Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors.
Identifieur interne : 001A84 ( PubMed/Curation ); précédent : 001A83; suivant : 001A85Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors.
Auteurs : Veena Nukoolkarn [Thaïlande] ; Vannajan Sanghiran Lee ; Maturos Malaisree ; Ornjira Aruksakulwong ; Supot HannongbuaSource :
- Journal of theoretical biology [ 1095-8541 ] ; 2008.
Descripteurs français
- KwdFr :
- Catalyse, Complexes multienzymatiques, Cysteine endopeptidases (), Inhibiteurs de protéase du VIH (usage thérapeutique), Liaison aux protéines, Liaison hydrogène, Ligands, Lopinavir, Modèles moléculaires, Protéines virales (), Pyrimidinones (usage thérapeutique), Ritonavir (usage thérapeutique), Simulation numérique.
- MESH :
English descriptors
- KwdEn :
- Catalysis, Computer Simulation, Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (drug effects), HIV Protease Inhibitors (therapeutic use), Hydrogen Bonding, Ligands, Lopinavir, Models, Molecular, Multienzyme Complexes, Protein Binding, Pyrimidinones (therapeutic use), Ritonavir (therapeutic use), Viral Proteins (chemistry), Viral Proteins (drug effects).
- MESH :
- chemical , chemistry : Cysteine Endopeptidases, Viral Proteins.
- chemical , drug effects : Cysteine Endopeptidases, Viral Proteins.
- chemical , therapeutic use : HIV Protease Inhibitors, Pyrimidinones, Ritonavir.
- Catalysis, Computer Simulation, Hydrogen Bonding, Ligands, Lopinavir, Models, Molecular, Multienzyme Complexes, Protein Binding.
Abstract
Since the emergence of the severe acute respiratory syndrome (SARS) to date, neither an effective antiviral drug nor a vaccine against SARS is available. However, it was found that a mixture of two HIV-1 proteinase inhibitors, lopinavir and ritonavir, exhibited some signs of effectiveness against the SARS virus. To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out for the SARS-CoV 3CL(pro) free enzyme (free SARS) and its complexes with lopinavir (SARS-LPV) and ritonavir (SARS-RTV). The results show that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CL(pro). The binding affinities of LPV and RTV to SARS-CoV 3CL(pro) do not show any significant difference. In addition, six hydrogen bonds were detected in the SARS-LPV system, while seven hydrogen bonds were found in SARS-RTV complex.
DOI: 10.1016/j.jtbi.2008.07.030
PubMed: 18706430
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Malaisree</name></author><author><name sortKey="Aruksakulwong, Ornjira" sort="Aruksakulwong, Ornjira" uniqKey="Aruksakulwong O" first="Ornjira" last="Aruksakulwong">Ornjira Aruksakulwong</name></author><author><name sortKey="Hannongbua, Supot" sort="Hannongbua, Supot" uniqKey="Hannongbua S" first="Supot" last="Hannongbua">Supot Hannongbua</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18706430</idno><idno type="pmid">18706430</idno><idno type="doi">10.1016/j.jtbi.2008.07.030</idno><idno type="wicri:Area/PubMed/Corpus">001A84</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001A84</idno><idno type="wicri:Area/PubMed/Curation">001A84</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001A84</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors.</title><author><name sortKey="Nukoolkarn, Veena" sort="Nukoolkarn, Veena" uniqKey="Nukoolkarn V" first="Veena" last="Nukoolkarn">Veena Nukoolkarn</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Vannajan Sanghiran" sort="Lee, Vannajan Sanghiran" uniqKey="Lee V" first="Vannajan Sanghiran" last="Lee">Vannajan Sanghiran Lee</name></author><author><name sortKey="Malaisree, Maturos" sort="Malaisree, Maturos" uniqKey="Malaisree M" first="Maturos" last="Malaisree">Maturos Malaisree</name></author><author><name sortKey="Aruksakulwong, Ornjira" sort="Aruksakulwong, Ornjira" uniqKey="Aruksakulwong O" first="Ornjira" last="Aruksakulwong">Ornjira Aruksakulwong</name></author><author><name sortKey="Hannongbua, Supot" sort="Hannongbua, Supot" uniqKey="Hannongbua S" first="Supot" last="Hannongbua">Supot Hannongbua</name></author></analytic><series><title level="j">Journal of theoretical biology</title><idno type="eISSN">1095-8541</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Catalysis</term><term>Computer Simulation</term><term>Cysteine Endopeptidases (chemistry)</term><term>Cysteine Endopeptidases (drug effects)</term><term>HIV Protease Inhibitors (therapeutic use)</term><term>Hydrogen Bonding</term><term>Ligands</term><term>Lopinavir</term><term>Models, Molecular</term><term>Multienzyme Complexes</term><term>Protein Binding</term><term>Pyrimidinones (therapeutic use)</term><term>Ritonavir (therapeutic use)</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (drug effects)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Catalyse</term><term>Complexes multienzymatiques</term><term>Cysteine endopeptidases ()</term><term>Inhibiteurs de protéase du VIH (usage thérapeutique)</term><term>Liaison aux protéines</term><term>Liaison hydrogène</term><term>Ligands</term><term>Lopinavir</term><term>Modèles moléculaires</term><term>Protéines virales ()</term><term>Pyrimidinones (usage thérapeutique)</term><term>Ritonavir (usage thérapeutique)</term><term>Simulation numérique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="drug effects" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="therapeutic use" xml:lang="en"><term>HIV Protease Inhibitors</term><term>Pyrimidinones</term><term>Ritonavir</term></keywords><keywords scheme="MESH" qualifier="usage thérapeutique" xml:lang="fr"><term>Inhibiteurs de protéase du VIH</term><term>Pyrimidinones</term><term>Ritonavir</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Catalysis</term><term>Computer Simulation</term><term>Hydrogen Bonding</term><term>Ligands</term><term>Lopinavir</term><term>Models, Molecular</term><term>Multienzyme Complexes</term><term>Protein Binding</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Catalyse</term><term>Complexes multienzymatiques</term><term>Cysteine endopeptidases</term><term>Liaison aux protéines</term><term>Liaison hydrogène</term><term>Ligands</term><term>Lopinavir</term><term>Modèles moléculaires</term><term>Protéines virales</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Since the emergence of the severe acute respiratory syndrome (SARS) to date, neither an effective antiviral drug nor a vaccine against SARS is available. However, it was found that a mixture of two HIV-1 proteinase inhibitors, lopinavir and ritonavir, exhibited some signs of effectiveness against the SARS virus. To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out for the SARS-CoV 3CL(pro) free enzyme (free SARS) and its complexes with lopinavir (SARS-LPV) and ritonavir (SARS-RTV). The results show that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CL(pro). The binding affinities of LPV and RTV to SARS-CoV 3CL(pro) do not show any significant difference. In addition, six hydrogen bonds were detected in the SARS-LPV system, while seven hydrogen bonds were found in SARS-RTV complex.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18706430</PMID><DateCompleted><Year>2008</Year><Month>12</Month><Day>05</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>26</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1095-8541</ISSN><JournalIssue CitedMedium="Internet"><Volume>254</Volume><Issue>4</Issue><PubDate><Year>2008</Year><Month>Oct</Month><Day>21</Day></PubDate></JournalIssue><Title>Journal of theoretical biology</Title><ISOAbbreviation>J. Theor. Biol.</ISOAbbreviation></Journal><ArticleTitle>Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors.</ArticleTitle><Pagination><MedlinePgn>861-7</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jtbi.2008.07.030</ELocationID><Abstract><AbstractText>Since the emergence of the severe acute respiratory syndrome (SARS) to date, neither an effective antiviral drug nor a vaccine against SARS is available. However, it was found that a mixture of two HIV-1 proteinase inhibitors, lopinavir and ritonavir, exhibited some signs of effectiveness against the SARS virus. To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out for the SARS-CoV 3CL(pro) free enzyme (free SARS) and its complexes with lopinavir (SARS-LPV) and ritonavir (SARS-RTV). The results show that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CL(pro). The binding affinities of LPV and RTV to SARS-CoV 3CL(pro) do not show any significant difference. In addition, six hydrogen bonds were detected in the SARS-LPV system, while seven hydrogen bonds were found in SARS-RTV complex.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nukoolkarn</LastName><ForeName>Veena</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Vannajan Sanghiran</ForeName><Initials>VS</Initials></Author><Author ValidYN="Y"><LastName>Malaisree</LastName><ForeName>Maturos</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Aruksakulwong</LastName><ForeName>Ornjira</ForeName><Initials>O</Initials></Author><Author ValidYN="Y"><LastName>Hannongbua</LastName><ForeName>Supot</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>07</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Theor Biol</MedlineTA><NlmUniqueID>0376342</NlmUniqueID><ISSNLinking>0022-5193</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017320">HIV Protease Inhibitors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008024">Ligands</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009097">Multienzyme Complexes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011744">Pyrimidinones</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral 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