Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors.
Identifieur interne : 003071 ( Main/Curation ); précédent : 003070; suivant : 003072Molecular 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
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001A84
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :001A84
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001A86
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :001D18
- to stream Ncbi, to step Curation: Pour aller vers cette notice dans l'étape Curation :001D18
- to stream Ncbi, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001D18
- to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :003149
Links to Exploration step
pubmed:18706430Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><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><wicri:noRegion>Bangkok 10400</wicri:noRegion></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></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><idno type="wicri:Area/PubMed/Checkpoint">001A86</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001A86</idno><idno type="wicri:Area/Ncbi/Merge">001D18</idno><idno type="wicri:Area/Ncbi/Curation">001D18</idno><idno type="wicri:Area/Ncbi/Checkpoint">001D18</idno><idno type="wicri:Area/Main/Merge">003149</idno><idno type="wicri:Area/Main/Curation">003071</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><wicri:noRegion>Bangkok 10400</wicri:noRegion></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></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003071 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 003071 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= SrasV1
|flux= Main
|étape= Curation
|type= RBID
|clé= pubmed:18706430
|texte= Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i -Sk "pubmed:18706430" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |