1
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Birtles D, Guiyab L, Abbas W, Lee J. Positive residues of the SARS-CoV-2 fusion domain are key contributors to the initiation of membrane fusion. J Biol Chem 2024; 300:107564. [PMID: 39002677 PMCID: PMC11357847 DOI: 10.1016/j.jbc.2024.107564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
SARS-CoV-2 is one of the most infectious viruses ever recorded. Despite a plethora of research over the last several years, the viral life cycle is still not well understood, particularly membrane fusion. This process is initiated by the fusion domain (FD), a highly conserved stretch of amino acids consisting of a fusion peptide (FP) and fusion loop (FL), which in synergy perturbs the target cells' lipid membrane to lower the energetic cost necessary for fusion. In this study, through a mutagenesis-based approach, we have investigated the basic residues within the FD (K825, K835, R847, K854) utilizing an in vitro fusion assay and 19F NMR, validated by traditional 13C 15N techniques. Alanine and charge-conserving mutants revealed every basic residue plays a highly specific role within the mechanism of initiating fusion. Intriguingly, K825A led to increased fusogenecity which was found to be correlated to the number of amino acids within helix one, further implicating the role of this specific helix within the FD's fusion mechanism. This work has found basic residues to be important within the FDs fusion mechanism and highlights K825A, a specific mutation made within the FD of the SARS-CoV-2 spike protein, as requiring further investigation due to its potential to contribute to a more virulent strain of SARS-CoV-2.
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Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Lijon Guiyab
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Wafa Abbas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA.
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2
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Ali MA, Caetano-Anollés G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants. BIOLOGY 2024; 13:134. [PMID: 38534404 DOI: 10.3390/biology13030134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development.
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Affiliation(s)
- Muhammad Asif Ali
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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3
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Zannella C, Chianese A, Monti A, Giugliano R, Morone MV, Secci F, Sanna G, Manzin A, De Filippis A, Doti N, Galdiero M. SARS-CoV-2 Fusion Peptide Conjugated to a Tetravalent Dendrimer Selectively Inhibits Viral Infection. Pharmaceutics 2023; 15:2791. [PMID: 38140131 PMCID: PMC10748278 DOI: 10.3390/pharmaceutics15122791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Fusion is a key event for enveloped viruses, through which viral and cell membranes come into close contact. This event is mediated by viral fusion proteins, which are divided into three structural and functional classes. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein belongs to class I fusion proteins, characterized by a trimer of helical hairpins and an internal fusion peptide (FP), which is exposed once fusion occurs. Many efforts have been directed at finding antivirals capable of interfering with the fusion mechanism, mainly by designing peptides on the two heptad-repeat regions present in class I viral fusion proteins. Here, we aimed to evaluate the anti-SARS-CoV-2 activity of the FP sequence conjugated to a tetravalent dendrimer through a classical organic nucleophilic substitution reaction (SN2) using a synthetic bromoacetylated peptide mimicking the FP and a branched scaffold of poly-L-Lysine functionalized with cysteine residues. We found that the FP peptide conjugated to the dendrimer, unlike the monomeric FP sequence, has virucidal activity by impairing the attachment of SARS-CoV-2 to cells. Furthermore, we found that the peptide dendrimer does not have the same effects on other coronaviruses, demonstrating that it is selective against SARS-CoV-2.
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Affiliation(s)
- Carla Zannella
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (R.G.); (M.V.M.); (A.D.F.)
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (R.G.); (M.V.M.); (A.D.F.)
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Naples, Italy; (A.M.); (N.D.)
| | - Rosa Giugliano
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (R.G.); (M.V.M.); (A.D.F.)
| | - Maria Vittoria Morone
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (R.G.); (M.V.M.); (A.D.F.)
| | - Francesco Secci
- Department of Chemical and Geological Sciences, University of Cagliari, University Campus, 09042 Cagliari, Italy;
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, University Campus, 09042 Cagliari, Italy; (G.S.); (A.M.)
| | - Aldo Manzin
- Department of Biomedical Sciences, University of Cagliari, University Campus, 09042 Cagliari, Italy; (G.S.); (A.M.)
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (R.G.); (M.V.M.); (A.D.F.)
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Naples, Italy; (A.M.); (N.D.)
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (R.G.); (M.V.M.); (A.D.F.)
- UOC of Virology and Microbiology, University Hospital of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
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4
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Wu L, Zheng A, Tang Y, Chai Y, Chen J, Cheng L, Hu Y, Qu J, Lei W, Liu WJ, Wu G, Zeng S, Yang H, Wang Q, Gao GF. A pan-coronavirus peptide inhibitor prevents SARS-CoV-2 infection in mice by intranasal delivery. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2201-2213. [PMID: 37574525 DOI: 10.1007/s11427-023-2410-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023]
Abstract
Coronaviruses (CoVs) have brought serious threats to humans, particularly severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which continually evolves into multiple variants. These variants, especially Omicron, reportedly escape therapeutic antibodies and vaccines, indicating an urgent need for new antivirals with pan-SARS-CoV-2 inhibitory activity. We previously reported that a peptide fusion inhibitor, P3, targeting heptad repeated-1 (HR1) of SARS-CoV-2 spike (S) protein, could inhibit viral infections. Here, we further designed multiple derivatives of the P3 based on structural analysis and found that one derivative, the P315V3, showed the most efficient antiviral activity against SARS-CoV-2 variants and several other sarbecoviruses, as well as other human-CoVs (HCoVs). P315V3 also exhibited effective prophylactic efficacy against the SARS-CoV-2 Delta and Omicron variants in mice via intranasal administration. These results suggest that P315V3, which is in Phase II clinical trial, is promising for further development as a nasal pan-SARS-CoV-2 or pan-CoVs inhibitor to prevent or treat CoV diseases.
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Affiliation(s)
- Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangming Tang
- Hybio Pharmaceutical Co., Ltd., Shenzhen, 518109, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiantao Chen
- Hybio Pharmaceutical Co., Ltd., Shenzhen, 518109, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Yu Hu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Jing Qu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - William Jun Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shaogui Zeng
- Hybio Pharmaceutical Co., Ltd., Shenzhen, 518109, China
| | - Hang Yang
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Hubei Jiangxia Laboratory, Wuhan, 430299, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
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5
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Strizzi S, Bernardo L, D'Ursi P, Urbinati C, Bianco A, Limanaqi F, Manconi A, Milanesi M, Macchi A, Di Silvestre D, Cavalleri A, Pareschi G, Rusnati M, Clerici M, Mauri P, Biasin M. An innovative strategy to investigate microbial protein modifications in a reliable fast and sensitive way: A therapy oriented proof of concept based on UV-C irradiation of SARS-CoV-2 spike protein. Pharmacol Res 2023; 194:106862. [PMID: 37479104 DOI: 10.1016/j.phrs.2023.106862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
The characterization of modifications of microbial proteins is of primary importance to dissect pathogen lifecycle mechanisms and could be useful in identifying therapeutic targets. Attempts to solve this issue yielded only partial and non-exhaustive results. We developed a multidisciplinary approach by coupling in vitro infection assay, mass spectrometry (MS), protein 3D modelling, and surface plasma resonance (SPR). As a proof of concept, the effect of low UV-C (273 nm) irradiation on SARS-CoV-2 spike (S) protein was investigated. Following UV-C exposure, MS analysis identified, among other modifications, the disruption of a disulphide bond within the conserved S2 subunit of S protein. Computational analyses revealed that this bond breakage associates with an allosteric effect resulting in the generation of a closed conformation with a reduced ability to bind the ACE2 receptor. The UV-C-induced reduced affinity of S protein for ACE2 was further confirmed by SPR analyses and in vitro infection assays. This comprehensive approach pinpoints the S2 domain of S protein as a potential therapeutic target to prevent SARS-CoV-2 infection. Notably, this workflow could be used to screen a wide variety of microbial protein domains, resulting in a precise molecular fingerprint and providing new insights to adequately address future epidemics.
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Affiliation(s)
- Sergio Strizzi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Letizia Bernardo
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Pasqualina D'Ursi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Chiara Urbinati
- Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Andrea Bianco
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Fiona Limanaqi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Andrea Manconi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Maria Milanesi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy; Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Macchi
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Adalberto Cavalleri
- Epidemiology and Prevention Unit, IRCCS Foundation, Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy
| | - Giovanni Pareschi
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Marco Rusnati
- Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy; Don C. Gnocchi Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Foundation, Via A. Capecelatro 66, 20148 Milan, íItaly
| | - PierLuigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy; Interdisciplinary Research Center "Health Science", Sant'Anna School of Advanced Studies, 56127 Pisa, Italy.
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
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6
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The Evolutionary Dance between Innate Host Antiviral Pathways and SARS-CoV-2. Pathogens 2022; 11:pathogens11050538. [PMID: 35631059 PMCID: PMC9147806 DOI: 10.3390/pathogens11050538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 02/04/2023] Open
Abstract
Compared to what we knew at the start of the SARS-CoV-2 global pandemic, our understanding of the interplay between the interferon signaling pathway and SARS-CoV-2 infection has dramatically increased. Innate antiviral strategies range from the direct inhibition of viral components to reprograming the host’s own metabolic pathways to block viral infection. SARS-CoV-2 has also evolved to exploit diverse tactics to overcome immune barriers and successfully infect host cells. Herein, we review the current knowledge of the innate immune signaling pathways triggered by SARS-CoV-2 with a focus on the type I interferon response, as well as the mechanisms by which SARS-CoV-2 impairs those defenses.
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7
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Dzuvor CKO, Tettey EL, Danquah MK. Aptamers as promising nanotheranostic tools in the COVID-19 pandemic era. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1785. [PMID: 35238490 PMCID: PMC9111085 DOI: 10.1002/wnan.1785] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
The emergence of SARS-COV-2, the causative agent of new coronavirus disease (COVID-19) has become a pandemic threat. Early and precise detection of the virus is vital for effective diagnosis and treatment. Various testing kits and assays, including nucleic acid detection methods, antigen tests, serological tests, and enzyme-linked immunosorbent assay (ELISA), have been implemented or are being explored to detect the virus and/or characterize cellular and antibody responses to the infection. However, these approaches have inherent drawbacks such as nonspecificity, high cost, are characterized by long turnaround times for test results, and can be labor-intensive. Also, the circulating SARS-COV-2 variant of concerns, reduced antibody sensitivity and/or neutralization, and possible antibody-dependent enhancement (ADE) have warranted the search for alternative potent therapeutics. Aptamers, which are single-stranded oligonucleotides, generated artificially by SELEX (Evolution of Ligands by Exponential Enrichment) may offer the capacity to generate high-affinity neutralizers and/or bioprobes for monitoring relevant SARS-COV-2 and COVID-19 biomarkers. This article reviews and discusses the prospects of implementing aptamers for rapid point-of-care detection and treatment of SARS-COV-2. We highlight other SARS-COV-2 targets (N protein, spike protein stem-helix), SELEX augmented with competition assays and in silico technologies for rapid discovery and isolation of theranostic aptamers against COVID-19 and future pandemics. It further provides an overview on site-specific bioconjugation approaches, customizable molecular scaffolding strategies, and nanotechnology platforms to engineer these aptamers into ultrapotent blockers, multivalent therapeutics, and vaccines to boost both humoral and cellular immunity against the virus. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Biosensing Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease.
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Affiliation(s)
- Christian K. O. Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological EngineeringMonash UniversityClaytonVictoriaAustralia
| | | | - Michael K. Danquah
- Department of Chemical EngineeringUniversity of TennesseeChattanoogaTennesseeUSA
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8
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Magazine N, Zhang T, Wu Y, McGee MC, Veggiani G, Huang W. Mutations and Evolution of the SARS-CoV-2 Spike Protein. Viruses 2022; 14:640. [PMID: 35337047 PMCID: PMC8949778 DOI: 10.3390/v14030640] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 spike protein mediates target recognition, cellular entry, and ultimately the viral infection that leads to various levels of COVID-19 severities. Positive evolutionary selection of mutations within the spike protein has led to the genesis of new SARS-CoV-2 variants with greatly enhanced overall fitness. Given the trend of variants with increased fitness arising from spike protein alterations, it is critical that the scientific community understand the mechanisms by which these mutations alter viral functions. As of March 2022, five SARS-CoV-2 strains were labeled "variants of concern" by the World Health Organization: the Alpha, Beta, Gamma, Delta, and Omicron variants. This review summarizes the potential mechanisms by which the common mutations on the spike protein that occur within these strains enhance the overall fitness of their respective variants. In addressing these mutations within the context of the SARS-CoV-2 spike protein structure, spike/receptor binding interface, spike/antibody binding, and virus neutralization, we summarize the general paradigms that can be used to estimate the effects of future mutations along SARS-CoV-2 evolution.
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Affiliation(s)
- Nicholas Magazine
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70802, USA; (N.M.); (T.Z.); (M.C.M.)
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70802, USA; (N.M.); (T.Z.); (M.C.M.)
| | - Yingying Wu
- Center of Mathematical Sciences and Applications, Harvard University, Cambridge, MA 02138, USA;
| | - Michael C. McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70802, USA; (N.M.); (T.Z.); (M.C.M.)
| | - Gianluca Veggiani
- The Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada;
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70802, USA; (N.M.); (T.Z.); (M.C.M.)
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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9
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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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10
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Akram F, Haq IU, Aqeel A, Ahmed Z, Shah FI, Nawaz A, Zafar J, Sattar R. Insights into the evolutionary and prophylactic analysis of SARS-CoV-2: A review. J Virol Methods 2022; 300:114375. [PMID: 34838536 PMCID: PMC8610842 DOI: 10.1016/j.jviromet.2021.114375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 10/29/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023]
Abstract
In late 2019, following the emergence of a β-originated SARS-CoV-2, phylogenetic and evolutionary approaches have been demonstrated to strengthen the diagnostic and prophylactic stratagem of COVID-19 at an unprecedented level. Despite its clinical prominence, the SARS-CoV-2 gene set remains largely irrefutable by impeding the dissection of COVID-19 biology. However, many pieces of molecular and serological evidence have predicted that SARS-CoV-2 related viruses carry their roots from bats and pangolins of South East Asia. Analysis of viral genome predicts that point mutations at a rate of 10-4 nucleotides per base in the receptor-binding domain allow the emergence of new SARS-CoV-2 genomic variants at regular intervals. Research in the evolution of molecular pathways involved in emergence of pandemic is critical for the development of therapeutics and vaccines as well as the prevention of future zoonosis. By determining the phyletic lineages of the SARS-CoV-2 genomic variants and those of the conserved regions in the accessory and spike proteins of all the SARS-related coronaviruses, a universal vaccine against all human coronaviruses could be formulated which would revolutionize the field of medicine. This review highlighted the current development and future prospects of antiviral drugs, inhibitors, mesenchymal stem cells, passive immunization, targeted immune therapy and CRISPR-Cas-based prophylactic and therapeutic strategies against SARS-CoV-2. However, further investigations on Covid-19 pathogenesis is required for the successful fabrication of successful antivirals.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ali Nawaz
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Javaria Zafar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Rukhma Sattar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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11
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Düzgüneş N, Fernandez-Fuentes N, Konopka K. Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design. Pathogens 2021; 10:1599. [PMID: 34959554 PMCID: PMC8709411 DOI: 10.3390/pathogens10121599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Fusion of lipid-enveloped viruses with the cellular plasma membrane or the endosome membrane is mediated by viral envelope proteins that undergo large conformational changes following binding to receptors. The HIV-1 fusion protein gp41 undergoes a transition into a "six-helix bundle" after binding of the surface protein gp120 to the CD4 receptor and a co-receptor. Synthetic peptides that mimic part of this structure interfere with the formation of the helix structure and inhibit membrane fusion. This approach also works with the S spike protein of SARS-CoV-2. Here we review the peptide inhibitors of membrane fusion involved in infection by influenza virus, HIV-1, MERS and SARS coronaviruses, hepatitis viruses, paramyxoviruses, flaviviruses, herpesviruses and filoviruses. We also describe recent computational methods used for the identification of peptide sequences that can interact strongly with protein interfaces, with special emphasis on SARS-CoV-2, using the PePI-Covid19 database.
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Affiliation(s)
- Nejat Düzgüneş
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, UK;
| | - Krystyna Konopka
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
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12
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Panchal D, Kataria J, Patel K, Crowe K, Pai V, Azizogli A, Kadian N, Sanyal S, Roy A, Dodd‐o J, Acevedo‐Jake AM, Kumar VA. Peptide-Based Inhibitors for SARS-CoV-2 and SARS-CoV. ADVANCED THERAPEUTICS 2021; 4:2100104. [PMID: 34514085 PMCID: PMC8420164 DOI: 10.1002/adtp.202100104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/14/2021] [Indexed: 12/20/2022]
Abstract
The COVID-19 (coronavirus disease) global pandemic, caused by the spread of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus, currently has limited treatment options which include vaccines, anti-virals, and repurposed therapeutics. With their high specificity, tunability, and biocompatibility, small molecules like peptides are positioned to act as key players in combating SARS-CoV-2, and can be readily modified to match viral mutation rate. A recent expansion of the understanding of the viral structure and entry mechanisms has led to the proliferation of therapeutic viral entry inhibitors. In this comprehensive review, inhibitors of SARS and SARS-CoV-2 are investigated and discussed based on therapeutic design, inhibitory mechanistic approaches, and common targets. Peptide therapeutics are highlighted, which have demonstrated in vitro or in vivo efficacy, discuss advantages of peptide therapeutics, and common strategies in identifying targets for viral inhibition.
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Affiliation(s)
- Disha Panchal
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Jeena Kataria
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Kamiya Patel
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Kaytlyn Crowe
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Varun Pai
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Abdul‐Rahman Azizogli
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Neil Kadian
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Sreya Sanyal
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Abhishek Roy
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Joseph Dodd‐o
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
| | | | - Vivek A. Kumar
- Department of Biomedical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
- Department of Biomedical EngineeringDepartment of ChemicalBiological and Pharmaceutical EngineeringNew Jersey Institute of TechnologyNewarkNJ07102USA
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13
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Jalalvand A, Khatouni SB, Najafi ZB, Fatahinia F, Ismailzadeh N, Farahmand B. Computational drug repurposing study of antiviral drugs against main protease, RNA polymerase, and spike proteins of SARS-CoV-2 using molecular docking method. J Basic Clin Physiol Pharmacol 2021; 33:85-95. [PMID: 34265888 DOI: 10.1515/jbcpp-2020-0369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/16/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES The new Coronavirus (SARS-CoV-2) created a pandemic in the world in late 2019 and early 2020. Unfortunately, despite the increasing prevalence of the disease, there is no effective drug for the treatment. A computational drug repurposing study would be an appropriate and rapid way to provide an effective drug in the treatment of the coronavirus disease of 2019 (COVID-19) pandemic. In this study, the inhibitory potential of more than 50 antiviral drugs on three important proteins of SARS-CoV-2, was investigated using the molecular docking method. METHODS By literature review, three important proteins, including main protease, RNA-dependent RNA polymerase (RdRp), and spike, were selected as the drug targets. The three-dimensional (3D) structure of protease, spike, and RdRp proteins was obtained from the Protein Data Bank. Proteins were energy minimized. More than 50 antiviral drugs were considered as candidates for protein inhibition, and their 3D structure was obtained from Drug Bank. Molecular docking settings were defined using Autodock 4.2 software and the algorithm was executed. RESULTS Based on the estimated binding energy of docking and hydrogen bond analysis and the position of drug binding, five drugs including, indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, had the highest inhibitory potential for all three proteins. CONCLUSIONS According to the results, among the mentioned drugs, saquinavir and lopinavir showed the highest inhibitory potential for all three proteins compared to the other drugs. This study suggests that saquinavir and lopinavir could be included in the laboratory phase studies as a two-drug treatment for SARS-CoV-2 inhibition.
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Affiliation(s)
- Alireza Jalalvand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Somayeh Behjat Khatouni
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Zahra Bahri Najafi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Division of Genetics, Department of Cell and Molecular Biology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Foroozan Fatahinia
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Narges Ismailzadeh
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Department of Chemistry, Faculty of Science, University of Tarbiat Modarres, Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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14
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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: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
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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15
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Remington JM, McKay KT, Ferrell JB, Schneebeli ST, Li J. Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein. Biophys J 2021; 120:2848-2858. [PMID: 34087207 PMCID: PMC8169235 DOI: 10.1016/j.bpj.2021.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses.
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Affiliation(s)
| | - Kyle T McKay
- Department of Chemistry, University of Vermont, Burlington, Vermont
| | | | | | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, Vermont.
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16
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Pu J, Zhou JT, Liu P, Yu F, He X, Lu L, Jiang S. Viral Entry Inhibitors Targeting Six-Helical Bundle Core Against Highly Pathogenic Enveloped Viruses with Class I Fusion Proteins. Curr Med Chem 2021; 29:700-718. [PMID: 33992055 DOI: 10.2174/0929867328666210511015808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/22/2022]
Abstract
TypeⅠ enveloped viruses bind to cell receptors through surface glycoproteins to initiate infection or undergo receptor-mediated endocytosis. They also initiate membrane fusion in the acidic environment of endocytic compartments, releasing genetic material into the cell. In the process of membrane fusion, envelope protein exposes fusion peptide, followed by insertion into the cell membrane or endosomal membrane. Further conformational changes ensue in which the type 1 envelope protein forms a typical six-helix bundle structure, shortening the distance between viral and cell membranes so that fusion can occur. Entry inhibitors targeting viral envelope proteins, or host factors, are effective antiviral agents and have been widely studied. Some have been used clinically, such as T20 and Maraviroc for human immunodeficiency virus 1 (HIV-1) or Myrcludex B for hepatitis D virus (HDV). This review focuses on entry inhibitors that target the six-helical bundle core against highly pathogenic enveloped viruses with class I fusion proteins, including retroviruses, coronaviruses, influenza A viruses, paramyxoviruses, and filoviruses.
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Affiliation(s)
- Jing Pu
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Joey Tianyi Zhou
- Institute of High Performance Computing, The Agency for Science, Technology and Research, Singapore
| | - Ping Liu
- Institute of High Performance Computing, The Agency for Science, Technology and Research, Singapore
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaoyang He
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
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17
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Ashaolu TJ, Nawaz A, Walayat N, Khalifa I. Potential "biopeptidal" therapeutics for severe respiratory syndrome coronaviruses: a review of antiviral peptides, viral mechanisms, and prospective needs. Appl Microbiol Biotechnol 2021; 105:3457-3470. [PMID: 33876282 PMCID: PMC8054851 DOI: 10.1007/s00253-021-11267-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/25/2021] [Accepted: 04/04/2021] [Indexed: 01/10/2023]
Abstract
Although great advances have been made on large-scale manufacturing of vaccines and antiviral-based drugs, viruses persist as the major cause of human diseases nowadays. The recent pandemic of coronavirus disease-2019 (COVID-19) mounts a lot of stress on the healthcare sector and the scientific society to search continuously for novel components with antiviral possibility. Herein, we narrated the different tactics of using biopeptides as antiviral molecules that could be used as an interesting alternative to treat COVID-19 patients. The number of peptides with antiviral effects is still low, but such peptides already displayed huge potentials to become pharmaceutically obtainable as antiviral medications. Studies showed that animal venoms, mammals, plant, and artificial sources are the main sources of antiviral peptides, when bioinformatics tools are used. This review spotlights bioactive peptides with antiviral activities against human viruses, especially the coronaviruses such as severe acute respiratory syndrome (SARS) virus, Middle East respiratory syndrome (MERS) virus, and severe acute respiratory syndrome coronavirus 2 (SARS-COV-2 or SARS-nCOV19). We also showed the data about well-recognized peptides that are still under investigations, while presenting the most potent ones that may become medications for clinical use.
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Affiliation(s)
- Tolulope Joshua Ashaolu
- Institute of Research and Development, Duy Tan University, Da Nang, 550000 Vietnam
- Faculty of Environmental and Chemical Engineering, Duy Tan University, Da Nang, 550000 Vietnam
| | - Asad Nawaz
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, People’s Republic of China
| | - Noman Walayat
- Department of Food Science and Engineering, College of Ocean, Zhejiang University of Technology, Hangzhou, People’s Republic of China
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Banha University, 13736, Moshtohor, Cairo, Egypt
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18
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Verma J, Subbarao N. A comparative study of human betacoronavirus spike proteins: structure, function and therapeutics. Arch Virol 2021; 166:697-714. [PMID: 33483791 PMCID: PMC7821988 DOI: 10.1007/s00705-021-04961-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/20/2020] [Indexed: 01/24/2023]
Abstract
Coronaviruses are the paradigm of emerging 21st century zoonotic viruses, triggering numerous outbreaks and a severe global health crisis. The current COVID-19 pandemic caused by SARS-CoV-2 has affected more than 51 million people across the globe as of 12 November 2020. The crown-like spikes on the surface of the virion are the unique structural feature of viruses in the family Coronaviridae. The spike (S) protein adopts distinct conformations while mediating entry of the virus into the host. This multifunctional protein mediates the entry process by recognizing its receptor on the host cell, followed by the fusion of the viral membrane with the host cell membrane. This review article focuses on the structural and functional comparison of S proteins of the human betacoronaviruses, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we review the current state of knowledge about receptor recognition, the membrane fusion mechanism, structural epitopes, and glycosylation sites of the S proteins of these viruses. We further discuss various vaccines and other therapeutics such as monoclonal antibodies, peptides, and small molecules based on the S protein of these three viruses.
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Affiliation(s)
- Jyoti Verma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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19
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Abstract
Vaccines are urgently needed to control the coronavirus disease 2019 (COVID-19) pandemic and to help the return to pre-pandemic normalcy. A great many vaccine candidates are being developed, several of which have completed late-stage clinical trials and are reporting positive results. In this Progress article, we discuss which viral elements are used in COVID-19 vaccine candidates, why they might act as good targets for the immune system and the implications for protective immunity.
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Affiliation(s)
- Lianpan Dai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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20
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Schütz D, Ruiz-Blanco YB, Münch J, Kirchhoff F, Sanchez-Garcia E, Müller JA. Peptide and peptide-based inhibitors of SARS-CoV-2 entry. Adv Drug Deliv Rev 2020; 167:47-65. [PMID: 33189768 PMCID: PMC7665879 DOI: 10.1016/j.addr.2020.11.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022]
Abstract
To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.
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Affiliation(s)
- Desiree Schütz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany.
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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21
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Silva LR, da Silva Santos-Júnior PF, de Andrade Brandão J, Anderson L, Bassi ÊJ, Xavier de Araújo-Júnior J, Cardoso SH, da Silva-Júnior EF. Druggable targets from coronaviruses for designing new antiviral drugs. Bioorg Med Chem 2020; 28:115745. [PMID: 33007557 PMCID: PMC7836322 DOI: 10.1016/j.bmc.2020.115745] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 01/18/2023]
Abstract
Severe respiratory infections were highlighted in the SARS-CoV outbreak in 2002, as well as MERS-CoV, in 2012. Recently, the novel CoV (COVID-19) has led to severe respiratory damage to humans and deaths in Asia, Europe, and Americas, which allowed the WHO to declare the pandemic state. Notwithstanding all impacts caused by Coronaviruses, it is evident that the development of new antiviral agents is an unmet need. In this review, we provide a complete compilation of all potential antiviral agents targeting macromolecular structures from these Coronaviruses (Coronaviridae), providing a medicinal chemistry viewpoint that could be useful for designing new therapeutic agents.
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Affiliation(s)
- Leandro Rocha Silva
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | | | - Júlia de Andrade Brandão
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Letícia Anderson
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; CESMAC University Center, Cônego Machado Street, Maceió 57051-160, Brazil
| | - Ênio José Bassi
- IMUNOREG - Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Campus AC. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - João Xavier de Araújo-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Sílvia Helena Cardoso
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil.
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22
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Varghese PM, Tsolaki AG, Yasmin H, Shastri A, Ferluga J, Vatish M, Madan T, Kishore U. Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies. Immunobiology 2020; 225:152008. [PMID: 33130519 PMCID: PMC7434692 DOI: 10.1016/j.imbio.2020.152008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023]
Abstract
The current coronavirus pandemic, COVID-19, is the third outbreak of disease caused by the coronavirus family, after Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome. It is an acute infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This severe disease is characterised by acute respiratory distress syndrome, septic shock, metabolic acidosis, coagulation dysfunction, and multiple organ dysfunction syndromes. Currently, no drugs or vaccines exist against the disease and the only course of treatment is symptom management involving mechanical ventilation, immune suppressants, and repurposed drugs. The severe form of the disease has a relatively high mortality rate. The last six months have seen an explosion of information related to the host receptors, virus transmission, virus structure-function relationships, pathophysiology, co-morbidities, immune response, treatment and the most promising vaccines. This review takes a critically comprehensive look at various aspects of the host-pathogen interaction in COVID-19. We examine the genomic aspects of SARS-CoV-2, modulation of innate and adaptive immunity, complement-triggered microangiopathy, and host transmission modalities. We also examine its pathophysiological impact during pregnancy, in addition to emphasizing various gaps in our knowledge. The lessons learnt from various clinical trials involving repurposed drugs have been summarised. We also highlight the rationale and likely success of the most promising vaccine candidates.
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Affiliation(s)
- Praveen Mathews Varghese
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, London, United Kingdom; School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Anthony G Tsolaki
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, London, United Kingdom
| | - Hadida Yasmin
- Immunology and Cell Biology Laboratory, Department of Zoology, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
| | - Abhishek Shastri
- Central and North West London NHS Foundation Trust, London, United Kingdom
| | - Janez Ferluga
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, London, United Kingdom
| | - Manu Vatish
- Department of Obstetrics and Gynaecology, Women's Centre, John Radcliffe Oxford University Hospital, Oxford, OX3 9DU, United Kingdom
| | - Taruna Madan
- Department of Innate Immunity, ICMR - National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai, Maharashtra, India
| | - Uday Kishore
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, London, United Kingdom.
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Ling R, Dai Y, Huang B, Huang W, Yu J, Lu X, Jiang Y. In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. Peptides 2020; 130:170328. [PMID: 32380200 PMCID: PMC7198429 DOI: 10.1016/j.peptides.2020.170328] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/16/2020] [Accepted: 04/30/2020] [Indexed: 12/24/2022]
Abstract
An outbreak caused by 2019 novel coronavirus (2019-nCoV) was first identified in Wuhan City, Hubei Province, China. The new virus was later named SARS-CoV-2. The virus has affected tens of thousands of patients in the world. The infection of SARS-CoV-2 causes severe pneumonia and even death. It is urgently needed to find a therapeutic method to treat patients with SARS-CoV-2 infection. Studies showed that the surface spike (S) protein is essential for the coronavirus binding and entry of host cells. The heptad repeats 1 and 2 (HR1 and HR2) in the S protein play a decisive role in the fusion of the viral membrane with the host cell membrane. We predicted the HR1 and HR2 regions in S protein by sequence alignment. We simulated a computational model of HR1/2 regions and the fusion core. The binding energy of HR1 and HR2 of the fusion core was -33.4 kcal/mol. We then designed antivirus peptides by molecular dynamics simulation of the fusion core. The binding energy of HR2-based antiviral peptide to HR1 was -43.0 kcal/mol, which was stronger than the natural stage of the fusion core, suggesting that the predicted antiviral peptide can competitively bind with HR1 to prevent forming of the fusion core. The antiviral peptides can prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infections.
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Affiliation(s)
- Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yarong Dai
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Boxuan Huang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Wenjie Huang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jianfeng Yu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xifeng Lu
- Department of Physiology, Health Science Center, Shenzhen University, Guangdong 518055, China.
| | - Yizhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China.
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Protective Immunity against SARS Subunit Vaccine Candidates Based on Spike Protein: Lessons for Coronavirus Vaccine Development. J Immunol Res 2020; 2020:7201752. [PMID: 32695833 PMCID: PMC7368938 DOI: 10.1155/2020/7201752] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022] Open
Abstract
The recent outbreak of the novel coronavirus disease, COVID-19, has highlighted the threat that highly pathogenic coronaviruses have on global health security and the imminent need to design an effective vaccine for prevention purposes. Although several attempts have been made to develop vaccines against human coronavirus infections since the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in 2003, there is no available licensed vaccine yet. A better understanding of previous coronavirus vaccine studies may help to design a vaccine for the newly emerged virus, SARS-CoV-2, that may also cover other pathogenic coronaviruses as a potentially universal vaccine. In general, coronavirus spike protein is the major antigen for the vaccine design as it can induce neutralizing antibodies and protective immunity. By considering the high genetic similarity between SARS-CoV and SARS-CoV-2, here, protective immunity against SARS-CoV spike subunit vaccine candidates in animal models has been reviewed to gain advances that can facilitate coronavirus vaccine development in the near future.
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Fan X, Cao D, Kong L, Zhang X. Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein. Nat Commun 2020; 11:3618. [PMID: 32681106 PMCID: PMC7367865 DOI: 10.1038/s41467-020-17371-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/25/2020] [Indexed: 12/28/2022] Open
Abstract
Global emergencies caused by the severe acute respiratory syndrome coronavirus (SARS-CoV), Middle-East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2 significantly endanger human health. The spike (S) glycoprotein is the key antigen and its conserved S2 subunit contributes to viral entry by mediating host-viral membrane fusion. However, structural information of the post-fusion S2 from these highly pathogenic human-infecting coronaviruses is still lacking. We used single-particle cryo-electron microscopy to show that the post-fusion SARS-CoV S2 forms a further rotated HR1-HR2 six-helix bundle and a tightly bound linker region upstream of the HR2 motif. The structures of pre- and post-fusion SARS-CoV S glycoprotein dramatically differ, resembling that of the Mouse hepatitis virus (MHV) and other class I viral fusion proteins. This structure suggests potential targets for the development of vaccines and therapies against a wide range of SARS-like coronaviruses. The spike (S) protein of coronaviruses is responsible for receptor recognition and the fusion between the viral membrane and the of cell host membrane. Here the authors report a cryo-EM structure of SARS-CoV post-fusion S2 trimer, providing insights into the fusion mechanism that could be useful for therapeutic development against coronaviruses.
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Affiliation(s)
- Xiaoyi Fan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Lingfei Kong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,Center for Biological Imaging, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
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Molecular Basis of Binding between Middle East Respiratory Syndrome Coronavirus and CD26 from Seven Bat Species. J Virol 2020; 94:JVI.01387-19. [PMID: 31776269 PMCID: PMC7022362 DOI: 10.1128/jvi.01387-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/13/2019] [Indexed: 02/05/2023] Open
Abstract
In this study, we found that bat CD26s (bCD26s) from different species exhibit large diversities, especially in the region responsible for binding to the receptor binding domain (RBD) of Middle East respiratory syndrome coronavirus (MERS-CoV). However, they maintain the interaction with MERS-RBD at varied affinities and support the entry of pseudotyped MERS-CoV. These bat receptors polymorphisms seem to confer evolutionary pressure for the adaptation of CD26-binding virus, such as the ancestor of MERS-CoV, and led to the generation of diversified CD26-engaging CoV strains. Thus, our data add more evidence to support that bats are the reservoir of MERS-CoV and similar viruses, as well as further emphasize the necessity to survey MERS-CoV and other CoVs among bats. Continued reports of Middle East respiratory syndrome coronavirus (MERS-CoV) infecting humans have occurred since the identification of this virus in 2012. MERS-CoV is prone to cause endemic disease in the Middle East, with several dozen spillover infections to other continents. It is hypothesized that MERS-CoV originated from bat coronaviruses and that dromedary camels are its natural reservoir. Although gene segments identical to MERS-CoV were sequenced from certain species of bats and one species experimentally shed the virus, it is still unknown whether other bats can transmit the virus. Here, at the molecular level, we found that all purified bat CD26s (bCD26s) from a diverse range of species interact with the receptor binding domain (RBD) of MERS-CoV, with equilibrium dissociation constant values ranging from several to hundreds at the micromolar level. Moreover, all bCD26s expressed in this study mediated the entry of pseudotyped MERS-CoV to receptor-expressing cells, indicating the broad potential engagement of bCD26s as MERS-CoV receptors. Further structural analysis indicated that in the bat receptor, compared to the human receptor, substitutions of key residues and their adjacent amino acids leads to decreased binding affinity to the MERS-RBD. These results add more evidence to the existing belief that bats are the original source of MERS-CoV and suggest that bCD26s in many species can mediate the entry of the virus, which has significant implications for the surveillance and control of MERS-CoV infection. IMPORTANCE In this study, we found that bat CD26s (bCD26s) from different species exhibit large diversities, especially in the region responsible for binding to the receptor binding domain (RBD) of Middle East respiratory syndrome coronavirus (MERS-CoV). However, they maintain the interaction with MERS-RBD at varied affinities and support the entry of pseudotyped MERS-CoV. These bat receptors polymorphisms seem to confer evolutionary pressure for the adaptation of CD26-binding virus, such as the ancestor of MERS-CoV, and led to the generation of diversified CD26-engaging CoV strains. Thus, our data add more evidence to support that bats are the reservoir of MERS-CoV and similar viruses, as well as further emphasize the necessity to survey MERS-CoV and other CoVs among bats.
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Han X, Qi J, Song H, Wang Q, Zhang Y, Wu Y, Lu G, Yuen KY, Shi Y, Gao GF. Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein. Virology 2017; 507:101-109. [PMID: 28432925 PMCID: PMC7111649 DOI: 10.1016/j.virol.2017.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/10/2017] [Accepted: 04/15/2017] [Indexed: 02/05/2023]
Abstract
Accumulating evidence indicates that MERS-CoV originated from bat coronaviruses (BatCoVs). Previously, we demonstrated that both MERS-CoV and BatCoV HKU4 use CD26 as a receptor, but how the BatCoVs evolved to bind CD26 is an intriguing question. Here, we solved the crystal structure of the S1 subunit C-terminal domain of HKU5 (HKU5-CTD), another BatCoV that is phylogenetically related to MERS-CoV but cannot bind to CD26. We observed that the conserved core subdomain and those of other betacoronaviruses (betaCoVs) have a similar topology of the external subdomain, indicating the same ancestor of lineage C betaCoVs. However, two deletions in two respective loops located in HKU5-CTD result in conformational variations in CD26-binding interface and are responsible for the non-binding of HKU5-CTD to CD26. Combined with sequence variation in the HKU5-CTD receptor binding interface, we propose the necessity for surveilling the mutation in BatCoV HKU5 spike protein in case of bat-to-human interspecies transmission.
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Affiliation(s)
- Xue Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Song
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administration Region; Department of Microbiology, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administration Region; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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28
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Shen ZT, Sigalov AB. SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice. Sci Rep 2016; 6:28672. [PMID: 27349522 PMCID: PMC4923882 DOI: 10.1038/srep28672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/06/2016] [Indexed: 12/29/2022] Open
Abstract
During the co-evolution of viruses and their hosts, the viruses have evolved numerous strategies to counter and evade host antiviral immune responses in order to establish a successful infection, replicate and persist in the host. Recently, based on our model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, we suggested specific molecular mechanisms used by different viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) to modulate the host immune response mediated by members of the family of multichain immune recognition receptors (MIRRs). This family includes T cell receptor (TCR) that is critically involved in immune diseases such as autoimmune arthritis. In the present study, we provide compelling experimental in vivo evidence in support of our hypothesis. Using the SCHOOL approach and the SARS-CoV fusion peptide sequence, we rationally designed a novel immunomodulatory peptide that targets TCR. We showed that this peptide ameliorates collagen-induced arthritis in DBA/1J mice and protects against bone and cartilage damage. Incorporation of the peptide into self-assembling lipopeptide nanoparticles that mimic native human high density lipoproteins significantly increases peptide dosage efficacy. Together, our data further confirm that viral immune evasion strategies that target MIRRs can be transferred to therapeutic strategies that require similar functionalities.
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Affiliation(s)
- Zu T. Shen
- SignaBlok, Inc, P.O. Box 4064, Shrewsbury, MA 01545, United States of America
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29
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Lu L, Yu F, Cai L, Debnath AK, Jiang S. Development of Small-molecule HIV Entry Inhibitors Specifically Targeting gp120 or gp41. Curr Top Med Chem 2016; 16:1074-90. [PMID: 26324044 PMCID: PMC4775441 DOI: 10.2174/1568026615666150901114527] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/17/2015] [Accepted: 05/27/2015] [Indexed: 12/31/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope (Env) glycoprotein surface subunit gp120 and transmembrane subunit gp41 play important roles in HIV-1 entry, thus serving as key targets for the development of HIV-1 entry inhibitors. T20 peptide (enfuvirtide) is the first U.S. FDA-approved HIV entry inhibitor; however, its clinical application is limited by the lack of oral availability. Here, we have described the structure and function of the HIV-1 gp120 and gp41 subunits and reviewed advancements in the development of small-molecule HIV entry inhibitors specifically targeting these two Env glycoproteins. We then compared the advantages and disadvantages of different categories of HIV entry inhibitor candidates and further predicted the future trend of HIV entry inhibitor development.
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Affiliation(s)
| | | | | | | | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Medical College, Fudan University, 130 Dong An Road, Building #13, Shanghai 200032, China.
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30
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Lu G, Wang Q, Gao GF. Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond. Trends Microbiol 2015. [PMID: 26206723 PMCID: PMC7125587 DOI: 10.1016/j.tim.2015.06.003] [Citation(s) in RCA: 399] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bats are natural reservoirs of many coronaviruses that can infect humans. Mechanisms of cross-species transmission of coronaviruses are important scientific questions. The coronaviral spike protein is an important viral determinant of cross-species transmission. Receptor-binding characteristics and cleavage priming of the spike protein are summarized.
Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic pathogens that crossed the species barriers to infect humans. The mechanism of viral interspecies transmission is an important scientific question to be addressed. These coronaviruses contain a surface-located spike (S) protein that initiates infection by mediating receptor-recognition and membrane fusion and is therefore a key factor in host specificity. In addition, the S protein needs to be cleaved by host proteases before executing fusion, making these proteases a second determinant of coronavirus interspecies infection. Here, we summarize the progress made in the past decade in understanding the cross-species transmission of SARS-CoV and MERS-CoV by focusing on the features of the S protein, its receptor-binding characteristics, and the cleavage process involved in priming.
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Affiliation(s)
- Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Office of Director-General, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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31
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Developments in the Search for Small-Molecule Inhibitors for Treatment of Severe Acute Respiratory Syndrome Coronavirus. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Aydin H, Al-Khooly D, Lee JE. Influence of hydrophobic and electrostatic residues on SARS-coronavirus S2 protein stability: insights into mechanisms of general viral fusion and inhibitor design. Protein Sci 2014; 23:603-17. [PMID: 24519901 PMCID: PMC4005712 DOI: 10.1002/pro.2442] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/09/2014] [Accepted: 02/10/2014] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome (SARS) is an acute respiratory disease caused by the SARS-coronavirus (SARS-CoV). SARS-CoV entry is facilitated by the spike protein (S), which consists of an N-terminal domain (S1) responsible for cellular attachment and a C-terminal domain (S2) that mediates viral and host cell membrane fusion. The SARS-CoV S2 is a potential drug target, as peptidomimetics against S2 act as potent fusion inhibitors. In this study, site-directed mutagenesis and thermal stability experiments on electrostatic, hydrophobic, and polar residues to dissect their roles in stabilizing the S2 postfusion conformation was performed. It was shown that unlike the pH-independent retroviral fusion proteins, SARS-CoV S2 is stable over a wide pH range, supporting its ability to fuse at both the plasma membrane and endosome. A comprehensive SARS-CoV S2 analysis showed that specific hydrophobic positions at the C-terminal end of the HR2, rather than electrostatics are critical for fusion protein stabilization. Disruption of the conserved C-terminal hydrophobic residues destabilized the fusion core and reduced the melting temperature by 30°C. The importance of the C-terminal hydrophobic residues led us to identify a 42-residue substructure on the central core that is structurally conserved in all existing CoV S2 fusion proteins (root mean squared deviation = 0.4 Å). This is the first study to identify such a conserved substructure and likely represents a common foundation to facilitate viral fusion. We have discussed the role of key residues in the design of fusion inhibitors and the potential of the substructure as a general target for the development of novel therapeutics against CoV infections.
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Affiliation(s)
- Halil Aydin
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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33
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Lu L, Liu Q, Zhu Y, Chan KH, Qin L, Li Y, Wang Q, Chan JFW, Du L, Yu F, Ma C, Ye S, Yuen KY, Zhang R, Jiang S. Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor. Nat Commun 2014; 5:3067. [PMID: 24473083 PMCID: PMC7091805 DOI: 10.1038/ncomms4067] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/04/2013] [Indexed: 01/12/2023] Open
Abstract
A novel human coronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), has caused outbreaks of a SARS-like illness with high case fatality rate. The reports of its person-to-person transmission through close contacts have raised a global concern about its pandemic potential. Here we characterize the six-helix bundle fusion core structure of MERS-CoV spike protein S2 subunit by X-ray crystallography and biophysical analysis. We find that two peptides, HR1P and HR2P, spanning residues 998-1039 in HR1 and 1251-1286 in HR2 domains, respectively, can form a stable six-helix bundle fusion core structure, suggesting that MERS-CoV enters into the host cell mainly through membrane fusion mechanism. HR2P can effectively inhibit MERS-CoV replication and its spike protein-mediated cell-cell fusion. Introduction of hydrophilic residues into HR2P results in significant improvement of its stability, solubility and antiviral activity. Therefore, the HR2P analogues have good potential to be further developed into effective viral fusion inhibitors for treating MERS-CoV infection.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, 200032 China
| | - Qi Liu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, 200032 China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Kwok-Hung Chan
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Lili Qin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yuan Li
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, 200032 China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, 200032 China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065 New York USA
| | - Fei Yu
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065 New York USA
| | - Cuiqing Ma
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065 New York USA
| | - Sheng Ye
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Kwok-Yung Yuen
- Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rongguang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, 200032 China
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065 New York USA
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Kilianski A, Baker SC. Cell-based antiviral screening against coronaviruses: developing virus-specific and broad-spectrum inhibitors. Antiviral Res 2013; 101:105-12. [PMID: 24269477 PMCID: PMC3931262 DOI: 10.1016/j.antiviral.2013.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 10/31/2013] [Accepted: 11/09/2013] [Indexed: 01/19/2023]
Abstract
To combat the public health threat from emerging coronaviruses (CoV), the development of antiviral therapies with either virus-specific or pan-coronaviral activities is necessary. An important step in antiviral drug development is the screening of potential inhibitors in cell-based systems. The recent emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) necessitates adapting methods that have been used to identify antivirals against severe acute respiratory syndrome coronavirus (SARS-CoV) and developing new approaches to more efficiently screen antiviral drugs. In this article we review cell-based assays using infectious virus (BSL-3) and surrogate assays (BSL-2) that can be implemented to accelerate antiviral development against MERS-CoV and future emergent coronaviruses. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses."
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Affiliation(s)
- Andy Kilianski
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, United States
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, United States.
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35
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Structure of the fusion core and inhibition of fusion by a heptad repeat peptide derived from the S protein of Middle East respiratory syndrome coronavirus. J Virol 2013; 87:13134-40. [PMID: 24067982 DOI: 10.1128/jvi.02433-13] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) recently emerged as a severe worldwide public health concern. The virus is highly pathogenic, manifesting in infected patients with an approximately 50% fatality rate. It is known that the surface spike (S) proteins of coronaviruses mediate receptor recognition and membrane fusion, thereby playing an indispensable role in initiating infection. In this process, heptad repeats 1 and 2 (HR1 and HR2) of the S protein assemble into a complex called the fusion core, which represents a key membrane fusion architecture. To date, however, the MERS-CoV fusion core remains uncharacterized. In this study, we performed a series of biochemical and biophysical analyses characterizing the HR1/HR2 complexes of this novel virus. The HR sequences were variably truncated and then connected with a flexible amino acid linker. In each case, the recombinant protein automatically assembled into a trimer in solution, displaying a typical α-helical structure. One of these trimers was successfully crystallized, and its structure was solved at a resolution of 1.9 Å. A canonical 6-helix bundle, like those reported for other coronaviruses, was revealed, with three HR1 helices forming the central coiled-coil core and three HR2 chains surrounding the core in the HR1 side grooves. This demonstrates that MERS-CoV utilizes a mechanism similar to those of other class I enveloped viruses for membrane fusion. With this notion, we further identified an HR2-based peptide that could potently inhibit MERS-CoV fusion and entry by using a pseudotyped-virus system. These results lay the groundwork for future inhibitory peptidic drug design.
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Lu G, Hu Y, Wang Q, Qi J, Gao F, Li Y, Zhang Y, Zhang W, Yuan Y, Bao J, Zhang B, Shi Y, Yan J, Gao GF. Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26. Nature 2013; 500:227-31. [PMID: 23831647 PMCID: PMC7095341 DOI: 10.1038/nature12328] [Citation(s) in RCA: 527] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/30/2013] [Indexed: 12/17/2022]
Abstract
The newly emergent Middle East respiratory syndrome coronavirus (MERS-CoV) can cause severe pulmonary disease in humans, representing the second example of a highly pathogenic coronavirus, the first being SARS-CoV. CD26 (also known as dipeptidyl peptidase 4, DPP4) was recently identified as the cellular receptor for MERS-CoV. The engagement of the MERS-CoV spike protein with CD26 mediates viral attachment to host cells and virus-cell fusion, thereby initiating infection. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Furthermore, binding between the RBD and CD26 is measured using real-time surface plasmon resonance with a dissociation constant of 16.7 nM. The viral RBD is composed of a core subdomain homologous to that of the SARS-CoV spike protein, and a unique strand-dominated external receptor binding motif that recognizes blades IV and V of the CD26 β-propeller. The atomic details at the interface between the two binding entities reveal a surprising protein-protein contact mediated mainly by hydrophilic residues. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition.
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Affiliation(s)
- Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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37
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Lu G, Liu D. SARS-like virus in the Middle East: a truly bat-related coronavirus causing human diseases. Protein Cell 2013; 3:803-5. [PMID: 23143870 PMCID: PMC4875465 DOI: 10.1007/s13238-012-2811-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Di Liu
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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Heald-Sargent T, Gallagher T. Ready, set, fuse! The coronavirus spike protein and acquisition of fusion competence. Viruses 2012; 4:557-80. [PMID: 22590686 PMCID: PMC3347323 DOI: 10.3390/v4040557] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 03/29/2012] [Accepted: 04/02/2012] [Indexed: 12/16/2022] Open
Abstract
Coronavirus-cell entry programs involve virus-cell membrane fusions mediated by viral spike (S) proteins. Coronavirus S proteins acquire membrane fusion competence by receptor interactions, proteolysis, and acidification in endosomes. This review describes our current understanding of the S proteins, their interactions with and their responses to these entry triggers. We focus on receptors and proteases in prompting entry and highlight the type II transmembrane serine proteases (TTSPs) known to activate several virus fusion proteins. These and other proteases are essential cofactors permitting coronavirus infection, conceivably being in proximity to cell-surface receptors and thus poised to split entering spike proteins into the fragments that refold to mediate membrane fusion. The review concludes by noting how understanding of coronavirus entry informs antiviral therapies.
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Affiliation(s)
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Medical Center, 2160 South First Avenue, Maywood, IL 60153, USA;
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Sigalov AB. The SCHOOL of nature: III. From mechanistic understanding to novel therapies. SELF/NONSELF 2010; 1:192-224. [PMID: 21487477 PMCID: PMC3047783 DOI: 10.4161/self.1.3.12794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/10/2010] [Accepted: 06/11/2010] [Indexed: 11/19/2022]
Abstract
Protein-protein interactions play a central role in biological processes and thus represent an appealing target for innovative drug design and development. They can be targeted by small molecule inhibitors, modulatory peptides and peptidomimetics, which represent a superior alternative to protein therapeutics that carry many disadvantages. Considering that transmembrane signal transduction is an attractive process to therapeutically control multiple diseases, it is fundamentally and clinically important to mechanistically understand how signal transduction occurs. Uncovering specific protein-protein interactions critical for signal transduction, a general platform for receptor-mediated signaling, the signaling chain homooligomerization (SCHOOL) platform, suggests these interactions as universal therapeutic targets. Within the platform, the general principles of signaling are similar for a variety of functionally unrelated receptors. This suggests that global therapeutic strategies targeting key protein-protein interactions involved in receptor triggering and transmembrane signal transduction may be used to treat a diverse set of diseases. This also assumes that clinical knowledge and therapeutic strategies can be transferred between seemingly disparate disorders, such as T cell-mediated skin diseases and platelet disorders or combined to develop novel pharmacological approaches. Intriguingly, human viruses use the SCHOOL-like strategies to modulate and/or escape the host immune response. These viral mechanisms are highly optimized over the millennia, and the lessons learned from viral pathogenesis can be used practically for rational drug design. Proof of the SCHOOL concept in the development of novel therapies for atopic dermatitis, rheumatoid arthritis, cancer, platelet disorders and other multiple indications with unmet needs opens new horizons in therapeutics.
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40
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Jiang S, Li R, Du L, Liu S. Roles of the hemagglutinin of influenza A virus in viral entry and development of antiviral therapeutics and vaccines. Protein Cell 2010; 1:342-354. [PMID: 21203946 PMCID: PMC4728157 DOI: 10.1007/s13238-010-0054-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 03/31/2010] [Indexed: 11/25/2022] Open
Abstract
Seasonal influenza epidemics and influenza pandemics caused by influenza A virus (IAV) has resulted in millions of deaths in the world. The development of anti-IAV vaccines and therapeutics is urgently needed for prevention and treatment of IAV infection and for controlling future influenza pandemics. Hemagglutinin (HA) of IAV plays a critical role in viral binding, fusion and entry, and contains the major neutralizing epitopes. Therefore, HA is an attractive target for developing anti-IAV drugs and vaccines. Here we have reviewed the recent progress in study of conformational changes of HA during viral fusion process and development of HA-based antiviral therapeutics and vaccines.
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Affiliation(s)
- Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA. .,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Runming Li
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Shuwen Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Cellular Entry of the SARS Coronavirus: Implications for Transmission, Pathogenicity and Antiviral Strategies. MOLECULAR BIOLOGY OF THE SARS-CORONAVIRUS 2010. [PMCID: PMC7176234 DOI: 10.1007/978-3-642-03683-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Ma Y, Feng Y, Liu D, Gao GF. Avian influenza virus, Streptococcus suis serotype 2, severe acute respiratory syndrome-coronavirus and beyond: molecular epidemiology, ecology and the situation in China. Philos Trans R Soc Lond B Biol Sci 2009; 364:2725-37. [PMID: 19687041 PMCID: PMC2865088 DOI: 10.1098/rstb.2009.0093] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The outbreak and spread of severe acute respiratory syndrome-associated coronavirus and the subsequent identification of its animal origin study have heightened the world's awareness of animal-borne or zoonotic pathogens. In addition to SARS, the highly pathogenic avian influenza virus (AIV), H5N1, and the lower pathogenicity H9N2 AIV have expanded their host ranges to infect human beings and other mammalian species as well as birds. Even the ‘well-known’ reservoir animals for influenza virus, migratory birds, became victims of the highly pathogenic H5N1 virus. Not only the viruses, but bacteria can also expand their host range: a new disease, streptococcal toxic shock syndrome, caused by human Streptococcus suis serotype 2 infection, has been observed in China with 52 human fatalities in two separate outbreaks (1998 and 2005, respectively). Additionally, enterohaemorrhagic Escherichia coli O157:H7 infection has increased worldwide with severe disease. Several outbreaks and sporadic isolations of this pathogen in China have made it an important target for disease control. A new highly pathogenic variant of porcine reproductive and respiratory syndrome virus (PRRSV) has been isolated in both China and Vietnam recently; although PRRSV is not a zoonotic human pathogen, its severe outbreaks have implications for food safety. All of these pathogens occur in Southeast Asia, including China, with severe consequences; therefore, we discuss the issues in this article by addressing the situation of the zoonotic threat in China.
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Affiliation(s)
- Ying Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, The People's Republic of China
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Du L, Zhao G, Chan CCS, Sun S, Chen M, Liu Z, Guo H, He Y, Zhou Y, Zheng BJ, Jiang S. Recombinant receptor-binding domain of SARS-CoV spike protein expressed in mammalian, insect and E. coli cells elicits potent neutralizing antibody and protective immunity. Virology 2009; 393:144-50. [PMID: 19683779 PMCID: PMC2753736 DOI: 10.1016/j.virol.2009.07.018] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 07/10/2009] [Accepted: 07/17/2009] [Indexed: 01/05/2023]
Abstract
Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease. The potential recurrence of the disease from animal reservoirs highlights the significance of development of safe and efficient vaccines to prevent a future SARS epidemic. In this study, we expressed the recombinant receptor-binding domain (rRBD) in mammalian (293T) cells, insect (Sf9) cells, and E. coli, respectively, and compared their immunogenicity and protection against SARS-CoV infection in an established mouse model. Our results show that all rRBD proteins expressed in the above systems maintained intact conformation, being able to induce highly potent neutralizing antibody responses and complete protective immunity against SARS-CoV challenge in mice, albeit the rRBD expressed in 293T cells elicited stronger humoral immune responses with significantly higher neutralizing activity (P < 0.05) than those expressed in Sf9 and E. coli cells. These results suggest that all three rRBDs are effective in eliciting immune responses and protection against SARS-CoV and any of the above expression systems can be used for production of rRBD-based SARS subunit vaccines. Preference will be given to rRBD expressed in mammalian cells for future evaluation of the vaccine efficacy in a non-human primate model of SARS because of its ability to refold into a native conformation more readily and to induce higher level of neutralizing antibody responses than those expressed in E. coli and insect cells.
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Affiliation(s)
- Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
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Abstract
We report a simple method for identifying foldable viral surface protein fragments in a random but systematic manner. The method involves digestion and reassembly of a target gene to generate a pool of smaller DNA fragments with random ends but controllable lengths, followed by screening for foldable fragments using green fluorescent protein (GFP) as a folding reporter. The surface glycoproteins of SARS-CoV and HIV-1 were used as model proteins. Two foldable fragments for SARS-CoV spike protein were identified, which coincide with various anti-SARS-CoV peptides. A similar treatment of the HIV-1 gp120 yielded a number of fragments that are associated with the critical CD4 binding site, or the partially buried CCR5 binding site of the protein. The random dissection approach described here should be applicable to other viral proteins for isolating soluble viral surface protein fragments, and may provide alternatives to the full-length proteins (subunits) or linear short peptides in search for antigen or vaccine candidates.
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Affiliation(s)
- Barry W. Hicks
- Department of Chemistry, 2355 Fairchild Drive, US Airforce Academy, CO 80840 USA
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45
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Liu IJ, Kao CL, Hsieh SC, Wey MT, Kan LS, Wang WK. Identification of a minimal peptide derived from heptad repeat (HR) 2 of spike protein of SARS-CoV and combination of HR1-derived peptides as fusion inhibitors. Antiviral Res 2008; 81:82-7. [PMID: 18983873 PMCID: PMC7114320 DOI: 10.1016/j.antiviral.2008.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Revised: 09/29/2008] [Accepted: 10/01/2008] [Indexed: 12/28/2022]
Abstract
The heptad repeats (HR1 and HR2) of the spike protein of SARS-CoV are highly conserved regions forming a critical 6-helix bundle during the fusion step of virus entry and are attractive targets of entry inhibitors. In this study, we report that a minimal HR2 peptide, P6 of 23-mer, can block the fusion of SARS-CoV with an IC(50) of 1.04+/-0.22 microM. This finding supports the structural prediction of the deep groove of HR1 trimer as a target for fusion inhibitors, and suggests P6 as a potential lead peptide for future drug development. Moreover, combination of an HR-1 peptide, N46, and its mutated version, N46eg, shows synergistic inhibition with an IC(50) of 1.39+/-0.05 microM and combination index of 0.75+/-0.15, suggesting a common strategy to achieve promising inhibition by HR1 peptide for other class I envelope viruses.
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Affiliation(s)
- I-Jung Liu
- Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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46
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Chu LHM, Chan SH, Tsai SN, Wang Y, Cheng CHK, Wong KB, Waye MMY, Ngai SM. Fusion core structure of the severe acute respiratory syndrome coronavirus (SARS-CoV): in search of potent SARS-CoV entry inhibitors. J Cell Biochem 2008; 104:2335-47. [PMID: 18442051 PMCID: PMC7166385 DOI: 10.1002/jcb.21790] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Severe acute respiratory coronavirus (SARS‐CoV) spike (S) glycoprotein fusion core consists of a six‐helix bundle with the three C‐terminal heptad repeat (HR2) helices packed against a central coiled‐coil of the other three N‐terminal heptad repeat (HR1) helices. Each of the three peripheral HR2 helices shows prominent contacts with the hydrophobic surface of the central HR1 coiled‐coil. The concerted protein–protein interactions among the HR helices are responsible for the fusion event that leads to the release of the SARS‐CoV nucleocapsid into the target host‐cell. In this investigation, we applied recombinant protein and synthetic peptide‐based biophysical assays to characterize the biological activities of the HR helices. In a parallel experiment, we employed a HIV‐luc/SARS pseudotyped virus entry inhibition assay to screen for potent inhibitory activities on HR peptides derived from the SARS‐CoV S protein HR regions and a series of other small‐molecule drugs. Three HR peptides and five small‐molecule drugs were identified as potential inhibitors. ADS‐J1, which has been used to interfere with the fusogenesis of HIV‐1 onto CD4+ cells, demonstrated the highest HIV‐luc/SARS pseudotyped virus‐entry inhibition activity among the other small‐molecule drugs. Molecular modeling analysis suggested that ADS‐J1 may bind to the deep pocket of the hydrophobic groove on the surface of the central coiled‐coil of SARS‐CoV S HR protein and prevent the entrance of the SARS‐CoV into the host cells. J. Cell. Biochem. 104: 2335–2347, 2008. © 2008 Wiley‐Liss, Inc.
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Affiliation(s)
- Ling-Hon Matthew Chu
- Molecular Biotechnology Program, The Chinese University of Hong Kong, Hong Kong, China
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47
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Guillén J, Kinnunen PKJ, Villalaín J. Membrane insertion of the three main membranotropic sequences from SARS-CoV S2 glycoprotein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2765-74. [PMID: 18721794 PMCID: PMC7157930 DOI: 10.1016/j.bbamem.2008.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/09/2008] [Accepted: 07/23/2008] [Indexed: 12/02/2022]
Abstract
In order to complete the fusion process of SARS-CoV virus, several regions of the S2 virus envelope glycoprotein are necessary. Recent studies have identified three membrane-active regions in the S2 domain of SARS-CoV glycoprotein, one situated downstream of the minimum furin cleavage, which is considered the fusion peptide (SARSFP), an internal fusion peptide located immediately upstream of the HR1 region (SARSIFP) and the pre-transmembrane domain (SARSPTM). We have explored the capacity of these selected membrane-interacting regions of the S2 SARS-CoV fusion protein, alone or in equimolar mixtures, to insert into the membrane as well as to perturb the dipole potential of the bilayer. We show that the three peptides interact with lipid membranes depending on lipid composition and experiments using equimolar mixtures of these peptides show that different segments of the protein may act in a synergistic way suggesting that several membrane-active regions could participate in the fusion process of the SARS-CoV.
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Affiliation(s)
- Jaime Guillén
- Instituto de Biología Molecular y Celular, Campus de Elche, Universidad Miguel Hernández, E-03202 Elche-Alicante, Spain
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48
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Guillén J, de Almeida RFM, Prieto M, Villalaín J. Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes. J Phys Chem B 2008; 112:6997-7007. [PMID: 18489147 DOI: 10.1021/jp7118229] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The SARS coronavirus (SARS-CoV) envelope spike (S) glycoprotein, a Class I viral fusion protein, is responsible for the fusion between the membranes of the virus and the target cell. In the present work, we report a study of the binding and interaction with model membranes of a peptide pertaining to the putative fusion domain of SARS-CoV, SARS FP, as well as the structural changes that take place in both the phospholipid and the peptide molecules upon this interaction. From fluorescence and infrared spectroscopies, the peptide ability to induce membrane leakage, aggregation and fusion, as well as its affinity toward specific phospholipids, was assessed. We demonstrate that SARS FP strongly partitions into phospholipid membranes, more specifically with those containing negatively charged phospholipids, increasing the water penetration depth and displaying membrane-activity modulated by the lipid composition of the membrane. Interestingly, peptide organization is different depending if SARS FP is in water or bound to the membrane. These data suggest that SARS FP could be involved in the merging of the viral and target cell membranes by perturbing the membrane outer leaflet phospholipids and specifically interacting with negatively charged phospholipids located in the inner leaflet.
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Affiliation(s)
- Jaime Guillén
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche-Alicante, Spain
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49
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Abstract
Protein-protein interactions play a central role in biological processes and thus are an appealing target for innovative drug design a nd development. They can be targeted bysmall molecule inhibitors, peptides and peptidomimetics, which represent an alternative to protein therapeutics that carry many disadvantages. In this chapter, I describe specific protein-protein interactions suggested by a novel model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, to be critical for cell activation mediated by multichain immune recognition receptors (MIRRs) expressed on different cells of the hematopoietic system. Unraveling a long-standing mystery of MIRR triggering and transmembrane signaling, the SCHOOL model reveals the intrareceptor transmembrane interactions and interreceptor cytoplasmic homointeractions as universal therapeutic targets for a diverse variety of disorders mediated by immune cells. Further, assuming that the general principles underlying MIRR-mediated transmembrane signaling mechanisms are similar, the SCHOOL model can be applied to any particular receptor of the MIRR family. Thus, an important application of the SCHOOL model is that global therapeutic strategies targeting key protein-protein interactions involved in MIRR triggering and transmembrane signal transduction may be used to treat a diverse set of immune-mediated diseases. This assumes that clinical knowledge and therapeutic strategies can be transferred between seemingly disparate disorders, such as T-cell-mediated skin diseases and platelet disorders, or combined to develop novel pharmacological approaches. Intriguingly, the SCHOOL model unravels the molecular mechanisms underlying ability of different human viruses such as human immunodeficiency virus, cytomegalovirus and severe acute respiratory syndrome coronavirus to modulate and/or escape the host immune response. It also demonstrates how the lessons learned from viral pathogenesis can be used practically for rational drug design. Application of this model to platelet collagen receptor signaling has already led to the development of a novel concept of platelet inhibition and the invention of new platelet inhibitors, thus proving the suggested hypothesis and highlighting the importance and broad perspectives of the SCHOOL model in the development of new targeting strategies.
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50
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Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev 2007; 20:660-94. [PMID: 17934078 DOI: 10.1128/cmr.00023-07] [Citation(s) in RCA: 657] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Before the emergence of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in 2003, only 12 other animal or human coronaviruses were known. The discovery of this virus was soon followed by the discovery of the civet and bat SARS-CoV and the human coronaviruses NL63 and HKU1. Surveillance of coronaviruses in many animal species has increased the number on the list of coronaviruses to at least 36. The explosive nature of the first SARS epidemic, the high mortality, its transient reemergence a year later, and economic disruptions led to a rush on research of the epidemiological, clinical, pathological, immunological, virological, and other basic scientific aspects of the virus and the disease. This research resulted in over 4,000 publications, only some of the most representative works of which could be reviewed in this article. The marked increase in the understanding of the virus and the disease within such a short time has allowed the development of diagnostic tests, animal models, antivirals, vaccines, and epidemiological and infection control measures, which could prove to be useful in randomized control trials if SARS should return. The findings that horseshoe bats are the natural reservoir for SARS-CoV-like virus and that civets are the amplification host highlight the importance of wildlife and biosecurity in farms and wet markets, which can serve as the source and amplification centers for emerging infections.
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