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Wilde V, Canard B, Ferron F. Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond. Viruses 2023; 15:1628. [PMID: 37631971 PMCID: PMC10458308 DOI: 10.3390/v15081628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses.
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Affiliation(s)
- Vincent Wilde
- Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, France; (V.W.); (B.C.)
- Marseille and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, France; (V.W.); (B.C.)
- Marseille and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, France; (V.W.); (B.C.)
- Marseille and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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2
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Touret F, Baronti C, Goethals O, Van Loock M, de Lamballerie X, Querat G. Phylogenetically based establishment of a dengue virus panel, representing all available genotypes, as a tool in dengue drug discovery. Antiviral Res 2019; 168:109-113. [DOI: 10.1016/j.antiviral.2019.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022]
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3
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Rogée S, Larrous F, Jochmans D, Ben-Khalifa Y, Neyts J, Bourhy H. Pyrimethamine inhibits rabies virus replication in vitro. Antiviral Res 2019; 161:1-9. [DOI: 10.1016/j.antiviral.2018.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022]
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Hilgenfeld R. From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 2014; 281:4085-96. [PMID: 25039866 PMCID: PMC7163996 DOI: 10.1111/febs.12936] [Citation(s) in RCA: 437] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023]
Abstract
This review focuses on the important contributions that macromolecular crystallography has made over the past 12 years to elucidating structures and mechanisms of the essential proteases of coronaviruses, the main protease (M(pro) ) and the papain-like protease (PL(pro) ). The role of X-ray crystallography in structure-assisted drug discovery against these targets is discussed. Aspects dealt with in this review include the emergence of the SARS coronavirus in 2002-2003 and of the MERS coronavirus 10 years later and the origins of these viruses. The crystal structure of the free SARS coronavirus M(pro) and its dependence on pH is discussed, as are efforts to design inhibitors on the basis of these structures. The mechanism of maturation of the enzyme from the viral polyprotein is still a matter of debate. The crystal structure of the SARS coronavirus PL(pro) and its complex with ubiquitin is also discussed, as is its orthologue from MERS coronavirus. Efforts at predictive structure-based inhibitor development for bat coronavirus M(pro) s to increase the preparedness against zoonotic transmission to man are described as well. The paper closes with a brief discussion of structure-based discovery of antivirals in an academic setting.
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Affiliation(s)
- Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, and German Center for Infection Research, University of Lübeck, Germany
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5
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Structure-based antivirals for emerging and neglected RNA viruses: an emerging field for medicinal chemistry in academia. Future Med Chem 2011; 2:1061-7. [PMID: 21426155 DOI: 10.4155/fmc.10.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
"Many [neglected viruses] predominantly hit developing countries in tropical and subtropical regions of the world (40% of the world's population are now at risk of contracting dengue fever), but developed countries are by no means immune to their impact."
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6
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Norder H, De Palma AM, Selisko B, Costenaro L, Papageorgiou N, Arnan C, Coutard B, Lantez V, De Lamballerie X, Baronti C, Solà M, Tan J, Neyts J, Canard B, Coll M, Gorbalenya AE, Hilgenfeld R. Picornavirus non-structural proteins as targets for new anti-virals with broad activity. Antiviral Res 2011; 89:204-18. [DOI: 10.1016/j.antiviral.2010.12.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 08/23/2010] [Accepted: 12/23/2010] [Indexed: 12/12/2022]
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7
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Charrel RN, Coutard B, Baronti C, Canard B, Nougairede A, Frangeul A, Morin B, Jamal S, Schmidt CL, Hilgenfeld R, Klempa B, de Lamballerie X. Arenaviruses and hantaviruses: from epidemiology and genomics to antivirals. Antiviral Res 2011; 90:102-14. [PMID: 21356244 DOI: 10.1016/j.antiviral.2011.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Revised: 02/16/2011] [Accepted: 02/17/2011] [Indexed: 12/11/2022]
Abstract
The arenaviruses and hantaviruses are segmented genome RNA viruses that are hosted by rodents. Due to their association with rodents, they are globally widespread and can infect humans via direct or indirect routes of transmission, causing considerable human morbidity and mortality. Nevertheless, despite their obvious and emerging importance as pathogens, there are currently no effective antiviral drugs (except ribavirin which proved effective against Lassa virus) with which to treat humans infected by any of these viruses. The EU-funded VIZIER project (Comparative Structural Genomics of Viral Enzymes Involved in Replication) was instigated with an ultimate view of contributing to the development of antiviral therapies for RNA viruses, including the arenaviruses and bunyaviruses. This review highlights some of the major features of the arenaviruses and hantaviruses that have been investigated during recent years. After describing their classification and epidemiology, we review progress in understanding the genomics as well as the structure and function of replicative enzymes achieved under the VIZIER program and the development of new disease control strategies.
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Affiliation(s)
- R N Charrel
- Unité des Virus Emergents UMR190, Université de la Méditerranée, Marseille, France.
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8
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Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription. Antiviral Res 2010; 87:149-61. [DOI: 10.1016/j.antiviral.2010.02.322] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 02/20/2010] [Indexed: 01/19/2023]
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Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA. Practical application of bioinformatics by the multidisciplinary VIZIER consortium. Antiviral Res 2010; 87:95-110. [PMID: 20153379 PMCID: PMC7172516 DOI: 10.1016/j.antiviral.2010.02.005] [Citation(s) in RCA: 39] [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: 12/22/2009] [Revised: 02/03/2010] [Accepted: 02/04/2010] [Indexed: 01/03/2023]
Abstract
This review focuses on bioinformatics technologies employed by the EU-sponsored multidisciplinary VIZIER consortium (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 PROJECT: 2004-511960, active from 1 November 2004 to 30 April 2009), to achieve its goals. From the management of the information flow of the project, to bioinformatics-mediated selection of RNA viruses and prediction of protein targets, to the analysis of 3D protein structures and antiviral compounds, these technologies provided a communication framework and integrated solutions for steady and timely advancement of the project. RNA viruses form a large class of major pathogens that affect humans and domestic animals. Such RNA viruses as HIV, Influenza virus and Hepatitis C virus are of prime medical concern today, but the identities of viruses that will threaten human population tomorrow are far from certain. To contain outbreaks of common or newly emerging infections, prototype drugs against viruses representing the Virus Universe must be developed. This concept was championed by the VIZIER project which brought together experts in diverse fields to produce a concerted and sustained effort for identifying and validating targets for antivirus therapy in dozens of RNA virus lineages.
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Affiliation(s)
- Alexander E. Gorbalenya
- Molecular Virology Laboratory, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, E4-P, 2300 RC Leiden, The Netherlands
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Philippe Lieutaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille, France
| | - Mark R. Harris
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bruno Canard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille, France
| | - Gerard J. Kleywegt
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Alexander A. Kravchenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Dmitry V. Samborskiy
- Molecular Virology Laboratory, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, E4-P, 2300 RC Leiden, The Netherlands
| | - Igor A. Sidorov
- Molecular Virology Laboratory, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, E4-P, 2300 RC Leiden, The Netherlands
| | - Andrey M. Leontovich
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - T. Alwyn Jones
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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Bourhy H, Dacheux L, Ribadeau-Dumas F. [The use of passive rabies immunotherapy: from the past to the future]. Biol Aujourdhui 2010; 204:71-80. [PMID: 20950578 DOI: 10.1051/jbio/2009049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Rabies is a fatal disease transmitted by infected animals by bite, scratch, licking on broken skin or contamination of mucosis by saliva. The regimen of post-exposure prophylaxis for people not previously vaccinated, that is currently recommended by WHO, consists of a combination of wound cleaning, active immunization and passive immunization when the exposure is of category 3. Most of the products available on the market, in particular human rabies immunoglobulins, highly purified equine rabies immunoglobulins and the derived F(ab')(2) fragments, are now characterized by high potency and safety. Although the interest of passive anti-rabies immunization was first demonstrated in the first half of the 20th century, there is still an inadequate supply of these products to the target populations mostly in developing countries. Therefore, it is urgent to set-up training and information actions for healthcare personnel on the need to use passive immunotherapy and the lack of adverse effects of the related products. For the future, we hope that a scale up of production and a lower price will improve the accessibility to these products. The development of new products based on monoclonal antibodies and molecular biology, and which may be cheaper, is promising.
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Affiliation(s)
- Hervé Bourhy
- Centre National de Référence de la Rage, Centre Collaborateur de l'Organisation Mondiale de la Santé de Référence et de Recherche pour la Rage, Unité Dynamique des Lyssavirus et Adaptation à l'Hôte, Institut Pasteur, 25-28 rue du Docteur Roux, Paris Cedex 15, France.
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11
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Zonta N, Coluccia A, Brancale A. Advanced in silico Approaches in Antiviral Research. ACTA ACUST UNITED AC 2010; 20:147-51. [DOI: 10.3851/imp1500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Computer-aided drug design has seen constantly increasing application over the past two decades in every area of drug discovery. It can offer significant advantages over conventional approaches, being far less expensive and faster than conventional methods, or offering the possibility to predict molecular behaviours that cannot be elucidated in any other way. Recent developments in software and hardware make it possible to simulate increasingly complex molecular environments, widening the applicability of in silico studies from the interactions of small molecules with key protein residues, to the simulation of the dynamic evolution of complex biological systems with atomic resolution. Antiviral research offers several open challenges, from a biological, biochemical and pharmaceutical point of view. Computational approaches are already providing some answers and will undoubtedly give more in the near future. Here, we present a brief overview of the cutting-edge computational methods that play a major role in present and future antiviral research.
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Affiliation(s)
- Nicola Zonta
- Welsh School of Pharmacy, Cardiff University, Cardiff, Wales, UK
| | - Antonio Coluccia
- Welsh School of Pharmacy, Cardiff University, Cardiff, Wales, UK
| | - Andrea Brancale
- Welsh School of Pharmacy, Cardiff University, Cardiff, Wales, UK
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12
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Coutard B, Canard B. The VIZIER project: overview; expectations; and achievements. Antiviral Res 2010; 87:85-94. [PMID: 20226212 PMCID: PMC7114346 DOI: 10.1016/j.antiviral.2010.02.326] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 02/14/2010] [Indexed: 02/06/2023]
Abstract
VIZIER is an acronym for a research project entitled “Comparative Structural Genomics of Viral Enzymes Involved in Replication” funded by the European Commission between November 1st, 2004 and April 30th, 2009. It involved 25 partners from 12 countries. In this paper, we describe the organization of the project and the culture created by its multidisciplinary essence. We discuss the main thematic sections of the project and the strategy adopted to optimize the integration of various scientific fields into a common objective: to obtain crystal structures of the widest variety of RNA virus replication enzymes documented and validated as potential drug targets. We discuss the thematic sections and their overall organization, their successes and bottlenecks around the protein production pipeline, the “low hanging fruit” strategy, and measures directed to problem solving. We discuss possible future options for such large-scale projects in the area of antiviral drug design. In a series of accompanying papers in Antiviral Research, the project and its achievements are presented for each virus family.
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Affiliation(s)
- Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, Universités Aix-Marseille I et II, ESIL Case 925, 163 Avenue de Luminy, 13288 Marseille, France
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13
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Weigelt J. Structural genomics-impact on biomedicine and drug discovery. Exp Cell Res 2010; 316:1332-8. [PMID: 20211166 DOI: 10.1016/j.yexcr.2010.02.041] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 02/28/2010] [Indexed: 11/24/2022]
Abstract
The field of structural genomics emerged as one of many 'omics disciplines more than a decade ago, and a multitude of large scale initiatives have been launched across the world. Development and implementation of methods for high-throughput structural biology represents a common denominator among different structural genomics programs. From another perspective a distinction between "biology-driven" versus "structure-driven" approaches can be made. This review outlines the general themes of structural genomics, its achievements and its impact on biomedicine and drug discovery. The growing number of high resolution structures of known and potential drug target proteins is expected to have tremendous value for future drug discovery programs. Moreover, the availability of large numbers of purified proteins enables generation of tool reagents, such as chemical probes and antibodies, to further explore protein function in the cell.
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Affiliation(s)
- Johan Weigelt
- Structural Genomics Consortium, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, 171 77 Stockholm, Sweden.
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Castel G, Tordo N. [New strategies for the development of antiviral molecules]. REVUE FRANCOPHONE DES LABORATOIRES : RFL 2009; 2009:91-100. [PMID: 32288807 PMCID: PMC7140268 DOI: 10.1016/s1773-035x(09)70313-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/30/2009] [Indexed: 11/29/2022]
Abstract
Antiviral research is a recent discipline and the number of molecules available to fight against viral infections remains still insufficient. However, both diseases caused by emerging endemic viruses and the existence of resistance from some viruses against antiviral make necessary a constant search for new antiviral drugs. Parallel to the development of traditional molecules such as nucleoside analogues, whose effectiveness is well demonstrated, pharmaceutical industry is now turning to new solutions such as antiviral peptides, which constitute a new exploration field in therapy. The recent progress in disciplines such as genomics, proteomics and structural biology have improved our fundamental understanding of the viral world. These advances can be used to efficiently create new drugs more selective and more effective. Identification and development of these molecules require the use of newer techniques such as high-throughput screening of combinatorial compound libraries and the use of new bioinformatics tools. This review aims to present some recent methods for the development of antiviral molecules.
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Affiliation(s)
- Guillaume Castel
- Unité postulante des stratégies antivirales – CNRS URA-3015, Institut Pasteur, 25, rue du Docteur-Roux, 75724 Paris cedex 15
| | - Noël Tordo
- Unité postulante des stratégies antivirales – CNRS URA-3015, Institut Pasteur, 25, rue du Docteur-Roux, 75724 Paris cedex 15
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15
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Abstract
The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging, or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.
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Affiliation(s)
- W F Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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16
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Gould EA, Coutard B, Malet H, Morin B, Jamal S, Weaver S, Gorbalenya A, Moureau G, Baronti C, Delogu I, Forrester N, Khasnatinov M, Gritsun T, de Lamballerie X, Canard B. Understanding the alphaviruses: recent research on important emerging pathogens and progress towards their control. Antiviral Res 2009; 87:111-24. [PMID: 19616028 PMCID: PMC7114216 DOI: 10.1016/j.antiviral.2009.07.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Revised: 07/07/2009] [Accepted: 07/11/2009] [Indexed: 11/28/2022]
Abstract
The alphaviruses were amongst the first arboviruses to be isolated, characterized and assigned a taxonomic status. They are globally very widespread, infecting a large variety of terrestrial animals, insects and even fish, and circulate both in the sylvatic and urban/peri-urban environment, causing considerable human morbidity and mortality. Nevertheless, despite their obvious importance as pathogens, there are currently no effective antiviral drugs with which to treat humans or animals infected by any of these viruses. The EU-supported project-VIZIER (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 PROJECT: 2004-511960) was instigated with an ultimate view of contributing to the development of antiviral therapies for RNA viruses, including the alphaviruses [Coutard, B., Gorbalenya, A.E., Snijder, E.J., Leontovich, A.M., Poupon, A., De Lamballerie, X., Charrel, R., Gould, E.A., Gunther, S., Norder, H., Klempa, B., Bourhy, H., Rohayemj, J., L'hermite, E., Nordlund, P., Stuart, D.I., Owens, R.J., Grimes, J.M., Tuckerm, P.A., Bolognesi, M., Mattevi, A., Coll, M., Jones, T.A., Aqvist, J., Unger, T., Hilgenfeld, R., Bricogne, G., Neyts, J., La Colla, P., Puerstinger, G., Gonzalez, J.P., Leroy, E., Cambillau, C., Romette, J.L., Canard, B., 2008. The VIZIER project: preparedness against pathogenic RNA viruses. Antiviral Res. 78, 37-46]. This review highlights some of the major features of alphaviruses that have been investigated during recent years. After describing their classification, epidemiology and evolutionary history and the expanding geographic distribution of Chikungunya virus, we review progress in understanding the structure and function of alphavirus replicative enzymes achieved under the VIZIER programme and the development of new disease control strategies.
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Affiliation(s)
- E A Gould
- Institut de Recherche pour le Développement UMR190/Unité des Virus Emergents, Université de la Méditerranée, Marseille, France.
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Speroni S, Rohayem J, Nenci S, Bonivento D, Robel I, Barthel J, Luzhkov VB, Coutard B, Canard B, Mattevi A. Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 A resolution. J Mol Biol 2009; 387:1137-52. [PMID: 19249313 DOI: 10.1016/j.jmb.2009.02.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 11/29/2022]
Abstract
Astroviruses are single-stranded RNA viruses with a replication strategy based on the proteolytic processing of a polyprotein precursor and subsequent release of the viral enzymes of replication. So far, the catalytic properties of the astrovirus protease as well as its structure have remained uncharacterized. In this study, the three-dimensional crystal structure of the predicted protease of human pathogenic astrovirus has been solved to 2.0 A resolution. The protein displays the typical properties of trypsin-like enzymes but also several characteristic features: (i) a catalytic Asp-His-Ser triad in which the aspartate side chain is oriented away from the histidine, being replaced by a water molecule; (ii) a non-common conformation and composition of the S1 pocket; and (iii) the lack of the typical surface beta-ribbons together with a "featureless" shape of the substrate-binding site. Hydrolytic activity assays indicate that the S1 pocket recognises Glu and Asp side chains specifically, which, therefore, are predicted to occupy the P1 position on the substrate cleavage site. The positive electrostatic potential featured by the S1 region underlies this specificity. The comparative structural analysis highlights the peculiarity of the astrovirus protease, and differentiates it from the human and viral serine proteases.
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Affiliation(s)
- Silvia Speroni
- Department of Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia, 27100 Italy
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18
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Highly pathogenic RNA viral infections: Challenges for antiviral research. Antiviral Res 2008; 78:1-8. [DOI: 10.1016/j.antiviral.2007.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 12/12/2007] [Accepted: 12/13/2007] [Indexed: 12/23/2022]
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