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Endo HM, Bandeca SCS, Olchanheski LR, Schemczssen-Graeff Z, Pileggi M. Probiotics and the reduction of SARS-CoV-2 infection through regulation of host cell calcium dynamics. Life Sci 2024; 350:122784. [PMID: 38848939 DOI: 10.1016/j.lfs.2024.122784] [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: 01/16/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Calcium is a secondary messenger that interacts with several cellular proteins, regulates various physiological processes, and plays a role in diseases such as viral infections. Next-generation probiotics and live biotherapeutic products are linked to the regulation of intracellular calcium levels. Some viruses can manipulate calcium channels, pumps, and membrane receptors to alter calcium influx and promote virion production and release. In this study, we examined the use of bacteria for the prevention and treatment of viral diseases, such as coronavirus of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Vaccination programs have helped reduce disease severity; however, there is still a lack of well-recognized drug regimens for the clinical management of COVID-19. SARS-CoV-2 interacts with the host cell calcium (Ca2+), manipulates proteins, and disrupts Ca2+ homeostasis. This article explores how viruses exploit, create, or exacerbate calcium imbalances, and the potential role of probiotics in mitigating viral infections by modulating calcium signaling. Pharmacological strategies have been developed to prevent viral replication and block the calcium channels that serve as viral receptors. Alternatively, probiotics may interact with cellular calcium influx, such as Lactobacillus spp. The interaction between Akkermansia muciniphila and cellular calcium homeostasis is evident. A scientific basis for using probiotics to manipulate calcium channel activity needs to be established for the treatment and prevention of viral diseases while maintaining calcium homeostasis. In this review article, we discuss how intracellular calcium signaling can affect viral replication and explore the potential therapeutic benefits of probiotics.
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Affiliation(s)
- Hugo Massami Endo
- Environmental Microbiology Laboratory, Life Sciences and Health Institute, Structural and Molecular Biology, and Genetics Department, Ponta Grossa State University, Ponta Grossa, Brazil
| | | | - Luiz Ricardo Olchanheski
- Environmental Microbiology Laboratory, Life Sciences and Health Institute, Structural and Molecular Biology, and Genetics Department, Ponta Grossa State University, Ponta Grossa, Brazil
| | - Zelinda Schemczssen-Graeff
- Comparative Immunology Laboratory, Department of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Marcos Pileggi
- Environmental Microbiology Laboratory, Life Sciences and Health Institute, Structural and Molecular Biology, and Genetics Department, Ponta Grossa State University, Ponta Grossa, Brazil.
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2
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Beiter J, Voth GA. Making the cut: Multiscale simulation of membrane remodeling. Curr Opin Struct Biol 2024; 87:102831. [PMID: 38740001 PMCID: PMC11283976 DOI: 10.1016/j.sbi.2024.102831] [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: 02/19/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Biological membranes are dynamic heterogeneous materials, and their shape and organization are tightly coupled to the properties of the proteins in and around them. However, the length scales of lipid and protein dynamics are far below the size of membrane-bound organelles, much less an entire cell. Therefore, multiscale modeling approaches are often necessary to build a comprehensive picture of the interplay of these factors, and have provided critical insights into our understanding of membrane dynamics. Here, we review computational methods for studying membrane remodeling, as well as passive and active examples of protein-driven membrane remodeling. As the field advances towards the modeling of key aspects of organelles and whole cells - an increasingly accessible regime of study - we summarize here recent successes and offer comments on future trends.
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Affiliation(s)
- Jeriann Beiter
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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3
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Máthé D, Szalay G, Cseri L, Kis Z, Pályi B, Földes G, Kovács N, Fülöp A, Szepesi Á, Hajdrik P, Csomos A, Zsembery Á, Kádár K, Katona G, Mucsi Z, Rózsa BJ, Kovács E. Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye. Cell Mol Biol Lett 2024; 29:105. [PMID: 39030477 PMCID: PMC11264913 DOI: 10.1186/s11658-024-00619-0] [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: 04/23/2024] [Accepted: 06/26/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND The organism-wide effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection are well studied, but little is known about the dynamics of how the infection spreads in time among or within cells due to the scarcity of suitable high-resolution experimental systems. It has been reported that SARS-CoV-2 infection pathways converge at calcium influx and subcellular calcium distribution changes. Imaging combined with a proper staining technique is an effective tool for studying subcellular calcium-related infection and replication mechanisms at such resolutions. METHODS Using two-photon (2P) fluorescence imaging with our novel Ca-selective dye, automated image analysis and clustering analysis were applied to reveal titer and variant effects on SARS-CoV-2-infected Vero E6 cells. RESULTS The application of a new calcium sensor molecule is shown, combined with a high-end 2P technique for imaging and identifying the patterns associated with cellular infection damage within cells. Vero E6 cells infected with SARS-CoV-2 variants, D614G or B.1.1.7, exhibit elevated cytosolic calcium levels, allowing infection monitoring by tracking the cellular changes in calcium level by the internalized calcium sensor. The imaging provides valuable information on how the level and intracellular distribution of calcium are perturbed during the infection. Moreover, two-photon calcium sensing allowed the distinction of infections by two studied viral variants via cluster analysis of the image parameters. This approach will facilitate the study of cellular correlates of infection and their quantification depending on viral variants and viral load. CONCLUSIONS We propose a new two-photon microscopy-based method combined with a cell-internalized sensor to quantify the level of SARS-CoV-2 infection. We optimized the applied dye concentrations to not interfere with viral fusion and viral replication events. The presented method ensured the proper monitoring of viral infection, replication, and cell fate. It also enabled distinguishing intracellular details of cell damage, such as vacuole and apoptotic body formation. Using clustering analysis, 2P microscopy calcium fluorescence images were suitable to distinguish two different viral variants in cell cultures. Cellular harm levels read out by calcium imaging were quantitatively related to the initial viral multiplicity of infection numbers. Thus, 2P quantitative calcium imaging might be used as a correlate of infection or a correlate of activity in cellular antiviral studies.
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Affiliation(s)
- Domokos Máthé
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó utca 37-47, 1094, Budapest, Hungary.
- In Vivo Imaging Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Tűzoltó utca 37-47, 1094, Budapest, Hungary.
- HUN-REN Physical Virology Research Group, Semmelweis University, Tűzoltó utca 37-47, 1094, Budapest, Hungary.
| | - Gergely Szalay
- Laboratory of 3D Functional Network and Dendritic Imaging, HUN-REN Institute of Experimental Medicine, Szigony utca 43, 1083, Budapest, Hungary
- BrainVisionCenter, Liliom utca 43-45, 1094, Budapest, Hungary
| | - Levente Cseri
- BrainVisionCenter, Liliom utca 43-45, 1094, Budapest, Hungary
- Femtonics Ltd., Tűzoltó utca 59, 1094, Budapest, Hungary
| | - Zoltán Kis
- National Center for Public Health, Albert Flórián út 2-6, 1097, Budapest, Hungary
| | - Bernadett Pályi
- National Center for Public Health, Albert Flórián út 2-6, 1097, Budapest, Hungary
| | - Gábor Földes
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Heart and Vascular Center, Semmelweis University, Városmajor utca. 68, 1122, Budapest, Hungary
| | - Noémi Kovács
- In Vivo Imaging Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Tűzoltó utca 37-47, 1094, Budapest, Hungary
| | - Anna Fülöp
- Femtonics Ltd., Tűzoltó utca 59, 1094, Budapest, Hungary
| | - Áron Szepesi
- Laboratory of 3D Functional Network and Dendritic Imaging, HUN-REN Institute of Experimental Medicine, Szigony utca 43, 1083, Budapest, Hungary
- BrainVisionCenter, Liliom utca 43-45, 1094, Budapest, Hungary
| | - Polett Hajdrik
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó utca 37-47, 1094, Budapest, Hungary
| | - Attila Csomos
- Femtonics Ltd., Tűzoltó utca 59, 1094, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Ákos Zsembery
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - Kristóf Kádár
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - Gergely Katona
- Two-Photon Measurement Technology Group, The Faculty of Information Technology, Pázmány Péter Catholic University, Szigony utca 50/A, 1083, Budapest, Hungary
| | - Zoltán Mucsi
- BrainVisionCenter, Liliom utca 43-45, 1094, Budapest, Hungary.
- Femtonics Ltd., Tűzoltó utca 59, 1094, Budapest, Hungary.
- Institute of Chemistry, Faculty of Materials Science and Engineering, University of Miskolc, Egyetem tér 1, 3515, Miskolc, Hungary.
| | - Balázs József Rózsa
- Laboratory of 3D Functional Network and Dendritic Imaging, HUN-REN Institute of Experimental Medicine, Szigony utca 43, 1083, Budapest, Hungary.
- BrainVisionCenter, Liliom utca 43-45, 1094, Budapest, Hungary.
- Two-Photon Measurement Technology Group, The Faculty of Information Technology, Pázmány Péter Catholic University, Szigony utca 50/A, 1083, Budapest, Hungary.
| | - Ervin Kovács
- Two-Photon Measurement Technology Group, The Faculty of Information Technology, Pázmány Péter Catholic University, Szigony utca 50/A, 1083, Budapest, Hungary.
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, 1117, Budapest, Hungary.
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4
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Wu Q, Rafatian N, Wagner KT, Blamer J, Smith J, Okhovatian S, Aggarwal P, Wang EY, Banerjee A, Zhao Y, Nash TR, Lu RXZ, Portillo-Esquivel LE, Li CY, Kuzmanov U, Mandla S, Virlee E, Landau S, Lai BF, Gramolini AO, Liu C, Fleischer S, Veres T, Vunjak-Novakovic G, Zhang B, Mossman K, Broeckel U, Radisic M. SARS-CoV-2 pathogenesis in an angiotensin II-induced heart-on-a-chip disease model and extracellular vesicle screening. Proc Natl Acad Sci U S A 2024; 121:e2403581121. [PMID: 38968108 PMCID: PMC11253010 DOI: 10.1073/pnas.2403581121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/17/2024] [Indexed: 07/07/2024] Open
Abstract
Adverse cardiac outcomes in COVID-19 patients, particularly those with preexisting cardiac disease, motivate the development of human cell-based organ-on-a-chip models to recapitulate cardiac injury and dysfunction and for screening of cardioprotective therapeutics. Here, we developed a heart-on-a-chip model to study the pathogenesis of SARS-CoV-2 in healthy myocardium established from human induced pluripotent stem cell (iPSC)-derived cardiomyocytes and a cardiac dysfunction model, mimicking aspects of preexisting hypertensive disease induced by angiotensin II (Ang II). We recapitulated cytopathic features of SARS-CoV-2-induced cardiac damage, including progressively impaired contractile function and calcium handling, apoptosis, and sarcomere disarray. SARS-CoV-2 presence in Ang II-treated hearts-on-a-chip decreased contractile force with earlier onset of contractile dysfunction and profoundly enhanced inflammatory cytokines compared to SARS-CoV-2 alone. Toward the development of potential therapeutics, we evaluated the cardioprotective effects of extracellular vesicles (EVs) from human iPSC which alleviated the impairment of contractile force, decreased apoptosis, reduced the disruption of sarcomeric proteins, and enhanced beta-oxidation gene expression. Viral load was not affected by either Ang II or EV treatment. We identified MicroRNAs miR-20a-5p and miR-19a-3p as potential mediators of cardioprotective effects of these EVs.
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Affiliation(s)
- Qinghua Wu
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ONM5G 2C4, Canada
| | - Naimeh Rafatian
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
| | - Karl T. Wagner
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ONM5S 3E5, Canada
| | - Jacob Blamer
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, WI53226
| | - Jacob Smith
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ONM5S 3E5, Canada
| | - Sargol Okhovatian
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ONM5G 2C4, Canada
| | - Praful Aggarwal
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, WI53226
| | - Erika Yan Wang
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
| | - Arinjay Banerjee
- Department of Medicine, McMaster University, Toronto, ONL8S 4L8, Canada
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SKS7N 5E3, Canada
| | - Yimu Zhao
- Department of Biomedical Engineering, Columbia University, New York, NY10027
| | - Trevor R. Nash
- Department of Biomedical Engineering, Columbia University, New York, NY10027
| | - Rick Xing Ze Lu
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
| | | | - Chen Yu Li
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ONM5S 3E5, Canada
| | - Uros Kuzmanov
- Department of Physiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ONM5G 1M1, Canada
| | - Serena Mandla
- Toronto General Hospital Research Institute, University Health Network, Toronto, ONM5G 2C4, Canada
| | - Elizabeth Virlee
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, WI53226
| | - Shira Landau
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
| | - Benjamin Fook Lai
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
| | - Anthony O. Gramolini
- Department of Physiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ONM5G 1M1, Canada
| | - Chuan Liu
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ONM5G 2C4, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY10027
| | - Teodor Veres
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ONM5S 3G8, Canada
- Medical Devices Research Center, Life Sciences Division, National Research Council Canada, Montreal, QCH4P 2R2, Canada
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY10027
- Department of Medicine, Columbia University, New York, NY10032
| | - Boyang Zhang
- Department of Chemical Engineering, McMaster University, Hamilton, ONL8S 4L8, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Toronto, ONL8S 4L8, Canada
| | - Ulrich Broeckel
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, WI53226
| | - Milica Radisic
- Institute of Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ONM5G 2C4, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ONM5S 3E5, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
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5
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Younes S. The role of nutrition on the treatment of Covid 19. HUMAN NUTRITION & METABOLISM 2024; 36:200255. [DOI: 10.1016/j.hnm.2024.200255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
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6
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Lei R, Qing E, Odle A, Yuan M, Gunawardene CD, Tan TJC, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. Nat Commun 2024; 15:4056. [PMID: 38744813 PMCID: PMC11094058 DOI: 10.1038/s41467-024-48104-8] [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: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chaminda D Gunawardene
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA.
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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7
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Carten JD, Khelashvili G, Bidon MK, Straus MR, Tang T, Jaimes JA, Whittaker GR, Weinstein H, Daniel S. A Mechanistic Understanding of the Modes of Ca 2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration. ACS Infect Dis 2024; 10:398-411. [PMID: 38270149 DOI: 10.1021/acsinfecdis.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates the fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca2+ binding that likely promote membrane insertion. We first individually mutated the negatively charged residues in the SARS CoV-1 FP to assay their roles in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants greatly reduced syncytia formation and pseudoparticle transduction of VeroE6 cells. Interestingly, one mutation (D812A) led to a modest increase in cell transduction, further indicating that FP function likely depends on calcium binding at specific residues and in specific combinations. To interpret these results mechanistically and identify specific modes of FP-Ca2+ binding that modulate membrane insertion, we performed molecular dynamics simulations of the SARS-CoV-1 FP and Ca2+ions. The preferred residue pairs for Ca2+ binding we identified (E801/D802, E801/D830, and D812/E821) include the two residues found to be essential for S function in our biological studies (D802 and D830). The three preferred Ca2+ binding pairs were also predicted to promote FP membrane insertion. We also identified a Ca2+ binding pair (E821/D825) predicted to inhibit FP membrane insertion. We then carried out simulations in the presence of membranes and found that binding of Ca2+ to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion by enabling the peptide to adopt conformations that shield the negative charges of the FP to reduce repulsion by the membrane phospholipid headgroups. This calcium binding mode also optimally positions the hydrophobic LLF region of the FP for membrane penetration. Conversely, Ca2+ binding to the FP E801/D802 and D821/D825 pairs eliminates the negative charge screening and instead creates a repulsive negative charge that hinders membrane penetration of the LLF motif. These computational results, taken together with our biological studies, provide an improved and nuanced mechanistic understanding of the dymanics of SARS-CoV-1 calcium binding and their potential effects on host cell entry.
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Affiliation(s)
- Juliana Debrito Carten
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - George Khelashvili
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Miya K Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Marco R Straus
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Javier A Jaimes
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Gary R Whittaker
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
- Public & Ecosystem Health, Cornell University, Ithaca, New York 14853, United States
| | - Harel Weinstein
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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8
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Ghafouri E, Bigdeli M, Khalafiyan A, Amirkhani Z, Ghanbari R, Hasan A, Khanahmad H, Boshtam M, Makvandi P. Unmasking the complex roles of hypocalcemia in cancer, COVID-19, and sepsis: Engineered nanodelivery and diagnosis. ENVIRONMENTAL RESEARCH 2023; 238:116979. [PMID: 37660871 DOI: 10.1016/j.envres.2023.116979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
Calcium (Ca2+) homeostasis is essential for maintaining physiological processes in the body. Disruptions in Ca2+ signaling can lead to various pathological conditions including inflammation, fibrosis, impaired immune function, and accelerated senescence. Hypocalcemia, a common symptom in diseases such as acute respiratory distress syndrome (ARDS), cancer, septic shock, and COVID-19, can have both potential protective and detrimental effects. This article explores the multifaceted role of Ca2+ dysregulation in inflammation, fibrosis, impaired immune function, and accelerated senescence, contributing to disease severity. Targeting Ca2+ signaling pathways may provide opportunities to develop novel therapeutics for age-related diseases and combat viral infections. However, the role of Ca2+ in viral infections is complex, and evidence suggests that hypocalcemia may have a protective effect against certain viruses, while changes in Ca2+ homeostasis can influence susceptibility to viral infections. The effectiveness and safety of Ca2+ supplements in COVID-19 patients remain a subject of ongoing research and debate. Further investigations are needed to understand the intricate interplay between Ca2+ signaling and disease pathogenesis.
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Affiliation(s)
- Elham Ghafouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zohre Amirkhani
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Roham Ghanbari
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China; School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, EH9 3JL, UK.
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9
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Lei R, Qing E, Odle A, Yuan M, Tan TJ, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569051. [PMID: 38076875 PMCID: PMC10705381 DOI: 10.1101/2023.11.28.569051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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10
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Van Doren SR, Scott BS, Koppisetti RK. SARS-CoV-2 fusion peptide sculpting of a membrane with insertion of charged and polar groups. Structure 2023; 31:1184-1199.e3. [PMID: 37625399 PMCID: PMC10592393 DOI: 10.1016/j.str.2023.07.015] [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: 12/14/2022] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike is essential for infection. How this charged and hydrophobic domain occupies and affects membranes needs clarification. Its depth in zwitterionic, bilayered micelles at pH 5 (resembling late endosomes) was measured by paramagnetic NMR relaxation enhancements used to bias molecular dynamics simulations. Asp830 inserted deeply, along with Lys825 or Lys835. Protonation of Asp830 appeared to enhance agreement of simulated and NMR-measured depths. While the fusion peptide occupied a leaflet of the DMPC bilayer, the opposite leaflet invaginated with influx of water and choline head groups in around Asp830 and bilayer-inserted polar side chains. NMR-detected hydrogen exchange found corroborating hydration of the backbone of Thr827-Phe833 inserted deeply in bicelles. Pinching of the membrane at the inserted charge and the intramembrane hydration of polar groups agree with theory. Formation of corridors of hydrated, inward-turned head groups was accompanied by flip-flop of head groups. Potential roles of the defects are discussed.
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Affiliation(s)
- Steven R Van Doren
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
| | - Benjamin S Scott
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Rama K Koppisetti
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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11
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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12
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Gregoriou I, Ioannides M, Ioannou C, Kalakouta O, Karagiannis C, Marcou M, Masia C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Shammas C, Stylianou DC, Zinieri B, Lemey P, Network TCOMESSAR, Kostrikis LG. Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacton Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021-Oct 2022). Viruses 2023; 15:1933. [PMID: 37766339 PMCID: PMC10535466 DOI: 10.3390/v15091933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021-January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed "Deltacron", was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation-a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus's local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus's epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic's dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Costakis Ioannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Markella Marcou
- Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Michail Mendris
- Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus
| | | | - Philippos C. Patsalis
- Medicover Genetics, 2409 Nicosia, Cyprus
- Medical School, University of Nicosia, 2417 Nicosia, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Christos Shammas
- S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Barbara Zinieri
- Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
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13
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Niort K, Dancourt J, Boedec E, Al Amir Dache Z, Lavieu G, Tareste D. Cholesterol and Ceramide Facilitate Membrane Fusion Mediated by the Fusion Peptide of the SARS-CoV-2 Spike Protein. ACS OMEGA 2023; 8:32729-32739. [PMID: 37720777 PMCID: PMC10500581 DOI: 10.1021/acsomega.3c03610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 09/19/2023]
Abstract
SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together and its fusion peptide (FP) that interacts with and perturbs the membrane structure to trigger fusion. Recent studies have suggested that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. Our findings reveal that both cholesterol and ceramide lipids facilitate fusion, suggesting that targeting these lipids could be effective against SARS-CoV-2. As a proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. Our results show that CPZ effectively inhibits S-mediated membrane fusion, thereby potentially impeding SARS-CoV-2 entry into the host cell.
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Affiliation(s)
- Kristina Niort
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Julia Dancourt
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Erwan Boedec
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Zahra Al Amir Dache
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Grégory Lavieu
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - David Tareste
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
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14
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Murugan AK, Alzahrani AS. Potential impacts of SARS-CoV-2 on parathyroid: current advances and trends. Endocrine 2023; 81:391-408. [PMID: 37328666 DOI: 10.1007/s12020-023-03415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection affects several important organs including endocrine glands. Experimental studies demonstrated that the virus exploits the ACE2, a transmembrane glycoprotein on the cell surface as a receptor for cellular entry. This entry process is exclusively facilitated by other intracellular protein molecules such as TMPRSS2, furin, NRP1, and NRP2. Recent findings documented the involvement of the SARS-CoV-2 in inducing various parathyroid disorders including hypoparathyroidism and hypocalcemia, which received significant attention. This review extensively describes rapidly evolving knowledge on the potential part of SARS-CoV-2 in emerging various parathyroid disorders due to SARS-CoV-2 infection particularly parathyroid malfunction in COVID-19 cases, and post-COVID-19 conditions. Further, it presents the expression level of various molecules such as ACE2, TMPRSS2, furin, NRP1, and NRP2 in the parathyroid cells that facilitate the SARS-CoV-2 entry into the cell, and discusses the possible mechanism of parathyroid gland infection. Besides, it explores parathyroid malfunction in COVID-19 vaccine-administered cases. It also explains the possible long-COVID-19 effect on parathyroid and post-COVID-19 management of parathyroid. A complete understanding of the mechanisms of SARS-CoV-2-triggered pathogenesis in parathyroid dysfunctions may curtail treatment options and aid in the management of SARS-CoV-2-infected cases.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia.
| | - Ali S Alzahrani
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
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15
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Su R, Zeng J, Marcink TC, Porotto M, Moscona A, O’Shaughnessy B. Host Cell Membrane Capture by the SARS-CoV-2 Spike Protein Fusion Intermediate. ACS CENTRAL SCIENCE 2023; 9:1213-1228. [PMID: 37396856 PMCID: PMC10255576 DOI: 10.1021/acscentsci.3c00158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 07/04/2023]
Abstract
Cell entry by SARS-CoV-2 is accomplished by the S2 subunit of the spike S protein on the virion surface by capture of the host cell membrane and fusion with the viral envelope. Capture and fusion require the prefusion S2 to transit to its potent fusogenic form, the fusion intermediate (FI). However, the FI structure is unknown, detailed computational models of the FI are unavailable, and the mechanisms and timing of membrane capture and fusion are not established. Here, we constructed a full-length model of the SARS-CoV-2 FI by extrapolating from known SARS-CoV-2 pre- and postfusion structures. In atomistic and coarse-grained molecular dynamics simulations the FI was remarkably flexible and executed giant bending and extensional fluctuations due to three hinges in the C-terminal base. The simulated configurations and their giant fluctuations are quantitatively consistent with SARS-CoV-2 FI configurations measured recently using cryo-electron tomography. Simulations suggested a host cell membrane capture time of ∼2 ms. Isolated fusion peptide simulations identified an N-terminal helix that directed and maintained binding to the membrane but grossly underestimated the binding time, showing that the fusion peptide environment is radically altered when attached to its host fusion protein. The large configurational fluctuations of the FI generated a substantial exploration volume that aided capture of the target membrane, and may set the waiting time for fluctuation-triggered refolding of the FI that draws the viral envelope and host cell membrane together for fusion. These results describe the FI as machinery that uses massive configurational fluctuations for efficient membrane capture and suggest novel potential drug targets.
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Affiliation(s)
- Rui Su
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Jin Zeng
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Tara C. Marcink
- Department
of Pediatrics, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
- Center
for Host−Pathogen Interaction, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
| | - Matteo Porotto
- Department
of Pediatrics, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
- Center
for Host−Pathogen Interaction, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
- Department
of Experimental Medicine, University of
Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Anne Moscona
- Department
of Pediatrics, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
- Center
for Host−Pathogen Interaction, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
- Department
of Microbiology & Immunology, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
- Department
of Physiology, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
| | - Ben O’Shaughnessy
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
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16
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Guo X, Feng Y, Zhao X, Qiao S, Ma Z, Li Z, Zheng H, Xiao S. Coronavirus Porcine Epidemic Diarrhea Virus Utilizes Chemokine Interleukin-8 to Facilitate Viral Replication by Regulating Ca 2+ Flux. J Virol 2023; 97:e0029223. [PMID: 37133374 PMCID: PMC10231212 DOI: 10.1128/jvi.00292-23] [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: 02/23/2023] [Accepted: 04/10/2023] [Indexed: 05/04/2023] Open
Abstract
Chemokine production by epithelial cells is crucial for neutrophil recruitment to sites of inflammation during viral infection. However, the effect of chemokine on epithelia and how chemokine is involved in coronavirus infection remains to be fully understood. Here, we identified an inducible chemokine interleukin-8 (CXCL8/IL-8), which could promote coronavirus porcine epidemic diarrhea virus (PEDV) infection in African green monkey kidney epithelial cells (Vero) and Lilly Laboratories cell-porcine kidney 1 epithelial cells (LLC-PK1). IL-8 deletion restrained cytosolic calcium (Ca2+), whereas IL-8 stimulation improved cytosolic Ca2+. The consumption of Ca2+ restricted PEDV infection. PEDV internalization and budding were obvious reductions when cytosolic Ca2+ was abolished in the presence of Ca2+ chelators. Further study revealed that the upregulated cytosolic Ca2+ redistributes intracellular Ca2+. Finally, we identified that G protein-coupled receptor (GPCR)-phospholipase C (PLC)-inositol trisphosphate receptor (IP3R)-store-operated Ca2+ (SOC) signaling was crucial for enhancive cytosolic Ca2+ and PEDV infection. To our knowledge, this study is the first to uncover the function of chemokine IL-8 during coronavirus PEDV infection in epithelia. PEDV induces IL-8 expression to elevate cytosolic Ca2+, promoting its infection. Our findings reveal a novel role of IL-8 in PEDV infection and suggest that targeting IL-8 could be a new approach to controlling PEDV infection. IMPORTANCE Coronavirus porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric coronavirus that caused severe economic losses worldwide, and more effort is needed to develop economical and efficient vaccines to control or eliminate this disease. The chemokine interleukin-8 (CXCL8/IL-8) is indispensable for the activation and trafficking of inflammatory mediators and tumor progression and metastasis. This study evaluated the effect of IL-8 on PEDV infection in epithelia. We found that IL-8 expression improved cytosolic Ca2+ in epithelia, facilitating PEDV rapid internalization and egress. G protein-coupled receptor (GPCR)-phospholipase C (PLC)-inositol trisphosphate receptor (IP3R)-SOC signaling was activated by IL-8, releasing the intracellular Ca2+ stores from endoplasmic reticulum (ER). These findings provide a better understanding of the role of IL-8 in PEDV-induced immune responses, which will help develop small-molecule drugs for coronavirus cure.
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Affiliation(s)
- Xuyang Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingtong Feng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojing Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuang Qiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiqian Ma
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Zhiwei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shuqi Xiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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17
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Villalaín J. SARS-CoV-2 Protein S Fusion Peptide Is Capable of Wrapping Negatively-Charged Phospholipids. MEMBRANES 2023; 13:344. [PMID: 36984731 PMCID: PMC10057416 DOI: 10.3390/membranes13030344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
COVID-19, caused by SARS-CoV-2, which is a positive-sense, single-stranded RNA enveloped virus, emerged in late 2019 and was declared a worldwide pandemic in early 2020 causing more than 600 million infections so far and more than 6 million deaths in the world. Although new vaccines have been implemented, the pandemic continues to impact world health dramatically. Membrane fusion, critical for the viral entry into the host cell, is one of the main targets for the development of novel antiviral therapies to combat COVID-19. The S2 subunit of the viral S protein, a class I membrane fusion protein, contains the fusion domain which is directly implicated in the fusion mechanism. The knowledge of the membrane fusion mechanism at the molecular level will undoubtedly result in the development of effective antiviral strategies. We have used all-atom molecular dynamics to analyse the binding of the SARS-CoV-2 fusion peptide to specific phospholipids in model membranes composed of only one phospholipid plus cholesterol in the presence of either Na+ or Ca2+. Our results show that the fusion peptide is capable of binding to the membrane, that its secondary structure does not change significantly upon binding, that it tends to preferentially bind electronegatively charged phospholipids, and that it does not bind cholesterol at all. Understanding the intricacies of the membrane fusion mechanism and the molecular interactions involved will lead us to the development of antiviral molecules that will allow a more efficient battle against these viruses.
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Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universitas "Miguel Hernández", E-03202 Elche, Spain
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18
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Adélaïde M, Salnikov E, Ramos-Martín F, Aisenbrey C, Sarazin C, Bechinger B, D’Amelio N. The Mechanism of Action of SAAP-148 Antimicrobial Peptide as Studied with NMR and Molecular Dynamics Simulations. Pharmaceutics 2023; 15:pharmaceutics15030761. [PMID: 36986623 PMCID: PMC10051583 DOI: 10.3390/pharmaceutics15030761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Background: SAAP-148 is an antimicrobial peptide derived from LL-37. It exhibits excellent activity against drug-resistant bacteria and biofilms while resisting degradation in physiological conditions. Despite its optimal pharmacological properties, its mechanism of action at the molecular level has not been explored. Methods: The structural properties of SAAP-148 and its interaction with phospholipid membranes mimicking mammalian and bacterial cells were studied using liquid and solid-state NMR spectroscopy as well as molecular dynamics simulations. Results: SAAP-148 is partially structured in solution and stabilizes its helical conformation when interacting with DPC micelles. The orientation of the helix within the micelles was defined by paramagnetic relaxation enhancements and found similar to that obtained using solid-state NMR, where the tilt and pitch angles were determined based on 15N chemical shift in oriented models of bacterial membranes (POPE/POPG). Molecular dynamic simulations revealed that SAAP-148 approaches the bacterial membrane by forming salt bridges between lysine and arginine residues and lipid phosphate groups while interacting minimally with mammalian models containing POPC and cholesterol. Conclusions: SAAP-148 stabilizes its helical fold onto bacterial-like membranes, placing its helix axis almost perpendicular to the surface normal, thus probably acting by a carpet-like mechanism on the bacterial membrane rather than forming well-defined pores.
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Affiliation(s)
- Morgane Adélaïde
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Evgeniy Salnikov
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS, 67000 Strasbourg, France
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
- Correspondence: (F.R.-M.); (N.D.); Tel.: +33-3-22-82-74-73 (F.R.-M. & N.D.)
| | - Christopher Aisenbrey
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS, 67000 Strasbourg, France
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Burkhard Bechinger
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS, 67000 Strasbourg, France
| | - Nicola D’Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
- Correspondence: (F.R.-M.); (N.D.); Tel.: +33-3-22-82-74-73 (F.R.-M. & N.D.)
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19
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Alkazmi L, Al-Kuraishy HM, Al-Gareeb AI, El-Bouseary MM, Ahmed EA, Batiha GES. Dantrolene and ryanodine receptors in COVID-19: The daunting task and neglected warden. Clin Exp Pharmacol Physiol 2023; 50:335-352. [PMID: 36732880 DOI: 10.1111/1440-1681.13756] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
Dantrolene (DTN) is a ryanodine receptor (RyR) antagonist that inhibits Ca2+ release from stores in the sarcoplasmic reticulum. DTN is mainly used in the management of malignant hyperthermia. RyRs are highly expressed in immune cells and are involved in different viral infections, including severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), because Ca2+ is necessary for viral replication, maturation and release. DTN can inhibit the proliferation of SARS-CoV-2, indicating its potential role in reducing entry and pathogenesis of SARS-CoV-2. DTN may increase clearance of SARS-CoV-2 and promote coronavirus disease 2019 (COVID-19) recovery by shortening the period of infection. DTN inhibits N-methyl-D-aspartate (NMDA) mediated platelets aggregations and thrombosis. Therefore, DTN may inhibit thrombosis and coagulopathy in COVID-19 through suppression of platelet NMDA receptors. Moreover, DTN has a neuroprotective effect against SARS-CoV-2 infection-induced brain injury through modulation of NMDA receptors, which are involved in excitotoxicity, neuronal injury and the development of neuropsychiatric disorders. In conclusion, DTN by inhibiting RyRs may attenuate inflammatory disorders in SARS-CoV-2 infection and associated cardio-pulmonary complications. Therefore, DNT could be a promising drug therapy against COVID-19. Preclinical and clinical studies are warranted in this regards.
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Affiliation(s)
- Luay Alkazmi
- Biology Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hayder M Al-Kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Ali I Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Maisra M El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Eman A Ahmed
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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20
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Chrysostomou AC, Aristokleous A, Rodosthenous JH, Christodoulou C, Stathi G, Kostrikis LG. Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay. Life (Basel) 2023; 13:life13020304. [PMID: 36836661 PMCID: PMC9960118 DOI: 10.3390/life13020304] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health.
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Affiliation(s)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | | | | | - Georgia Stathi
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
- Correspondence: ; Tel.: +35-72-289-2885
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21
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Pirhadi E, Vanegas JM, Farin M, Schertzer JW, Yong X. Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics. J Chem Theory Comput 2023; 19:363-372. [PMID: 36579901 DOI: 10.1021/acs.jctc.2c01026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biological membranes are fundamental components of living organisms that play an undeniable role in their survival. Molecular dynamics (MD) serves as an essential computational tool for studying biomembranes on molecular and atomistic scales. The status quo of MD simulations of biomembranes studies a nanometer-sized membrane patch periodically extended under periodic boundary conditions (PBCs). In nature, membranes are usually composed of different lipids in their two layers (referred to as leaflets). This compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets in a periodically constrained membrane, which needs to be set appropriately. The widely adopted methods of defining a leaflet lipid ratio suffer from the lack of control over the mechanical tension of each leaflet, which could significantly influence research findings. In this study, we investigate the role of membrane-building protocol and the resulting initial stress state on the interaction between small molecules and asymmetric membranes. We model the outer membrane of Pseudomonas aeruginosa bacteria using two different building protocols and probe their interactions with the Pseudomonas quinolone signal (PQS). Our results show that differential stress could shift the position of free energy minimum for the PQS molecule between the two leaflets of the asymmetric membrane. This work provides critical insights into the relationship between the initial per-leaflet tension and the spontaneous intercalation of PQS.
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Affiliation(s)
- Emad Pirhadi
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Juan M Vanegas
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Mithila Farin
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Jeffrey W Schertzer
- Department of Biological Sciences, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Xin Yong
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
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22
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Aristokleous A, Christodoulou C, Gregoriou I, Ioannides M, Kalakouta O, Karagiannis C, Koumbaris G, Loizides C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Richter J, Schmitt M, Shammas C, Stylianou DC, Themistokleous G, Lemey P, Kostrikis LG. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern. Viruses 2022; 15:108. [PMID: 36680148 PMCID: PMC9862594 DOI: 10.3390/v15010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | | | | | - Michail Mendris
- Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
| | | | - Philippos C. Patsalis
- NIPD Genetics, Nicosia 2409, Cyprus
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Markus Schmitt
- Eurofins Genomics Sequencing Europe, 85560 Ebersberg, Germany
| | - Christos Shammas
- S.C.I.N.A Bioanalysis Sciomedical Centre Ltd., Limassol 4040, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | | | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, Nicosia 1011, Cyprus
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23
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Russell T, Gangotia D, Barry G. Assessing the potential of repurposing ion channel inhibitors to treat emerging viral diseases and the role of this host factor in virus replication. Biomed Pharmacother 2022; 156:113850. [DOI: 10.1016/j.biopha.2022.113850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/25/2022] [Accepted: 10/06/2022] [Indexed: 12/03/2022] Open
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24
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Villalaín J. Interaction of Lassa virus fusion and membrane proximal peptides with late endosomal membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184031. [PMID: 35964711 DOI: 10.1016/j.bbamem.2022.184031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Mammarenaviruses include many significant worldwide-widespread human pathogens, among them Lassa virus (LASV), having a dramatic morbidity and mortality rate. They are a potential high-risk menace to the worldwide public health since there are no treatments and there is a high possibility of animal-to-human and human-to-human viral transmission. These viruses enter into the cells by endocytosis fusing its membrane envelope with the late endosomal membrane thanks to the glycoprotein GP2, a membrane fusion protein of class I. This protein contains different domains, among them the N-terminal fusion peptide (NFP), the internal fusion loop (IFL), the membrane proximal external region (MPER) and the transmembrane domain (TMD). All these domains are implicated in the membrane fusion process. In this work, we have used an all-atom molecular dynamics study to know the binding of these protein domains with a complex membrane mimicking the late endosome one. We show that the NFP/IFL domain is capable of spontaneously inserting into the membrane without a significant change of secondary structure, the MPER domain locates at the bilayer interface with an orientation parallel to the membrane surface and tends to interact with other MPER domains, and the TMD domain tilts inside the bilayer. Moreover, they predominantly interact with negatively charged phospholipids. Overall, these membrane-interacting domains would characterise a target that would make possible to find effective antiviral molecules against LASV in particular and Mammarenaviruses in general.
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Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universitas "Miguel Hernández", E-03202 Elche-Alicante, Spain.
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25
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Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022; 14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
Attachment to and fusion with cell membranes are two major steps in the replication cycle of many human viruses. We focus on these steps for three enveloped viruses, i.e., HIV-1, IAVs, and SARS-CoV-2. Viral spike proteins drive the membrane attachment and fusion of these viruses. Dynamic interactions between the spike proteins and membrane receptors trigger their specific attachment to the plasma membrane of host cells. A single virion on cell membranes can engage in binding with multiple receptors of the same or different types. Such dynamic and multivalent binding of these viruses result in an optimal attachment strength which in turn leads to their cellular entry and membrane fusion. The latter process is driven by conformational changes of the spike proteins which are also class I fusion proteins, providing the energetics of membrane tethering, bending, and fusion. These viruses exploit cellular and membrane factors in regulating the conformation changes and membrane processes. Herein, we describe the major structural and functional features of spike proteins of the enveloped viruses including highlights on their structural dynamics. The review delves into some of the case studies in the literature discussing the findings on multivalent binding, membrane hemifusion, and fusion of these viruses. The focus is on applications of biophysical tools with an emphasis on single-particle methods for evaluating mechanisms of these processes at the molecular and cellular levels.
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Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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26
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Sultan F, Ahuja K, Motiani RK. Potential of targeting host cell calcium dynamics to curtail SARS-CoV-2 infection and COVID-19 pathogenesis. Cell Calcium 2022; 106:102637. [PMID: 35986958 PMCID: PMC9367204 DOI: 10.1016/j.ceca.2022.102637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection and associated coronavirus disease 2019 (COVID-19) has severely impacted human well-being. Although vaccination programs have helped in reducing the severity of the disease, drug regimens for clinical management of COVID-19 are not well recognized yet. It is therefore important to identify and characterize the molecular pathways that could be therapeutically targeted to halt SARS-CoV-2 infection and COVID-19 pathogenesis. SARS-CoV-2 hijacks host cell molecular machinery for its entry, replication and egress. Interestingly, SARS-CoV-2 interacts with host cell Calcium (Ca2+) handling proteins and perturbs Ca2+ homeostasis. We here systematically review the literature that demonstrates a critical role of host cell Ca2+ dynamics in regulating SARS-CoV-2 infection and COVID-19 pathogenesis. Further, we discuss recent studies, which have reported that SARS-CoV-2 acts on several organelle-specific Ca2+ transport mechanisms. Moreover, we deliberate upon the possibility of curtailing SARS-CoV-2 infection by targeting host cell Ca2+ handling machinery. Importantly, we delve into the clinical trials that are examining the efficacy of FDA-approved small molecules acting on Ca2+ handling machinery for the management of COVID-19. Although an important role of host cell Ca2+ signaling in driving SARS-CoV-2 infection has emerged, the underlying molecular mechanisms remain poorly understood. In future, it would be important to investigate in detail the signaling cascades that connect perturbed Ca2+ dynamics to SARS-CoV-2 infection.
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Affiliation(s)
- Farina Sultan
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad, Delhi-NCR, India
| | - Kriti Ahuja
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad, Delhi-NCR, India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad, Delhi-NCR, India.
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27
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Costa BTD, Araújo GRL, da Silva Júnior RT, Santos LKDS, Lima de Souza Gonçalves V, Lima DBA, Cuzzuol BR, Santos Apolonio J, de Carvalho LS, Marques HS, Silva CS, Barcelos IDS, Oliveira MV, Freire de Melo F. Effects of nutrients on immunomodulation in patients with severe COVID-19: Current knowledge. World J Crit Care Med 2022; 11:201-218. [PMID: 36051942 PMCID: PMC9305681 DOI: 10.5492/wjccm.v11.i4.201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/24/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that critically ill patients with coronavirus disease 2019 (COVID-19) show significant immune system dysregulation. Due to that, some nutrients that influence immunomodulation have been suggested as a form of treatment against the infection. This review collected the information on the impact of vitamins on the prognosis of COVID-19, with the intention of facilitating treatment and prevention of the disease risk status in patients. The collected information was obtained using the PubMed electronic database by searching for articles that relate COVID-19 and the mechanisms/effects of the nutrients: Proteins, glucose, lipids, vitamin B12, vitamin D, calcium, iron, copper, zinc, and magnesium, including prospective, retrospective, and support articles. The findings reveal an optimal response related mainly to omega-3, eicosapentaenoic acid, docosahexaenoic acid, calcium, and iron that might represent benefits in the treatment of critically ill patients. However, nutrient supplementation should be done with caution due to the limited availability of randomized controlled studies.
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Affiliation(s)
- Bruna Teixeira da Costa
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Glauber Rocha Lima Araújo
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | | | - Luana Kauany de Sá Santos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | | | - Daniel Bastos Alves Lima
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Beatriz Rocha Cuzzuol
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Jonathan Santos Apolonio
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Lorena Sousa de Carvalho
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Hanna Santos Marques
- Campus Vitória da Conquista, Universidade Estadual do Sudoeste da Bahia, Vitória da Conquista 45083-900, Bahia, Brazil
| | - Camilo Santana Silva
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Isadora de Souza Barcelos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Márcio Vasconcelos Oliveira
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Fabrício Freire de Melo
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
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28
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Zhang C, Meng X, Zhao H. Comparison of Cell Fusions Induced by Influenza Virus and SARS-CoV-2. Int J Mol Sci 2022; 23:ijms23137365. [PMID: 35806369 PMCID: PMC9266613 DOI: 10.3390/ijms23137365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/10/2022] Open
Abstract
Virus–cell fusion is the key step for viral infection in host cells. Studies on virus binding and fusion with host cells are important for understanding the virus–host interaction and viral pathogenesis for the discovery of antiviral drugs. In this review, we focus on the virus–cell fusions induced by the two major pandemic viruses, including the influenza virus and SARS-CoV-2. We further compare the cell fusions induced by the influenza virus and SARS-CoV-2, especially the pH-dependent fusion of the influenza virus and the fusion of SARS-CoV-2 in the type-II transmembrane serine protease 2 negative (TMPRSS2-) cells with syncytia formation. Finally, we present the development of drugs used against SARA-CoV-2 and the influenza virus through the discovery of anti-fusion drugs and the prevention of pandemic respiratory viruses.
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Affiliation(s)
- Chuyuan Zhang
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (C.Z.); (X.M.)
| | - Xinjie Meng
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (C.Z.); (X.M.)
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Hanjun Zhao
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (C.Z.); (X.M.)
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Correspondence: or ; Tel.: +852-2255-4892
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Barrantes FJ. The constellation of cholesterol-dependent processes associated with SARS-CoV-2 infection. Prog Lipid Res 2022; 87:101166. [PMID: 35513161 PMCID: PMC9059347 DOI: 10.1016/j.plipres.2022.101166] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 01/11/2023]
Abstract
The role of cholesterol in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronavirus-host cell interactions is currently being discussed in the context of two main scenarios: i) the presence of the neutral lipid in cholesterol-rich lipid domains involved in different steps of the viral infection and ii) the alteration of metabolic pathways by the virus over the course of infection. Cholesterol-enriched lipid domains have been reported to occur in the lipid envelope membrane of the virus, in the host-cell plasma membrane, as well as in endosomal and other intracellular membrane cellular compartments. These membrane subdomains, whose chemical and physical properties distinguish them from the bulk lipid bilayer, have been purported to participate in diverse phenomena, from virus-host cell fusion to intracellular trafficking and exit of the virions from the infected cell. SARS-CoV-2 recruits many key proteins that participate under physiological conditions in cholesterol and lipid metabolism in general. This review analyses the status of cholesterol and lipidome proteins in SARS-CoV-2 infection and the new horizons they open for therapeutic intervention.
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Affiliation(s)
- Francisco J. Barrantes
- Corresponding author at: BIOMED UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
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30
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Baazaoui N, Iqbal K. COVID-19 and Neurodegenerative Diseases: Prion-Like Spread and Long-Term Consequences. J Alzheimers Dis 2022; 88:399-416. [DOI: 10.3233/jad-220105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
COVID-19 emerged as a global pandemic starting from Wuhan in China and spread at a lightning speed to the rest of the world. One of the potential long-term outcomes that we speculate is the development of neurodegenerative diseases as a long-term consequence of SARS-CoV-2 especially in people that have developed severe neurological symptoms. Severe inflammatory reactions and aging are two very strong common links between neurodegenerative diseases and COVID-19. Thus, patients that have very high viral load may be at high risk of developing long-term adverse neurological consequences such as dementia. We hypothesize that people with neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and aged people are at higher risk of getting the COVID-19 than normal adults. The basis of this hypothesis is the fact that SARS-CoV-2 uses as a receptor angiotensin-converting enzyme 2 to enter the host cell and that this interaction is calcium-dependent. This could then suggest a direct relationship between neurodegenerative diseases, ACE-2 expression, and the susceptibility to COVID-19. The analysis of the available literature showed that COVID-19 virus is neurotropic and was found in the brains of patients infected with this virus. Furthermore, that the risk of having the infection increases with dementia and that infected people with severe symptoms could develop dementia as a long-term consequence. Dementia could be developed following the acceleration of the spread of prion-like proteins. In the present review we discuss current reports concerning the prevalence of COVID-19 in dementia patients, the individuals that are at high risk of suffering from dementia and the potential acceleration of prion-like proteins spread following SARS-CoV-2 infection.
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Affiliation(s)
| | - Khalid Iqbal
- Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
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31
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Pennington H, Lee J. Lassa virus glycoprotein complex review: insights into its unique fusion machinery. Biosci Rep 2022; 42:BSR20211930. [PMID: 35088070 PMCID: PMC8844875 DOI: 10.1042/bsr20211930] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Lassa virus (LASV), an arenavirus endemic to West Africa, causes Lassa fever-a lethal hemorrhagic fever. Entry of LASV into the host cell is mediated by the glycoprotein complex (GPC), which is the only protein located on the viral surface and comprises three subunits: glycoprotein 1 (GP1), glycoprotein 2 (GP2), and a stable signal peptide (SSP). The LASV GPC is a class one viral fusion protein, akin to those found in viruses such as human immunodeficiency virus (HIV), influenza, Ebola virus (EBOV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These viruses are enveloped and utilize membrane fusion to deliver their genetic material to the host cell. Like other class one fusion proteins, LASV-mediated membrane fusion occurs through an orchestrated sequence of conformational changes in its GPC. The receptor-binding subunit, GP1, first engages with a host cell receptor then undergoes a unique receptor switch upon delivery to the late endosome. The acidic pH and change in receptor result in the dissociation of GP1, exposing the fusion subunit, GP2, such that fusion can occur. These events ultimately lead to the formation of a fusion pore so that the LASV genetic material is released into the host cell. Interestingly, the mature GPC retains its SSP as a third subunit-a feature that is unique to arenaviruses. Additionally, the fusion domain contains two separate fusion peptides, instead of a standard singular fusion peptide. Here, we give a comprehensive review of the LASV GPC components and their unusual features.
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Affiliation(s)
- Hallie N. Pennington
- Department of Chemistry and Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, MD 20740, U.S.A
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, MD 20740, U.S.A
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Tuerkova A, Kasson PM. Computational methods to study enveloped viral entry. Biochem Soc Trans 2021; 49:2527-2537. [PMID: 34783344 PMCID: PMC10184508 DOI: 10.1042/bst20210190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
The protein-membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become important adjuncts for integrating experimental data, developing mechanistic models, and suggesting testable hypotheses regarding viral function. However, the large molecular scales of virus-host interaction also create challenges for detailed molecular simulation. For this reason, continuum membrane models have played a large historical role, although they have become less favored for high-resolution models of protein assemblies and lipid organization. Here, we review recent progress in the field, with an emphasis on the insight that has been gained using a mixture of coarse-grained and atomic-resolution molecular dynamics simulations. Based on successes and challenges to date, we suggest a multiresolution strategy that should yield the best mixture of computational efficiency and physical fidelity. This strategy may facilitate further simulations of viral entry by a broader range of viruses, helping illuminate the diversity of viral entry strategies and the essential common elements that can be targeted for antiviral therapies.
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Affiliation(s)
- Alzbeta Tuerkova
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, U.S.A
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Lai AL, Freed JH. Importance of Negatively Charged Residues in the Membrane Ordering Activity of SARS-CoV-1 and -2 Fusion Peptides. Biophys J 2021; 121:207-227. [PMID: 34929193 PMCID: PMC8683214 DOI: 10.1016/j.bpj.2021.12.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022] Open
Abstract
Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. Previously, we identified the bona fide FPs for SARS-CoV ("SARS-1") and SARS-CoV-2 ("SARS-2") using ESR spectroscopy. We also found that their FPs induce membrane ordering in a Ca2+-dependent fashion. Here we study which negatively charged residues in SARS-1 FP are involved in this binding, to build a topological model and clarify the role of Ca2+. Our systematic mutation study on the SARS-1 FP shows that all six negatively charged residues contribute to the FP's membrane ordering activity, with D812 the dominant residue. The corresponding SARS-2 residue D830 plays an equivalent role. We provide a topological model of how the FP binds Ca2+ ions: its two segments FP1 and FP2 each bind one Ca2+. The binding of Ca2+, the folding of FP (both studied by ITC experiments), and the ordering activity correlate very well across the mutants, suggesting that the Ca2+ helps the folding of FP in membranes to enhance the ordering activity. Using a novel pseudotyped virus particle (PP)-liposome methodology, we monitored the membrane ordering induced by the FPs in the whole S protein in its trimer form in real time. We found that the SARS-1 and SARS-2 PPs also induce membrane ordering to the extent that separate FPs do, and mutations of the negatively charged residues also significantly suppress the membrane ordering activity. However, the slower kinetics of the FP ordering activity vs. that of the PP suggests the need for initial trimerization of the FPs.
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Affiliation(s)
- Alex L Lai
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
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Basso LGM, Zeraik AE, Felizatti AP, Costa-Filho AJ. Membranotropic and biological activities of the membrane fusion peptides from SARS-CoV spike glycoprotein: The importance of the complete internal fusion peptide domain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183697. [PMID: 34274319 PMCID: PMC8280623 DOI: 10.1016/j.bbamem.2021.183697] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/05/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022]
Abstract
Fusion peptides (FP) are prominent hydrophobic segments of viral fusion proteins that play critical roles in viral entry. FPs interact with and insert into the host lipid membranes, triggering conformational changes in the viral protein that leads to the viral-cell fusion. Multiple membrane-active domains from the severe acute respiratory syndrome (SARS) coronavirus (CoV) spike protein have been reported to act as the functional fusion peptide such as the peptide sequence located between the S1/S2 and S2' cleavage sites (FP1), the S2'-adjacent fusion peptide domain (FP2), and the internal FP sequence (cIFP). Using a combined biophysical approach, we demonstrated that the α-helical coiled-coil-forming internal cIFP displayed the highest membrane fusion and permeabilizing activities along with membrane ordering effect in phosphatidylcholine (PC)/phosphatidylglycerol (PG) unilamellar vesicles compared to the other two N-proximal fusion peptide counterparts. While the FP1 sequence displayed intermediate membranotropic activities, the well-conserved FP2 peptide was substantially less effective in promoting fusion, leakage, and membrane ordering in PC/PG model membranes. Furthermore, Ca2+ did not enhance the FP2-induced lipid mixing activity in PC/phosphatidylserine/cholesterol lipid membranes, despite its strong erythrocyte membrane perturbation. Nonetheless, we found that the three putative SARS-CoV membrane-active fusion peptide sequences here studied altered the physical properties of model and erythrocyte membranes to different extents. The importance of the distinct membranotropic and biological activities of all SARS-CoV fusion peptide domains and the pronounced effect of the internal fusion peptide sequence to the whole spike-mediated membrane fusion process are discussed.
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Affiliation(s)
- Luis Guilherme Mansor Basso
- Laboratório de Ciências Físicas, Centro de Ciência e Tecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
| | - Ana Eliza Zeraik
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Ana Paula Felizatti
- Laboratório de Produtos Naturais, Departamento de Química, Centro de Ciências Exatas e de Tecnologia, Universidade Federal de São Carlos, Rod. Washington Luiz, Km 235, Monjolinho, 13565905, São Carlos, SP, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Antonio José Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
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Birtles D, Lee J. Identifying Distinct Structural Features of the SARS-CoV-2 Spike Protein Fusion Domain Essential for Membrane Interaction. Biochemistry 2021; 60:2978-2986. [PMID: 34570469 PMCID: PMC8491435 DOI: 10.1021/acs.biochem.1c00543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/20/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 spike protein is the primary antigenic determinant of the virus and has been studied extensively, yet the process of membrane fusion remains poorly understood. The fusion domain (FD) of viral glycoproteins is well established as facilitating the initiation of membrane fusion. An improved understanding of the structural plasticity associated with these highly conserved regions aids in our knowledge of the molecular mechanisms that drive viral fusion. Within the spike protein, the FD of SARS-CoV-2 exists immediately following S2' cleavage at the N-terminus of the S2 domain. Here we have shown that following the introduction of a membrane at pH 7.4, the FD undergoes a transition from a random coil to a more structurally well-defined postfusion state. Furthermore, we have classified the domain into two distinct regions, a fusion peptide (FP, S816-G838) and a fusion loop (FL, D839-F855). The FP forms a helix-turn-helix motif upon association with a membrane, and the favorable entropy gained during this transition from a random coil is likely the driving force behind membrane insertion. Membrane depth experiments then revealed the FP is found inserted within the membrane below the lipid headgroups, while the interaction of the FL with the membrane is shallower in nature. Thus, we propose a structural model relevant to fusion at the plasma membrane in which the FP inserts itself just below the phospholipid headgroups and the FL lays upon the lipid membrane surface.
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Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Plant Alkaloids Inhibit Membrane Fusion Mediated by Calcium and Fragments of MERS-CoV and SARS-CoV/SARS-CoV-2 Fusion Peptides. Biomedicines 2021; 9:biomedicines9101434. [PMID: 34680551 PMCID: PMC8533497 DOI: 10.3390/biomedicines9101434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
To rationalize the antiviral actions of plant alkaloids, the ability of 20 compounds to inhibit calcium-mediated fusion of lipid vesicles composed of phosphatidylglycerol and cholesterol was investigated using the calcein release assay and dynamic light scattering. Piperine, tabersonine, hordenine, lupinine, quinine, and 3-isobutyl-1-methylxanthine demonstrated the most potent effects (inhibition index greater than 50%). The introduction of phosphatidylcholine into the phosphatidylglycerol/cholesterol mixture led to significant changes in quinine, hordenine, and 3-isobutyl-1-methylxanthine efficiency. Comparison of the fusion inhibitory ability of the tested alkaloids, and the results of the measurements of alkaloid-induced alterations in the physical properties of model membranes indicated a potent relationship between a decrease in the cooperativity of the phase transition of lipids and the ability of alkaloids to prevent calcium-mediated vesicle fusion. In order to use this knowledge to combat the novel coronavirus pandemic, the ability of the most effective compounds to suppress membrane fusion induced by fragments of MERS-CoV and SARS-CoV/SARS-CoV-2 fusion peptides was studied using the calcein release assay and confocal fluorescence microscopy. Piperine was shown to inhibit vesicle fusion mediated by both coronavirus peptides. Moreover, piperine was shown to significantly reduce the titer of SARS-CoV2 progeny in vitro in Vero cells when used in non-toxic concentrations.
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Straus MR, Bidon MK, Tang T, Jaimes JA, Whittaker GR, Daniel S. Inhibitors of L-Type Calcium Channels Show Therapeutic Potential for Treating SARS-CoV-2 Infections by Preventing Virus Entry and Spread. ACS Infect Dis 2021; 7:2807-2815. [PMID: 34498840 PMCID: PMC8442615 DOI: 10.1021/acsinfecdis.1c00023] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Indexed: 01/06/2023]
Abstract
COVID-19 is caused by a novel coronavirus, the severe acute respiratory syndrome coronavirus (CoV)-2 (SARS-CoV-2). The virus is responsible for an ongoing pandemic and concomitant public health crisis around the world. While vaccine development is proving to be highly successful, parallel drug development approaches are also critical in the response to SARS-CoV-2 and other emerging viruses. Coronaviruses require Ca2+ ions for host cell entry, and we have previously shown that Ca2+ modulates the interaction of the viral fusion peptide with host cell membranes. In an attempt to accelerate drug repurposing, we tested a panel of L-type calcium channel blocker (CCB) drugs currently developed for other conditions to determine whether they would inhibit SARS-CoV-2 infection in cell culture. All the CCBs tested showed varying degrees of inhibition, with felodipine and nifedipine strongly limiting SARS-CoV-2 entry and infection in epithelial lung cells at concentrations where cell toxicity was minimal. Further studies with pseudotyped particles displaying the SARS-CoV-2 spike protein suggested that inhibition occurs at the level of virus entry. Overall, our data suggest that certain CCBs have the potential to treat SARS-CoV-2 infections and are worthy of further examination for possible treatment of COVID-19.
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Affiliation(s)
- Marco R. Straus
- Department of Microbiology & Immunology, College
of Veterinary Medicine, Cornell University, Ithaca, New York
14853, United States
| | - Miya K. Bidon
- Robert Frederick Smith School of Chemical &
Biomolecular Engineering, Cornell University, Ithaca, New York
14853, United States
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical &
Biomolecular Engineering, Cornell University, Ithaca, New York
14853, United States
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College
of Veterinary Medicine, Cornell University, Ithaca, New York
14853, United States
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College
of Veterinary Medicine, Cornell University, Ithaca, New York
14853, United States
- Master of Public Health Program, Cornell
University, Ithaca, New York 14853, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical &
Biomolecular Engineering, Cornell University, Ithaca, New York
14853, United States
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Takeda M. Proteolytic activation of SARS-CoV-2 spike protein. Microbiol Immunol 2021; 66:15-23. [PMID: 34561887 PMCID: PMC8652499 DOI: 10.1111/1348-0421.12945] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 11/27/2022]
Abstract
Spike (S) protein cleavage is a crucial step in coronavirus infection. In this review, this process is discussed, with particular focus on the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Compared with influenza virus and paramyxovirus membrane fusion proteins, the cleavage activation mechanism of coronavirus S protein is much more complex. The S protein has two cleavage sites (S1/S2 and S2′), and the cleavage motif for furin protease at the S1/S2 site that results from a unique four‐amino acid insertion is one of the distinguishing features of SARS‐CoV‐2. The viral particle incorporates the S protein, which has already undergone S1/S2 cleavage by furin, and then undergoes further cleavage at the S2′ site, mediated by the type II transmembrane serine protease transmembrane protease serine 2 (TMPRSS2), after binding to the receptor angiotensin‐converting enzyme 2 (ACE2) to facilitate membrane fusion at the plasma membrane. In addition, SARS‐CoV‐2 can enter the cell by endocytosis and be proteolytically activated by cathepsin L, although this is not a major mode of SARS‐CoV‐2 infection. SARS‐CoV‐2 variants with enhanced infectivity have been emerging throughout the ongoing pandemic, and there is a close relationship between enhanced infectivity and changes in S protein cleavability. All four variants of concern carry the D614G mutation, which indirectly enhances S1/S2 cleavability by furin. The P681R mutation of the delta variant directly increases S1/S2 cleavability, enhancing membrane fusion and SARS‐CoV‐2 virulence. Changes in S protein cleavability can significantly impact viral infectivity, tissue tropism, and virulence. Understanding these mechanisms is critical to counteracting the coronavirus pandemic.
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Affiliation(s)
- Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
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Rotondo JC, Martini F, Maritati M, Mazziotta C, Di Mauro G, Lanzillotti C, Barp N, Gallerani A, Tognon M, Contini C. SARS-CoV-2 Infection: New Molecular, Phylogenetic, and Pathogenetic Insights. Efficacy of Current Vaccines and the Potential Risk of Variants. Viruses 2021; 13:1687. [PMID: 34578269 PMCID: PMC8473168 DOI: 10.3390/v13091687] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly discovered coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic. COVID-19 has rapidly become a public health emergency of international concern. Although remarkable scientific achievements have been reached since the beginning of the pandemic, the knowledge behind this novel coronavirus, in terms of molecular and pathogenic characteristics and zoonotic potential, is still relatively limited. Today, there is a vaccine, or rather several vaccines, which, for the first time in the history of highly contagious infectious diseases that have plagued mankind, has been manufactured in just one year. Currently, four vaccines are licensed by regulatory agencies, and they use RNA or viral vector technologies. The positive effects of the vaccination campaign are being felt in many parts of the world, but the disappearance of this new infection is still far from being a reality, as it is also threatened by the presence of novel SARS-CoV-2 variants that could undermine the effectiveness of the vaccine, hampering the immunization control efforts. Indeed, the current findings indicate that SARS-CoV-2 is adapting to transmission in humans more efficiently, while further divergence from the initial archetype should be considered. In this review, we aimed to provide a collection of the current knowledge regarding the molecular, phylogenetic, and pathogenetic insights into SARS-CoV-2. The most recent findings obtained with respect to the impact of novel emerging SARS-CoV-2 variants as well as the development and implementation of vaccines are highlighted.
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Affiliation(s)
- John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Martina Maritati
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Giulia Di Mauro
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Carmen Lanzillotti
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Nicole Barp
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Altea Gallerani
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Carlo Contini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
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40
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Schaefer SL, Jung H, Hummer G. Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. J Phys Chem B 2021; 125:7732-7741. [PMID: 34255499 PMCID: PMC8311640 DOI: 10.1021/acs.jpcb.1c04176] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
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During infection
the SARS-CoV-2 virus fuses its viral envelope
with cellular membranes of its human host. The viral spike (S) protein
mediates both the initial contact with the host cell and the subsequent
membrane fusion. Proteolytic cleavage of S at the S2′ site
exposes its fusion peptide (FP) as the new N-terminus. By binding
to the host membrane, the FP anchors the virus to the host cell. The
reorganization of S2 between virus and host then pulls the two membranes
together. Here we use molecular dynamics (MD) simulations to study
the two core functions of the SARS-CoV-2 FP: to attach quickly to
cellular membranes and to form an anchor strong enough to withstand
the mechanical force during membrane fusion. In eight 10 μs
long MD simulations of FP in proximity to endosomal and plasma membranes,
we find that FP binds spontaneously to the membranes and that binding
proceeds predominantly by insertion of two short amphipathic helices
into the membrane interface. Connected via a flexible linker, the
two helices can bind the membrane independently, yet binding of one
promotes the binding of the other by tethering it close to the target
membrane. By simulating mechanical pulling forces acting on the C-terminus
of the FP, we then show that the bound FP can bear forces up to 250
pN before detaching from the membrane. This detachment force is more
than 10-fold higher than an estimate of the force required to pull
host and viral membranes together for fusion. We identify a fully
conserved disulfide bridge in the FP as a major factor for the high
mechanical stability of the FP membrane anchor. We conclude, first,
that the sequential binding of two short amphipathic helices allows
the SARS-CoV-2 FP to insert quickly into the target membrane, before
the virion is swept away after shedding the S1 domain connecting it
to the host cell receptor. Second, we conclude that the double attachment
and the conserved disulfide bridge establish the strong anchoring
required for subsequent membrane fusion. Multiple distinct membrane-anchoring
elements ensure high avidity and high mechanical strength of FP–membrane
binding.
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Affiliation(s)
- Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Hendrik Jung
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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41
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Chrysostomou AC, Vrancken B, Koumbaris G, Themistokleous G, Aristokleous A, Masia C, Eleftheriou C, Iοannou C, Stylianou DC, Ioannides M, Petrou P, Georgiou V, Hatziyianni A, Lemey P, Vandamme AM, Patsalis PP, Kostrikis LG. A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Viruses 2021; 13:1098. [PMID: 34207490 PMCID: PMC8227210 DOI: 10.3390/v13061098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/19/2022] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island.
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Affiliation(s)
- Andreas C. Chrysostomou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
| | - George Koumbaris
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
| | - George Themistokleous
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Christina Eleftheriou
- Department of Health and Safety, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus;
| | - Costakis Iοannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Marios Ioannides
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
| | - Panagiotis Petrou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Amalia Hatziyianni
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
- Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Philippos P. Patsalis
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
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42
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Lai AL, Freed JH. SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca 2. J Mol Biol 2021; 433:166946. [PMID: 33744314 PMCID: PMC7969826 DOI: 10.1016/j.jmb.2021.166946] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 11/03/2022]
Abstract
Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our previous ESR studies, the local membrane ordering effect of the fusion peptide (FP) of various viral glycoproteins including the S of SARS-1 and MERS has been consistently observed. We previously determined that the sequence immediately downstream from the S2′ cleavage site is the bona fide SARS-1 FP. In this study, we used sequence alignment to identify the SARS-2 FP, and studied its membrane ordering effect. Although there are only three residue differences, SARS-2 FP induces even greater membrane ordering than SARS-1 FP, possibly due to its greater hydrophobicity. This may be a reason that SARS-2 is better able to infect host cells. In addition, the membrane binding enthalpy for SARS-2 is greater. Both the membrane ordering of SARS-2 and SARS-1 FPs are dependent on Ca2+, but that of SARS-2 shows a greater response to the presence of Ca2+. Both FPs bind two Ca2+ ions as does SARS-1 FP, but the two Ca2+ binding sites of SARS-2 exhibit greater cooperativity. This Ca2+ dependence by the SARS-2 FP is very ion-specific. These results show that Ca2+ is an important regulator that interacts with the SARS-2 FP and thus plays a significant role in SARS-2 viral entry. This could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca2+ channel.
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Affiliation(s)
- Alex L Lai
- ACERT, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Jack H Freed
- ACERT, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States.
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43
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Whittaker GR, Daniel S, Millet JK. Coronavirus entry: how we arrived at SARS-CoV-2. Curr Opin Virol 2021; 47:113-120. [PMID: 33744490 PMCID: PMC7942143 DOI: 10.1016/j.coviro.2021.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/08/2021] [Accepted: 02/25/2021] [Indexed: 01/12/2023]
Abstract
Because of the COVID-19 pandemic, the novel coronavirus SARS-CoV-2 has risen to shape scientific research during 2020, with its spike (S) protein being a predominant focus. The S protein is likely the most complicated of all viral glycoproteins and is a key factor in immunological responses and virus pathogenesis. It is also the driving force dictating virus entry mechanisms, which are highly ‘plastic’ for coronaviruses, allowing a plethora of options for different virus variants and strains in different cell types. Here we review coronavirus entry as a foundation for current work on SARS-CoV-2. We focus on the post-receptor binding events and cellular pathways that direct the membrane fusion events necessary for genome delivery, including S proteolytic priming and activation. We also address aspects of the entry process important for virus evolution and therapeutic development.
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Affiliation(s)
- Gary R Whittaker
- Department of Microbiology and Immunology and Master of Public Health Program, Cornell University, Ithaca, NY, USA.
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
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44
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Gorgun D, Lihan M, Kapoor K, Tajkhorshid E. Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane. Biophys J 2021; 120:2914-2926. [PMID: 33675757 PMCID: PMC7929786 DOI: 10.1016/j.bpj.2021.02.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
Infection of human cells by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics simulations that take advantage of the highly mobile membrane mimetic model to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas, each for 300 ns. In 73% of the simulations, the FP reaches a stable, membrane-bound configuration, in which the peptide deeply penetrated into the membrane. Clustering of the results reveals three major membrane-binding modes (binding modes 1-3), in which binding mode 1 populates over half of the data points. Taking into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, the significant depth of penetration of the whole peptide, and the dense population of the respective cluster, we propose that the most deeply inserted membrane-bound form (binding mode 1) represents more closely the biologically relevant form. Analysis of FP-lipid interactions shows the involvement of specific residues, previously described as the "fusion-active core residues," in membrane binding. Taken together, the results shed light on a key step involved in SARS-CoV2 infection, with potential implications in designing novel inhibitors.
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Affiliation(s)
- Defne Gorgun
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Muyun Lihan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Karan Kapoor
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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45
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Schlick T, Sundberg EJ, Schroeder SJ, Babu MM. Biophysicists' outstanding response to Covid-19. Biophys J 2021; 120:E1-E2. [PMID: 33689685 PMCID: PMC7931721 DOI: 10.1016/j.bpj.2021.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - M Madan Babu
- St Jude Children's Research Hospital, Memphis, Tennessee
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46
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Wenzhong L, Hualan L. COVID-19: the CaMKII-like system of S protein drives membrane fusion and induces syncytial multinucleated giant cells. Immunol Res 2021; 69:496-519. [PMID: 34410575 PMCID: PMC8374125 DOI: 10.1007/s12026-021-09224-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/24/2021] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 S protein on the membrane of infected cells can promote receptor-dependent syncytia formation, relating to extensive tissue damage and lymphocyte elimination. In this case, it is challenging to obtain neutralizing antibodies and prevent them through antibodies effectively. Considering that, in the current study, structural domain search methods are adopted to analyze the SARS-CoV-2 S protein to find the fusion mechanism. The results show that after the EF-hand domain of S protein bound to calcium ions, S2 protein had CaMKII protein activities. Besides, the CaMKII_AD domain of S2 changed S2 conformation, facilitating the formation of HR1-HR2 six-helix bundles. Apart from that, the Ca2+-ATPase of S2 pumped calcium ions from the virus cytoplasm to help membrane fusion, while motor structures of S drove the CaATP_NAI and CaMKII_AD domains to extend to the outside and combined the viral membrane and the cell membrane, thus forming a calcium bridge. Furthermore, the phospholipid-flipping-ATPase released water, triggering lipid mixing and fusion and generating fusion pores. Then, motor structures promoted fusion pore extension, followed by the cytoplasmic contents of the virus being discharged into the cell cytoplasm. After that, the membrane of the virus slid onto the cell membrane along the flowing membrane on the gap of the three CaATP_NAI. At last, the HR1-HR2 hexamer would fall into the cytoplasm or stay on the cell membrane. Therefore, the CaMKII_like system of S protein facilitated membrane fusion for further inducing syncytial multinucleated giant cells.
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Affiliation(s)
- Liu Wenzhong
- grid.412605.40000 0004 1798 1351School of Computer Science and Engineering, Sichuan University of Science & Engineering, Zigong, 643002 China ,grid.413041.30000 0004 1808 3369School of Life Science and Food Engineering, Yibin University, Yibin, 644000 China
| | - Li Hualan
- grid.413041.30000 0004 1808 3369School of Life Science and Food Engineering, Yibin University, Yibin, 644000 China
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