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Chen L, Gui C, Luo X, Yang Q, Günther S, Scandella E, Drosten C, Bai D, He X, Ludewig B, Chen J, Luo H, Yang Y, Yang Y, Zou J, Thiel V, Chen K, Shen J, Shen X, Jiang H. Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro. J Virol 2005; 79:7095-103. [PMID: 15890949 PMCID: PMC1112131 DOI: 10.1128/jvi.79.11.7095-7103.2005] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3C-like proteinase (3CLpro) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is one of the most promising targets for anti-SARS-CoV drugs due to its crucial role in the viral life cycle. In this study, a database containing structural information of more than 8,000 existing drugs was virtually screened by a docking approach to identify potential binding molecules of SARS-CoV 3CLpro. As a target for screening, both a homology model and the crystallographic structure of the binding pocket of the enzyme were used. Cinanserin (SQ 10,643), a well-characterized serotonin antagonist that has undergone preliminary clinical testing in humans in the 1960s, showed a high score in the screening and was chosen for further experimental evaluation. Binding of both cinanserin and its hydrochloride to bacterially expressed 3CLpro of SARS-CoV and the related human coronavirus 229E (HCoV-229E) was demonstrated by surface plasmon resonance technology. The catalytic activity of both enzymes was inhibited with 50% inhibitory concentration (IC50) values of 5 microM, as tested with a fluorogenic substrate. The antiviral activity of cinanserin was further evaluated in tissue culture assays, namely, a replicon system based on HCoV-229E and quantitative test assays with infectious SARS-CoV and HCoV-229E. All assays revealed a strong inhibition of coronavirus replication at nontoxic drug concentrations. The level of virus RNA and infectious particles was reduced by up to 4 log units, with IC50 values ranging from 19 to 34 microM. These findings demonstrate that the old drug cinanserin is an inhibitor of SARS-CoV replication, acting most likely via inhibition of the 3CL proteinase.
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Affiliation(s)
- Lili Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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202
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Ferron F, Rancurel C, Longhi S, Cambillau C, Henrissat B, Canard B. VaZyMolO: a tool to define and classify modularity in viral proteins. J Gen Virol 2005; 86:743-749. [PMID: 15722535 DOI: 10.1099/vir.0.80590-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viral structural genomic projects aim at unveiling the function of unknown viral proteins by employing high-throughput approaches to determine their 3D structure and to identify their function through fold-homology studies. The 'viral enzyme module localization' (VaZyMolO) tool has been developed, which aims at defining viral protein modules that might be expressed in a soluble and functionally active form, thereby identifying candidates for crystallization studies. VaZyMolO includes 114 complete viral genome sequences of both negative- and positive-sense, single-stranded RNA viruses available from NCBI. In VaZyMolO, a module is defined as a structural and/or functional unit. Modules were first identified by homology search and then validated by the convergence of results from sequence composition analysis, motif search, transmembrane region search and domain definitions, as found in the literature. The public interface of VaZyMolO, which is accessible from http://www.vazymolo.org, allows comparison of a query sequence to all VaZyMolO modules of known function.
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Affiliation(s)
- François Ferron
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France
| | - Corinne Rancurel
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France
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203
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Bernini A, Spiga O, Ciutti A, Chiellini S, Bracci L, Yan X, Zheng B, Huang J, He ML, Song HD, Hao P, Zhao G, Niccolai N. Prediction of quaternary assembly of SARS coronavirus peplomer. Biochem Biophys Res Commun 2005; 325:1210-4. [PMID: 15555555 PMCID: PMC7092937 DOI: 10.1016/j.bbrc.2004.10.156] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Indexed: 11/29/2022]
Abstract
The tertiary structures of the S1 and S2 domains of the spike protein of the coronavirus which is responsible of the severe acute respiratory syndrome (SARS) have been recently predicted. Here a molecular assembly of SARS coronavirus peplomer which accounts for the available functional data is suggested. The interaction between S1 and S2 appears to be stabilised by a large hydrophobic network of aromatic side chains present in both domains. This feature results to be common to all coronaviruses, suggesting potential targeting for drugs preventing coronavirus-related infections.
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Affiliation(s)
- Andrea Bernini
- Department of Molecular Biology, Biomolecular Structure Research Center, University of Siena, I-53100 Siena, Italy
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204
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Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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205
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Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol 2004; 3:e5. [PMID: 15630477 PMCID: PMC539059 DOI: 10.1371/journal.pbio.0030005] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Accepted: 10/13/2004] [Indexed: 11/19/2022] Open
Abstract
We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3′ end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 90° kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold. The SARS RNA genome contains a unique structure that resembles a portion of ribosomal RNA; this may allow the virus to hijack its hosts protein synthesis machinery
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Affiliation(s)
- Michael P Robertson
- 1The Center for the Molecular Biology of RNA, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
- 2Department of Chemistry and Biochemistry, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
| | - Haller Igel
- 1The Center for the Molecular Biology of RNA, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
- 3Department of Molecular, Celland Developmental Biology, University of California, Santa Cruz, CaliforniaUnited States of America
| | - Robert Baertsch
- 1The Center for the Molecular Biology of RNA, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
- 4Howard Hughes Medical Institute and Department of Biomolecular Engineering, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
| | - David Haussler
- 1The Center for the Molecular Biology of RNA, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
- 4Howard Hughes Medical Institute and Department of Biomolecular Engineering, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
| | - Manuel Ares
- 1The Center for the Molecular Biology of RNA, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
- 3Department of Molecular, Celland Developmental Biology, University of California, Santa Cruz, CaliforniaUnited States of America
| | - William G Scott
- 1The Center for the Molecular Biology of RNA, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
- 2Department of Chemistry and Biochemistry, University of CaliforniaSanta Cruz, CaliforniaUnited States of America
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206
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Abstract
The worldwide epidemic of severe acute respiratory syndrome (SARS) in 2003 was caused by a novel coronavirus called SARS-CoV. Coronaviruses and their closest relatives possess extremely large plus-strand RNA genomes and employ unique mechanisms and enzymes in RNA synthesis that separate them from all other RNA viruses. The SARS epidemic prompted a variety of studies on multiple aspects of the coronavirus replication cycle, yielding both rapid identification of the entry mechanisms of SARS-CoV into host cells and valuable structural and functional information on SARS-CoV proteins. These recent advances in coronavirus research have important implications for the development of anti-SARS drugs and vaccines.
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Key Words
- 2′-o-mt, 2′-o-ribose methyltransferase
- 3clpro, 3c-like main protease
- adrp, adp-ribose 1″-phosphatase
- cpd, cyclic phosphodiesterase
- exon, 3′-to-5′ exoribonuclease
- hcov-229e, human coronavirus 229e
- hr, heptad repeat
- nendou, nidoviral uridylate-specific endoribonuclease
- orf, open reading frame
- pl2pro, papain-like protease 2
- rdrp, rna-dependent rna polymerase
- sars, severe acute respiratory syndrome
- sars-cov, severe acute respiratory syndrome coronavirus
- sg mrna, subgenomic mrna
- trs, transcription-regulating sequence
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Affiliation(s)
- John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany.
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