Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
Identifieur interne : 000722 ( Istex/Corpus ); précédent : 000721; suivant : 000723Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
Auteurs : Marcin Hoffmann ; Krystian Eitner ; Marcin Von Grotthuss ; Leszek Rychlewski ; Ewa Banachowicz ; Tomasz Grabarkiewicz ; Tomasz Szkoda ; Andrzej KolinskiSource :
- Journal of Computer-Aided Molecular Design [ 0920-654X ] ; 2006-05-01.
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Abstract
Abstract: The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.
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DOI: 10.1007/s10822-006-9057-z
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This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. 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This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. 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Grant="Restricted"></ESMGrant></ArticleGrants></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1 Aff2" CorrespondingAffiliationID="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Marcin</GivenName><FamilyName>Hoffmann</FamilyName></AuthorName><Contact><Email>mmh@bioinfo.pl</Email></Contact></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Krystian</GivenName><FamilyName>Eitner</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Marcin</GivenName><Particle>von</Particle><FamilyName>Grotthuss</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Leszek</GivenName><FamilyName>Rychlewski</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff3"><AuthorName DisplayOrder="Western"><GivenName>Ewa</GivenName><FamilyName>Banachowicz</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Tomasz</GivenName><FamilyName>Grabarkiewicz</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff4"><AuthorName DisplayOrder="Western"><GivenName>Tomasz</GivenName><FamilyName>Szkoda</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff5"><AuthorName DisplayOrder="Western"><GivenName>Andrzej</GivenName><FamilyName>Kolinski</FamilyName></AuthorName></Author><Affiliation ID="Aff1"><OrgName>BioInfoBank Institute</OrgName><OrgAddress><Street>ul. Limanowskiego 24A</Street><Postcode>60-744</Postcode><City>Poznan</City><Country Code="PL">Poland</Country></OrgAddress></Affiliation><Affiliation ID="Aff2"><OrgDivision>Quantum Chemistry Group, Faculty of Chemistry</OrgDivision><OrgName>Adam Mickiewicz University</OrgName><OrgAddress><Street>ul. Grunwaldzka 6</Street><Postcode>60–780</Postcode><City>Poznan</City><Country Code="PL">Poland</Country></OrgAddress></Affiliation><Affiliation ID="Aff3"><OrgDivision>Bioinformatics Unit, Department of Physics</OrgDivision><OrgName>Adam Mickiewicz University</OrgName><OrgAddress><Street>ul. Umultowska 85</Street><Postcode>61–614</Postcode><City>Poznan</City><Country Code="PL">Poland</Country></OrgAddress></Affiliation><Affiliation ID="Aff4"><OrgDivision>Respiratory Virus Laboratory, Department of Virology</OrgDivision><OrgName>National Institute of Hygiene</OrgName><OrgAddress><Street>ul. Chocimska 24</Street><Postcode>00-791</Postcode><City>Warsaw</City><Country Code="PL">Poland</Country></OrgAddress></Affiliation><Affiliation ID="Aff5"><OrgDivision>Faculty of Chemistry</OrgDivision><OrgName>Warsaw University</OrgName><OrgAddress><Street>ul. Pasteura 1</Street><Postcode>02-093</Postcode><City>Warsaw</City><Country Code="PL">Poland</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Abstract</Heading><Para>The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.</Para></Abstract><KeywordGroup Language="En"><Heading>Keywords</Heading><Keyword>SARS</Keyword><Keyword>Inhibitors</Keyword><Keyword>Drug design</Keyword><Keyword>Computational chemistry</Keyword><Keyword>Bioinformatics</Keyword></KeywordGroup></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors</title></titleInfo><name type="personal" displayLabel="corresp"><namePart type="given">Marcin</namePart><namePart type="family">Hoffmann</namePart><affiliation>BioInfoBank Institute, ul. Limanowskiego 24A, 60-744, Poznan, Poland</affiliation><affiliation>Quantum Chemistry Group, Faculty of Chemistry, Adam Mickiewicz University, ul. Grunwaldzka 6, 60–780, Poznan, Poland</affiliation><affiliation>E-mail: mmh@bioinfo.pl</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Krystian</namePart><namePart type="family">Eitner</namePart><affiliation>BioInfoBank Institute, ul. Limanowskiego 24A, 60-744, Poznan, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Marcin</namePart><namePart type="family">von Grotthuss</namePart><affiliation>BioInfoBank Institute, ul. Limanowskiego 24A, 60-744, Poznan, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Leszek</namePart><namePart type="family">Rychlewski</namePart><affiliation>BioInfoBank Institute, ul. Limanowskiego 24A, 60-744, Poznan, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ewa</namePart><namePart type="family">Banachowicz</namePart><affiliation>Bioinformatics Unit, Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61–614, Poznan, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Tomasz</namePart><namePart type="family">Grabarkiewicz</namePart><affiliation>BioInfoBank Institute, ul. Limanowskiego 24A, 60-744, Poznan, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Tomasz</namePart><namePart type="family">Szkoda</namePart><affiliation>Respiratory Virus Laboratory, Department of Virology, National Institute of Hygiene, ul. Chocimska 24, 00-791, Warsaw, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Andrzej</namePart><namePart type="family">Kolinski</namePart><affiliation>Faculty of Chemistry, Warsaw University, ul. Pasteura 1, 02-093, Warsaw, Poland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>Kluwer Academic Publishers</publisher><place><placeTerm type="text">Dordrecht</placeTerm></place><dateCreated encoding="w3cdtf">2005-12-22</dateCreated><dateIssued encoding="w3cdtf">2006-05-01</dateIssued><copyrightDate encoding="w3cdtf">2006</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.</abstract><note>Original Paper</note><subject lang="en"><genre>Keywords</genre><topic>SARS</topic><topic>Inhibitors</topic><topic>Drug design</topic><topic>Computational chemistry</topic><topic>Bioinformatics</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Computer-Aided Molecular Design</title></titleInfo><titleInfo type="abbreviated"><title>J Comput Aided Mol Des</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">2006-10-24</dateIssued><copyrightDate encoding="w3cdtf">2006</copyrightDate></originInfo><subject><genre>Chemistry</genre><topic>Animal Anatomy / Morphology / Histology</topic><topic>Computer Applications in Chemistry</topic><topic>Physical Chemistry</topic></subject><identifier type="ISSN">0920-654X</identifier><identifier type="eISSN">1573-4951</identifier><identifier type="JournalID">10822</identifier><identifier type="IssueArticleCount">6</identifier><identifier type="VolumeIssueCount">12</identifier><part><date>2006</date><detail type="volume"><number>20</number><caption>vol.</caption></detail><detail type="issue"><number>5</number><caption>no.</caption></detail><extent unit="pages"><start>305</start><end>319</end></extent></part><recordInfo><recordOrigin>Springer Science+Business Media, LLC, 2006</recordOrigin></recordInfo></relatedItem><identifier type="istex">01425C7EEE0BB6928E80EE89666CCC077B3AADA5</identifier><identifier type="ark">ark:/67375/VQC-7T2WPFSP-B</identifier><identifier type="DOI">10.1007/s10822-006-9057-z</identifier><identifier type="ArticleID">9057</identifier><identifier type="ArticleID">s10822-006-9057-z</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer Science+Business Media B.V., 2006</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Springer Science+Business Media B.V., 2006</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-7T2WPFSP-B/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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