Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications.
Identifieur interne : 001460 ( PubMed/Corpus ); précédent : 001459; suivant : 001461Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications.
Auteurs : Rima Chaudhuri ; Sishi Tang ; Guijun Zhao ; Hui Lu ; David A. Case ; Michael E. JohnsonSource :
- Journal of molecular biology [ 1089-8638 ] ; 2011.
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.
DOI: 10.1016/j.jmb.2011.09.030
PubMed: 22004941
Links to Exploration step
pubmed:22004941Le document en format XML
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Case</name></author><author><name sortKey="Johnson, Michael E" sort="Johnson, Michael E" uniqKey="Johnson M" first="Michael E" last="Johnson">Michael E. Johnson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:22004941</idno><idno type="pmid">22004941</idno><idno type="doi">10.1016/j.jmb.2011.09.030</idno><idno type="wicri:Area/PubMed/Corpus">001460</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001460</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications.</title><author><name sortKey="Chaudhuri, Rima" sort="Chaudhuri, Rima" uniqKey="Chaudhuri R" first="Rima" last="Chaudhuri">Rima Chaudhuri</name><affiliation><nlm:affiliation>Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Tang, Sishi" sort="Tang, Sishi" uniqKey="Tang S" first="Sishi" last="Tang">Sishi Tang</name></author><author><name sortKey="Zhao, Guijun" sort="Zhao, Guijun" uniqKey="Zhao G" first="Guijun" last="Zhao">Guijun Zhao</name></author><author><name sortKey="Lu, Hui" sort="Lu, Hui" uniqKey="Lu H" first="Hui" last="Lu">Hui Lu</name></author><author><name sortKey="Case, David A" sort="Case, David A" uniqKey="Case D" first="David A" last="Case">David A. Case</name></author><author><name sortKey="Johnson, Michael E" sort="Johnson, Michael E" uniqKey="Johnson M" first="Michael E" last="Johnson">Michael E. Johnson</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="eISSN">1089-8638</idno><imprint><date when="2011" type="published">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="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptide Hydrolases</term><term>Protease Inhibitors</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" 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></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22004941</PMID><DateCompleted><Year>2012</Year><Month>01</Month><Day>13</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8638</ISSN><JournalIssue CitedMedium="Internet"><Volume>414</Volume><Issue>2</Issue><PubDate><Year>2011</Year><Month>Nov</Month><Day>25</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications.</ArticleTitle><Pagination><MedlinePgn>272-88</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jmb.2011.09.030</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2011 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chaudhuri</LastName><ForeName>Rima</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Sishi</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Guijun</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Hui</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Case</LastName><ForeName>David A</ForeName><Initials>DA</Initials></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>Michael E</ForeName><Initials>ME</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 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HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM57513</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P01 AI060915-05</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P01 AI060915</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM057513-08S1</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P01 AI060915-04</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P01 AI060915-03</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM057513-12</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R56 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