Comparison of SARS and NL63 Papain-Like Protease Binding Sites and Binding Site Dynamics: Inhibitor Design Implications
Identifieur interne : 002142 ( Main/Exploration ); précédent : 002141; suivant : 002143Comparison of SARS and NL63 Papain-Like Protease Binding Sites and Binding Site Dynamics: Inhibitor Design Implications
Auteurs : Rima Chaudhuri [États-Unis] ; Sishi Tang [États-Unis] ; Guijun Zhao [États-Unis] ; Hui Lu [États-Unis] ; David A. Case [États-Unis] ; Michael E. Johnson [États-Unis]Source :
- Journal of Molecular Biology [ 0022-2836 ] ; 2011.
Descripteurs français
- KwdFr :
- Conception de médicament, Coronavirus humain NL63 (enzymologie), Données de séquences moléculaires, Inhibiteurs de protéases (), Inhibiteurs de protéases (pharmacologie), Modèles moléculaires, Peptide hydrolases (), Peptide hydrolases (métabolisme), Similitude de séquences d'acides aminés, Simulation de dynamique moléculaire, Sites de fixation, Séquence d'acides aminés, Virus du SRAS (enzymologie), Électricité statique.
- MESH :
- enzymologie : Coronavirus humain NL63, Virus du SRAS.
- métabolisme : Peptide hydrolases.
- pharmacologie : Inhibiteurs de protéases.
- Conception de médicament, Données de séquences moléculaires, Inhibiteurs de protéases, Modèles moléculaires, Peptide hydrolases, Similitude de séquences d'acides aminés, Simulation de dynamique moléculaire, Sites de fixation, Séquence d'acides aminés, Électricité statique.
English descriptors
- KwdEn :
- Amino Acid Sequence, Binding Sites, Coronavirus NL63, Human (enzymology), Drug Design, Models, Molecular, Molecular Dynamics Simulation, Molecular Sequence Data, Peptide Hydrolases (chemistry), Peptide Hydrolases (metabolism), Protease Inhibitors (chemistry), Protease Inhibitors (pharmacology), SARS Virus (enzymology), Sequence Homology, Amino Acid, Static Electricity.
- MESH :
- chemical , chemistry : Peptide Hydrolases, Protease Inhibitors.
- enzymology : Coronavirus NL63, Human, SARS Virus.
- chemical , metabolism : Peptide Hydrolases.
- chemical , pharmacology : Protease Inhibitors.
- Amino Acid Sequence, Binding Sites, Drug Design, Models, Molecular, Molecular Dynamics Simulation, Molecular Sequence Data, Sequence Homology, Amino Acid, Static Electricity.
Abstract
The human severe acute respiratory syndrome coronavirus (SARS-CoV) and the NL63 coronaviruses are human respiratory pathogens for which no effective antiviral treatment exists. The papain-like cysteine proteases encoded by the coronavirus (SARS-CoV: PLpro; NL63: PLP1 and PLP2) represent potential targets for antiviral drug development. Three recent inhibitor-bound PLpro structures highlight the role of an extremely flexible six-residue loop in inhibitor binding. The high binding site plasticity is a major challenge in computational drug discovery/design efforts. From conventional molecular dynamics and accelerated molecular dynamics (aMD) simulations, we find that with conventional molecular dynamics simulation, PLpro translationally samples the open and closed conformation of BL2 loop on a picosecond–nanosecond timescale but does not reproduce the peptide bond inversion between loop residues Tyr269 and Gln270 that is observed on inhibitor GRL0617 binding. Only aMD simulation, starting from the closed loop conformation, reproduced the 180° ϕ–ψ dihedral rotation back to the open loop state. The Tyr–Gln peptide bond inversion appears to involve a progressive conformational change of the full loop, starting at one side, and progressing to the other. We used the SARS-CoV apo X-ray structure to develop a model of the NL63-PLP2 catalytic site. Superimposition of the PLP2 model on the PLpro X-ray structure identifies binding site residues in PLP2 that contribute to the distinct substrate cleavage site specificities between the two proteases. The topological and electrostatic differences between the two protease binding sites also help explain the selectivity of non-covalent PLpro inhibitors.
Url:
DOI: 10.1016/j.jmb.2011.09.030
PubMed: 22004941
PubMed Central: 3397151
Affiliations:
- États-Unis
- Illinois, New Jersey
- Chicago, New Brunswick (New Jersey)
- Université Rutgers, Université de l'Illinois à Chicago
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Le document en format XML
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de l'Illinois à Chicago</orgName></affiliation></author><author><name sortKey="Lu, Hui" sort="Lu, Hui" uniqKey="Lu H" first="Hui" last="Lu">Hui Lu</name><affiliation wicri:level="4"><nlm:aff id="af0010">Department of Bioengineering, Bioinformatics Program, University of Illinois at Chicago, Chicago, IL 60607, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, Bioinformatics Program, University of Illinois at Chicago, Chicago, IL 60607</wicri:regionArea><placeName><region type="state">Illinois</region><settlement type="city">Chicago</settlement></placeName><orgName type="university">Université de l'Illinois à Chicago</orgName></affiliation></author><author><name sortKey="Case, David A" sort="Case, David A" uniqKey="Case D" first="David A." last="Case">David A. Case</name><affiliation wicri:level="4"><nlm:aff id="af0015">BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 0885, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 0885</wicri:regionArea><placeName><region type="state">New Jersey</region><settlement type="city">New Brunswick (New Jersey)</settlement></placeName><orgName type="university">Université Rutgers</orgName></affiliation></author><author><name sortKey="Johnson, Michael E" sort="Johnson, Michael E" uniqKey="Johnson M" first="Michael E." last="Johnson">Michael E. Johnson</name><affiliation wicri:level="4"><nlm:aff id="af0005">Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607</wicri:regionArea><placeName><region type="state">Illinois</region><settlement type="city">Chicago</settlement></placeName><orgName type="university">Université de l'Illinois à Chicago</orgName></affiliation></author></analytic><series><title level="j">Journal of Molecular Biology</title><idno type="ISSN">0022-2836</idno><idno type="eISSN">1089-8638</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Coronavirus NL63, Human (enzymology)</term><term>Drug Design</term><term>Models, Molecular</term><term>Molecular Dynamics Simulation</term><term>Molecular Sequence Data</term><term>Peptide Hydrolases (chemistry)</term><term>Peptide Hydrolases (metabolism)</term><term>Protease Inhibitors (chemistry)</term><term>Protease Inhibitors (pharmacology)</term><term>SARS Virus (enzymology)</term><term>Sequence Homology, Amino Acid</term><term>Static Electricity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Conception de médicament</term><term>Coronavirus humain NL63 (enzymologie)</term><term>Données de séquences moléculaires</term><term>Inhibiteurs de protéases ()</term><term>Inhibiteurs de protéases (pharmacologie)</term><term>Modèles moléculaires</term><term>Peptide hydrolases ()</term><term>Peptide hydrolases (métabolisme)</term><term>Similitude de séquences d'acides aminés</term><term>Simulation de dynamique moléculaire</term><term>Sites de fixation</term><term>Séquence d'acides aminés</term><term>Virus du SRAS (enzymologie)</term><term>Électricité statique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptide Hydrolases</term><term>Protease Inhibitors</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Coronavirus humain NL63</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Coronavirus NL63, Human</term><term>SARS Virus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Peptide Hydrolases</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Peptide hydrolases</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Inhibiteurs de protéases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Protease Inhibitors</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Drug Design</term><term>Models, Molecular</term><term>Molecular Dynamics Simulation</term><term>Molecular Sequence Data</term><term>Sequence Homology, Amino Acid</term><term>Static Electricity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Conception de médicament</term><term>Données de séquences moléculaires</term><term>Inhibiteurs de protéases</term><term>Modèles moléculaires</term><term>Peptide hydrolases</term><term>Similitude de séquences d'acides aminés</term><term>Simulation de dynamique moléculaire</term><term>Sites de fixation</term><term>Séquence d'acides aminés</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The human severe acute respiratory syndrome coronavirus (SARS-CoV) and the NL63 coronaviruses are human respiratory pathogens for which no effective antiviral treatment exists. The papain-like cysteine proteases encoded by the coronavirus (SARS-CoV: PLpro; NL63: PLP1 and PLP2) represent potential targets for antiviral drug development. Three recent inhibitor-bound PLpro structures highlight the role of an extremely flexible six-residue loop in inhibitor binding. The high binding site plasticity is a major challenge in computational drug discovery/design efforts. From conventional molecular dynamics and accelerated molecular dynamics (aMD) simulations, we find that with conventional molecular dynamics simulation, PLpro translationally samples the open and closed conformation of BL2 loop on a picosecond–nanosecond timescale but does not reproduce the peptide bond inversion between loop residues Tyr269 and Gln270 that is observed on inhibitor GRL0617 binding. Only aMD simulation, starting from the closed loop conformation, reproduced the 180° ϕ–ψ dihedral rotation back to the open loop state. The Tyr–Gln peptide bond inversion appears to involve a progressive conformational change of the full loop, starting at one side, and progressing to the other. We used the SARS-CoV apo X-ray structure to develop a model of the NL63-PLP2 catalytic site. Superimposition of the PLP2 model on the PLpro X-ray structure identifies binding site residues in PLP2 that contribute to the distinct substrate cleavage site specificities between the two proteases. The topological and electrostatic differences between the two protease binding sites also help explain the selectivity of non-covalent PLpro inhibitors.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cavanagh, D" uniqKey="Cavanagh D">D. Cavanagh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Der Hoek, L" uniqKey="Van Der Hoek L">L. van der Hoek</name></author><author><name sortKey="Pyrc, K" uniqKey="Pyrc K">K. 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Taylor</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Illinois</li><li>New Jersey</li></region><settlement><li>Chicago</li><li>New Brunswick (New Jersey)</li></settlement><orgName><li>Université Rutgers</li><li>Université de l'Illinois à Chicago</li></orgName></list><tree><country name="États-Unis"><region name="Illinois"><name sortKey="Chaudhuri, Rima" sort="Chaudhuri, Rima" uniqKey="Chaudhuri R" first="Rima" last="Chaudhuri">Rima Chaudhuri</name></region><name sortKey="Case, David A" sort="Case, David A" uniqKey="Case D" first="David A." last="Case">David A. Case</name><name sortKey="Chaudhuri, Rima" sort="Chaudhuri, Rima" uniqKey="Chaudhuri R" first="Rima" last="Chaudhuri">Rima Chaudhuri</name><name sortKey="Johnson, Michael E" sort="Johnson, Michael E" uniqKey="Johnson M" first="Michael E." last="Johnson">Michael E. Johnson</name><name sortKey="Lu, Hui" sort="Lu, Hui" uniqKey="Lu H" first="Hui" last="Lu">Hui Lu</name><name sortKey="Tang, Sishi" sort="Tang, Sishi" uniqKey="Tang S" first="Sishi" last="Tang">Sishi Tang</name><name sortKey="Zhao, Guijun" sort="Zhao, Guijun" uniqKey="Zhao G" first="Guijun" last="Zhao">Guijun Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |