leads to a wide range of immune evasion. Herein, a unique trivalent mRNA vaccine based on ancestral SARS-CoV-2, Delta, and Omicron variant spike receptor-binding domain (RBD) mRNAs was developed to tackle the immune evasion of the variants. First, three RBD mRNAs of SARS-CoV-2, Delta, and Omicron were coencapsulated into lipid nanoparticles (LNPs) by using microfluidic technology. After that, the physicochemical properties and time-dependent storage stability of the trivalent mRNA vaccine nanoformulation were tested by using dynamic light scattering (DLS). In vitro, the trivalent mRNA vaccine exhibited better lysosomal escape ability, transfection efficiency, and biocompatibility than did the commercial transfection reagent Lipo3000. In addition, Western blot analyses confirmed that the three RBD proteins can be detected in cells transfected with the trivalent mRNA vaccine. Furthermore, ex vivo imaging analysis indicated that the livers of BALB/c mice had the strongest protein expression levels after intramuscular (IM) injection. Using a prime-boost strategy, this trivalent vaccine elicited robust humoral and T-cell immune responses in both the high-dose and low-dose groups and showed no toxicity in BALB/c mice. Three specific IgG antibodies in the high-dose group against SARS-CoV-2, Delta, and Omicron variants approached ∼1/1,833,333, ∼1/1,866,667, and ∼1/925,000, respectively. Taken together, two doses of inoculation with the trivalent mRNA vaccine may provide broad and effective immunization responses against SARS-CoV-2 and variants.
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Affiliation(s)
- Ji Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Yanhao Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Chao Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Wenhui Zha
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Shuo Dong
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Yang Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Yuhao Jiang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Hanlei Xing
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Xinsong Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
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Stuible M, Schrag JD, Sheff J, Zoubchenok D, Lord-Dufour S, Cass B, L'Abbé D, Pelletier A, Rossotti MA, Tanha J, Gervais C, Maurice R, El Bakkouri M, Acchione M, Durocher Y. Influence of variant-specific mutations, temperature and pH on conformations of a large set of SARS-CoV-2 spike trimer vaccine antigen candidates. Sci Rep 2023; 13:16498. [PMID: 37779126 PMCID: PMC10543594 DOI: 10.1038/s41598-023-43661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023] Open
Abstract
SARS-CoV-2 subunit vaccines continue to be the focus of intense clinical development worldwide. Protein antigens in these vaccines most commonly consist of the spike ectodomain fused to a heterologous trimerization sequence, designed to mimic the compact, prefusion conformation of the spike on the virus surface. Since 2020, we have produced dozens of such constructs in CHO cells, consisting of spike variants with different mutations fused to different trimerization sequences. This set of constructs displayed notable conformational heterogeneity, with two distinct trimer species consistently detected by analytical size exclusion chromatography. A recent report showed that spike ectodomain fusion constructs can adopt an alternative trimer conformation consisting of loosely associated ectodomain protomers. Here, we applied multiple biophysical and immunological techniques to demonstrate that this alternative conformation is formed to a significant extent by several SARS-CoV-2 variant spike proteins. We have also examined the influence of temperature and pH, which can induce inter-conversion of the two forms. The substantial structural differences between these trimer types may impact their performance as vaccine antigens.
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Affiliation(s)
- Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Joey Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Daria Zoubchenok
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Simon Lord-Dufour
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Brian Cass
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Denis L'Abbé
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Alex Pelletier
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Christian Gervais
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Roger Maurice
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Majida El Bakkouri
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Mauro Acchione
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.
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Thadani NN, Gurev S, Notin P, Youssef N, Rollins NJ, Ritter D, Sander C, Gal Y, Marks DS. Learning from prepandemic data to forecast viral escape. Nature 2023; 622:818-825. [PMID: 37821700 PMCID: PMC10599991 DOI: 10.1038/s41586-023-06617-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses to facilitate vaccine and therapeutic design. However, current strategies for viral evolution prediction are not available early in a pandemic-experimental approaches require host polyclonal antibodies to test against1-16, and existing computational methods draw heavily from current strain prevalence to make reliable predictions of variants of concern17-19. To address this, we developed EVEscape, a generalizable modular framework that combines fitness predictions from a deep learning model of historical sequences with biophysical and structural information. EVEscape quantifies the viral escape potential of mutations at scale and has the advantage of being applicable before surveillance sequencing, experimental scans or three-dimensional structures of antibody complexes are available. We demonstrate that EVEscape, trained on sequences available before 2020, is as accurate as high-throughput experimental scans at anticipating pandemic variation for SARS-CoV-2 and is generalizable to other viruses including influenza, HIV and understudied viruses with pandemic potential such as Lassa and Nipah. We provide continually revised escape scores for all current strains of SARS-CoV-2 and predict probable further mutations to forecast emerging strains as a tool for continuing vaccine development ( evescape.org ).
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Affiliation(s)
- Nicole N Thadani
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah Gurev
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Pascal Notin
- OATML Group, Department of Computer Science, University of Oxford, Oxford, UK
| | - Noor Youssef
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nathan J Rollins
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Seismic Therapeutic, Watertown, MA, USA
| | - Daniel Ritter
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Chris Sander
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yarin Gal
- OATML Group, Department of Computer Science, University of Oxford, Oxford, UK
| | - Debora S Marks
- Marks Group, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Verkhivker G, Alshahrani M, Gupta G. Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites. Viruses 2023; 15:2009. [PMID: 37896786 PMCID: PMC10610873 DOI: 10.3390/v15102009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron variants. By using a combination of atomistic simulations, a dynamics network analysis, and an allostery-guided network screening of binding pockets in the conformational ensembles of the BA.1 and BA.2 spike conformations, we identified all experimentally known allosteric sites and discovered significant variant-specific differences in the distribution of binding sites in the BA.1 and BA.2 trimers. This study provided a structural characterization of the predicted cryptic pockets and captured the experimentally known allosteric sites, revealing the critical role of conformational plasticity in modulating the distribution and cross-talk between functional binding sites. We found that mutational and dynamic changes in the BA.1 variant can induce the remodeling and stabilization of a known druggable pocket in the N-terminal domain, while this pocket is drastically altered and may no longer be available for ligand binding in the BA.2 variant. Our results predicted the experimentally known allosteric site in the receptor-binding domain that remains stable and ranks as the most favorable site in the conformational ensembles of the BA.2 variant but could become fragmented and less probable in BA.1 conformations. We also uncovered several cryptic pockets formed at the inter-domain and inter-protomer interface, including functional regions of the S2 subunit and stem helix region, which are consistent with the known role of pocket residues in modulating conformational transitions and antibody recognition. The results of this study are particularly significant for understanding the dynamic and network features of the universe of available binding pockets in spike proteins, as well as the effects of the Omicron-variant-specific modulation of preferential druggable pockets. The exploration of predicted druggable sites can present a new and previously underappreciated opportunity for therapeutic interventions for Omicron variants through the conformation-selective and variant-specific targeting of functional sites involved in allosteric changes.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557205. [PMID: 37745525 PMCID: PMC10515794 DOI: 10.1101/2023.09.11.557205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results of are significant for understanding functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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Sauvageau J, Koyuturk I, St Michael F, Brochu D, Goneau MF, Schoenhofen I, Perret S, Star A, Robotham A, Haqqani A, Kelly J, Gilbert M, Durocher Y. Simplifying glycan monitoring of complex antigens such as the SARS-CoV-2 spike to accelerate vaccine development. Commun Chem 2023; 6:189. [PMID: 37684364 PMCID: PMC10491790 DOI: 10.1038/s42004-023-00988-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Glycosylation is a key quality attribute that must be closely monitored for protein therapeutics. Established assays such as HILIC-Fld of released glycans and LC-MS of glycopeptides work well for glycoproteins with a few glycosylation sites but are less amenable for those with multiple glycosylation sites, resulting in complex datasets that are time consuming to generate and difficult to analyze. As part of efforts to improve preparedness for future pandemics, researchers are currently assessing where time can be saved in the vaccine development and production process. In this context, we evaluated if neutral and acidic monosaccharides analysis via HPAEC-PAD could be used as a rapid and robust alternative to LC-MS and HILIC-Fld for monitoring glycosylation between protein production batches. Using glycoengineered spike proteins we show that the HPAEC-PAD monosaccharide assays could quickly and reproducibly detect both major and minor glycosylation differences between batches. Moreover, the monosaccharide results aligned well with those obtained by HILIC-Fld and LC-MS.
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Affiliation(s)
- Janelle Sauvageau
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada.
| | - Izel Koyuturk
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Canada
- Human Health Therapeutics Research Centre, National Research Council of Canada, 6100 Avenue Royalmount, Montréal, QC, H4P 2R2, Canada
| | - Frank St Michael
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Denis Brochu
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Marie-France Goneau
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Ian Schoenhofen
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Sylvie Perret
- Human Health Therapeutics Research Centre, National Research Council of Canada, 6100 Avenue Royalmount, Montréal, QC, H4P 2R2, Canada
| | - Alexandra Star
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Arsalan Haqqani
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - John Kelly
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Michel Gilbert
- Human Health Therapeutics Research Centre, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON, K1A 0R6, Canada
| | - Yves Durocher
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Canada
- Human Health Therapeutics Research Centre, National Research Council of Canada, 6100 Avenue Royalmount, Montréal, QC, H4P 2R2, Canada
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Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X. Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Life Sci Alliance 2023; 6:e202201796. [PMID: 37402591 PMCID: PMC10320017 DOI: 10.26508/lsa.202201796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions.
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Affiliation(s)
- Xixi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yutong Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qian Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lutang Fu
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Peiyi Wang
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Xiaolin Zhong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Liang Jin
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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Soto J, Linsley C, Song Y, Chen B, Fang J, Neyyan J, Davila R, Lee B, Wu B, Li S. Engineering Materials and Devices for the Prevention, Diagnosis, and Treatment of COVID-19 and Infectious Diseases. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2455. [PMID: 37686965 PMCID: PMC10490511 DOI: 10.3390/nano13172455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
Following the global spread of COVID-19, scientists and engineers have adapted technologies and developed new tools to aid in the fight against COVID-19. This review discusses various approaches to engineering biomaterials, devices, and therapeutics, especially at micro and nano levels, for the prevention, diagnosis, and treatment of infectious diseases, such as COVID-19, serving as a resource for scientists to identify specific tools that can be applicable for infectious-disease-related research, technology development, and treatment. From the design and production of equipment critical to first responders and patients using three-dimensional (3D) printing technology to point-of-care devices for rapid diagnosis, these technologies and tools have been essential to address current global needs for the prevention and detection of diseases. Moreover, advancements in organ-on-a-chip platforms provide a valuable platform to not only study infections and disease development in humans but also allow for the screening of more effective therapeutics. In addition, vaccines, the repurposing of approved drugs, biomaterials, drug delivery, and cell therapy are promising approaches for the prevention and treatment of infectious diseases. Following a comprehensive review of all these topics, we discuss unsolved problems and future directions.
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Affiliation(s)
- Jennifer Soto
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chase Linsley
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yang Song
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Binru Chen
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jun Fang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Josephine Neyyan
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Raul Davila
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon Lee
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Benjamin Wu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department 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, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Alpuche-Lazcano SP, Stuible M, Akache B, Tran A, Kelly J, Hrapovic S, Robotham A, Haqqani A, Star A, Renner TM, Blouin J, Maltais JS, Cass B, Cui K, Cho JY, Wang X, Zoubchenok D, Dudani R, Duque D, McCluskie MJ, Durocher Y. Preclinical evaluation of manufacturable SARS-CoV-2 spike virus-like particles produced in Chinese Hamster Ovary cells. COMMUNICATIONS MEDICINE 2023; 3:116. [PMID: 37612423 PMCID: PMC10447459 DOI: 10.1038/s43856-023-00340-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/25/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND As the COVID-19 pandemic continues to evolve, novel vaccines need to be developed that are readily manufacturable and provide clinical efficacy against emerging SARS-CoV-2 variants. Virus-like particles (VLPs) presenting the spike antigen at their surface offer remarkable benefits over other vaccine antigen formats; however, current SARS-CoV-2 VLP vaccines candidates in clinical development suffer from challenges including low volumetric productivity, poor spike antigen density, expression platform-driven divergent protein glycosylation and complex upstream/downstream processing requirements. Despite their extensive use for therapeutic protein manufacturing and proven ability to produce enveloped VLPs, Chinese Hamster Ovary (CHO) cells are rarely used for the commercial production of VLP-based vaccines. METHODS Using CHO cells, we aimed to produce VLPs displaying the full-length SARS-CoV-2 spike. Affinity chromatography was used to capture VLPs released in the culture medium from engineered CHO cells expressing spike. The structure, protein content, and glycosylation of spikes in VLPs were characterized by several biochemical and biophysical methods. In vivo, the generation of neutralizing antibodies and protection against SARS-CoV-2 infection was tested in mouse and hamster models. RESULTS We demonstrate that spike overexpression in CHO cells is sufficient by itself to generate high VLP titers. These VLPs are evocative of the native virus but with at least three-fold higher spike density. In vivo, purified VLPs elicit strong humoral and cellular immunity at nanogram dose levels which grant protection against SARS-CoV-2 infection. CONCLUSIONS Our results show that CHO cells are amenable to efficient manufacturing of high titers of a potently immunogenic spike protein-based VLP vaccine antigen.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Bassel Akache
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - John Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Dr, Ottawa, ON, K1A 0R6, Canada
| | - Sabahudin Hrapovic
- Aquatic and Crop Resources Development Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Dr, Ottawa, ON, K1A 0R6, Canada
| | - Arsalan Haqqani
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Dr, Ottawa, ON, K1A 0R6, Canada
| | - Alexandra Star
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Dr, Ottawa, ON, K1A 0R6, Canada
| | - Tyler M Renner
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Julie Blouin
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Jean-Sébastien Maltais
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Brian Cass
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Kai Cui
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada
| | - Jae-Young Cho
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada
| | - Xinyu Wang
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada
| | - Daria Zoubchenok
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Renu Dudani
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Diana Duque
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Michael J McCluskie
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.
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Huang SH, Chen YT, Lin XY, Ly YY, Lien ST, Chen PH, Wang CT, Wu SC, Chen CC, Lin CY. In silico prediction of immune-escaping hot spots for future COVID-19 vaccine design. Sci Rep 2023; 13:13468. [PMID: 37596329 PMCID: PMC10439115 DOI: 10.1038/s41598-023-40741-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
The COVID-19 pandemic has had a widespread impact on a global scale, and the evolution of considerable dominants has already taken place. Some variants contained certain key mutations located on the receptor binding domain (RBD) of spike protein, such as E484K and N501Y. It is increasingly worrying that these variants could impair the efficacy of current vaccines or therapies. Therefore, analyzing and predicting the high-risk mutations of SARS-CoV-2 spike glycoprotein is crucial to design future vaccines against the different variants. In this work, we proposed an in silico approach, immune-escaping score (IES), to predict high-risk immune-escaping hot spots on the receptor-binding domain (RBD), implemented through integrated delta binding free energy measured by computational mutagenesis of spike-antibody complexes and mutation frequency calculated from viral genome sequencing data. We identified 23 potentially immune-escaping mutations on the RBD by using IES, nine of which occurred in omicron variants (R346K, K417N, N440K, L452Q, L452R, S477N, T478K, F490S, and N501Y), despite our dataset being curated before the omicron first appeared. The highest immune-escaping score (IES = 1) was found for E484K, which agrees with recent studies stating that the mutation significantly reduced the efficacy of neutralization antibodies. Furthermore, our predicted delta binding free energy and IES show a high correlation with high-throughput deep mutational scanning data (Pearson's r = 0.70) and experimentally measured neutralization titers data (mean Pearson's r = -0.80). In summary, our work presents a new method to identify the potentially immune-escaping mutations on the RBD and provides valuable insights into future COVID-19 vaccine design.
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Affiliation(s)
| | | | | | - Yi-Yi Ly
- Graphen Inc., New York, NY, 10110, USA
| | | | | | | | - Suh-Chin Wu
- Adimmune Corp., Taichung City, 427003, Taiwan
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45
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Oliveira ASF, Shoemark DK, Davidson AD, Berger I, Schaffitzel C, Mulholland AJ. SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid. J Mol Cell Biol 2023; 15:mjad021. [PMID: 36990513 PMCID: PMC10563148 DOI: 10.1093/jmcb/mjad021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/07/2022] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
The SARS-CoV-2 spike protein contains a functionally important fatty acid (FA) binding site, which is also found in some other coronaviruses, e.g. SARS-CoV and MERS-CoV. The occupancy of the FA site by linoleic acid (LA) reduces infectivity by 'locking' the spike in a less infectious conformation. Here, we use dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations to compare the allosteric responses of spike variants to LA removal. D-NEMD simulations show that the FA site is coupled to other functional regions of the protein, e.g. the receptor-binding motif (RBM), N-terminal domain (NTD), furin cleavage site, and regions surrounding the fusion peptide. D-NEMD simulations also identify the allosteric networks connecting the FA site to these functional regions. The comparison between the wild-type spike and four variants (Alpha, Delta, Delta plus, and Omicron BA.1) shows that the variants differ significantly in their responses to LA removal. The allosteric connections to the FA site on Alpha are generally similar to those on the wild-type protein, with the exception of the RBM and the S71-R78 region, which show a weaker link to the FA site. In contrast, Omicron is the most different variant, exhibiting significant differences in the RBM, NTD, V622-L629, and furin cleavage site. These differences in the allosteric modulation may be of functional relevance, potentially affecting transmissibility and virulence. Experimental comparison of the effects of LA on SARS-CoV-2 variants, including emerging variants, is warranted.
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Affiliation(s)
- A Sofia F Oliveira
- School of Chemistry, Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS, UK
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Imre Berger
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- School of Chemistry, Max Planck Bristol Centre for Minimal Biology, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- School of Chemistry, Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS, UK
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46
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Fernandez Z, de Arruda Rodrigues R, Torres JM, Marcon GEB, de Castro Ferreira E, de Souza VF, Sarti EFB, Bertolli GF, Araujo D, Demarchi LHF, Lichs G, Zardin MU, Gonçalves CCM, Cuenca V, Favacho A, Guilhermino J, Dos Santos LR, de Araujo FR, Silva MR. Development and validity assessment of ELISA test with recombinant chimeric protein of SARS-CoV-2. J Immunol Methods 2023; 519:113489. [PMID: 37179011 PMCID: PMC10174469 DOI: 10.1016/j.jim.2023.113489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/07/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Serological tests developed for COVID-19 diagnostic are based on antibodies specific for SARS-CoV-2 antigens. Most of the antigens consist of a fragment or a whole amino acid sequence of the nucleocapsid or spike proteins. We evaluated a chimeric recombinant protein as an antigen in an ELISA test, using the most conserved and hydrophilic portions of the S1-subunit of the S and Nucleocapsid (N) proteins. These proteins, individually, indicated a suitable sensitivity of 93.6 and 100% and a specificity of 94.5 and 91.3%, respectively. However, our study with the chimera containing S1 and N proteins of SARS-CoV-2 suggested that the recombinant protein could better balance both the sensitivity (95.7%) and the specificity (95.5%) of the serological assay when comparing with the ELISA test using the antigens N and S1, individually. Accordingly, the chimera showed a high area under the ROC curve of 0.98 (CI 95% 0.958-1). Thus, our chimeric approach could be used to assess the natural exposure against SARS-CoV-2 virus over time, however, other tests will be necessary to better understand the behaviour of the chimera in samples from people with different vaccination doses and/or infected with different variants of the virus.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Daniel Araujo
- Instituto Integrado de Saúde-Universidade Federal de Mato Grosso do Sul, Brazil
| | | | - Gislene Lichs
- Laboratório Central de Saúde do Mato Grosso do Sul, Brazil
| | | | | | - Valter Cuenca
- Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul, Brazil
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Wang D, Baudys J, Osman SH, Barr JR. Analysis of the N-glycosylation profiles of the spike proteins from the Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2. Anal Bioanal Chem 2023:10.1007/s00216-023-04771-y. [PMID: 37354227 DOI: 10.1007/s00216-023-04771-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/26/2023]
Abstract
N-Glycosylation plays an important role in the structure and function of membrane and secreted proteins. Viral proteins used in cell entry are often extensively glycosylated to assist in protein folding, provide stability, and shield the virus from immune recognition by its host (described as a "glycan shield"). The SARS-CoV-2 spike protein (S) is a prime example, having 22 potential sites of N-glycosylation per protein protomer, as predicted from the primary sequence. In this report, we conducted mass spectrometric analysis of the N-glycosylation profiles of recombinant spike proteins derived from four common SARS-CoV-2 variants classified as Variant of Concern, including Alpha, Beta, Gamma, and Delta along with D614G variant spike as a control. Our data reveal that the amino acid substitutions and deletions between variants impact the abundance and type of glycans on glycosylation sites of the spike protein. Some of the N-glycosylation sequons in S show differences between SARS-CoV-2 variants in the distribution of glycan forms. In comparison with our previously reported site-specific glycan analysis on the S-D614G and its ancestral protein, glycan types on later variants showed high similarity on the site-specific glycan content to S-D614G. Additionally, we applied multiple digestion methods on each sample, and confirmed the results for individual glycosylation sites from different experiment conditions to improve the identification and quantification of glycopeptides. Detailed site-specific glycan analysis of a wide variety of SARS-CoV-2 variants provides useful information toward the understanding of the role of protein glycosylation on viral protein structure and function and development of effective vaccines and therapeutics.
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Affiliation(s)
- Dongxia Wang
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Jakub Baudys
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sarah H Osman
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barr
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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48
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Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
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Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
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49
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Halma MTJ, Plothe C, Marik P, Lawrie TA. Strategies for the Management of Spike Protein-Related Pathology. Microorganisms 2023; 11:1308. [PMID: 37317282 PMCID: PMC10222799 DOI: 10.3390/microorganisms11051308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
In the wake of the COVID-19 crisis, a need has arisen to prevent and treat two related conditions, COVID-19 vaccine injury and long COVID-19, both of which can trace at least part of their aetiology to the spike protein, which can cause harm through several mechanisms. One significant mechanism of harm is vascular, and it is mediated by the spike protein, a common element of the COVID-19 illness, and it is related to receiving a COVID-19 vaccine. Given the significant number of people experiencing these two related conditions, it is imperative to develop treatment protocols, as well as to consider the diversity of people experiencing long COVID-19 and vaccine injury. This review summarizes the known treatment options for long COVID-19 and vaccine injury, their mechanisms, and their evidentiary basis.
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Affiliation(s)
| | - Christof Plothe
- Center for Biophysical Osteopathy, Am Wegweiser 27, 55232 Alzey, Germany
| | - Paul Marik
- Front Line COVID-19 Critical Care Alliance (FLCCC), 2001 L St. NW Suite 500, Washington, DC 20036, USA;
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50
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Lorenz P, Steinbeck F, Mai F, Reisinger EC, Müller-Hilke B. A linear B-cell epitope close to the furin cleavage site within the S1 domain of SARS-CoV-2 Spike protein discriminates the humoral immune response of nucleic acid- and protein-based vaccine cohorts. Front Immunol 2023; 14:1192395. [PMID: 37228598 PMCID: PMC10203960 DOI: 10.3389/fimmu.2023.1192395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Background Understanding the humoral immune response towards viral infection and vaccination is instrumental in developing therapeutic tools to fight and restrict the viral spread of global pandemics. Of particular interest are the specificity and breadth of antibody reactivity in order to pinpoint immune dominant epitopes that remain immutable in viral variants. Methods We used profiling with peptides derived from the Spike surface glycoprotein of SARS-CoV-2 to compare the antibody reactivity landscapes between patients and different vaccine cohorts. Initial screening was done with peptide microarrays while detailed results and validation data were obtained using peptide ELISA. Results Overall, antibody patterns turned out to be individually distinct. However, plasma samples of patients conspicuously recognized epitopes covering the fusion peptide region and the connector domain of Spike S2. Both regions are evolutionarily conserved and are targets of antibodies that were shown to inhibit viral infection. Among vaccinees, we discovered an invariant Spike region (amino acids 657-671) N-terminal to the furin cleavage site that elicited a significantly stronger antibody response in AZD1222- and BNT162b2- compared to NVX-CoV2373-vaccinees. Conclusions Understanding the exact function of antibodies recognizing amino acid region 657-671 of SARS-CoV-2 Spike glycoprotein and why nucleic acid-based vaccines elicit different responses from protein-based ones will be helpful for future vaccine design.
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Affiliation(s)
- Peter Lorenz
- Institute of Immunology, Rostock University Medical Center, Rostock, Germany
| | - Felix Steinbeck
- Institute of Immunology, Rostock University Medical Center, Rostock, Germany
| | - Franz Mai
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Rostock, Germany
| | - Emil C. Reisinger
- Division of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Brigitte Müller-Hilke
- Institute of Immunology, Rostock University Medical Center, Rostock, Germany
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Rostock, Germany
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