Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies.
Identifieur interne : 000E32 ( Main/Curation ); précédent : 000E31; suivant : 000E33Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies.
Auteurs : Nabajyoti Baildya [Inde] ; Narendra Nath Ghosh [Inde] ; Asoke P. Chattopadhyay [Inde]Source :
- Journal of molecular structure [ 0022-2860 ] ; 2020.
Abstract
The present work is an investigation to test hydroxychloroquine as an inhibitor for the COVID-19 main protease. Molecular docking studies revealed a high docking score and interaction energies and decent level of docking within the cavity in protease moiety. Molecular dynamics simulations also lead to the evaluation of conformational energies, average H-bonding distance, RMSD plots etc. Large RMSD fluctuations for the first 2 ns seem to provide the conformational and rotational changes associated with the drug molecule when it comes into the vicinity on the protease matrix. Snapshots of structural changes with respect to time vividly indicates that drug molecule has a profound impact on the binding sites as well as overall geometry of the protease moiety. On the whole, hydroxyxhloroquine confers good inhibitory response to COVID-19 main protease. We hope the present study should help workers in the field to develop potential vaccines and therapeutics against the novel coronavirus.
DOI: 10.1016/j.molstruc.2020.128595
PubMed: 32834108
PubMed Central: PMC7266611
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Chattopadhyay</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Kalyani, Kalyani, 741235, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Chemistry, University of Kalyani, Kalyani, 741235</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of molecular structure</title><idno type="ISSN">0022-2860</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The present work is an investigation to test hydroxychloroquine as an inhibitor for the COVID-19 main protease. Molecular docking studies revealed a high docking score and interaction energies and decent level of docking within the cavity in protease moiety. Molecular dynamics simulations also lead to the evaluation of conformational energies, average H-bonding distance, RMSD plots etc. Large RMSD fluctuations for the first 2 ns seem to provide the conformational and rotational changes associated with the drug molecule when it comes into the vicinity on the protease matrix. Snapshots of structural changes with respect to time vividly indicates that drug molecule has a profound impact on the binding sites as well as overall geometry of the protease moiety. On the whole, hydroxyxhloroquine confers good inhibitory response to COVID-19 main protease. We hope the present study should help workers in the field to develop potential vaccines and therapeutics against the novel coronavirus.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32834108</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0022-2860</ISSN><JournalIssue CitedMedium="Print"><Volume>1219</Volume><PubDate><Year>2020</Year><Month>Nov</Month><Day>05</Day></PubDate></JournalIssue><Title>Journal of molecular structure</Title><ISOAbbreviation>J Mol Struct</ISOAbbreviation></Journal><ArticleTitle>Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies.</ArticleTitle><Pagination><MedlinePgn>128595</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.molstruc.2020.128595</ELocationID><Abstract><AbstractText>The present work is an investigation to test hydroxychloroquine as an inhibitor for the COVID-19 main protease. Molecular docking studies revealed a high docking score and interaction energies and decent level of docking within the cavity in protease moiety. Molecular dynamics simulations also lead to the evaluation of conformational energies, average H-bonding distance, RMSD plots etc. Large RMSD fluctuations for the first 2 ns seem to provide the conformational and rotational changes associated with the drug molecule when it comes into the vicinity on the protease matrix. Snapshots of structural changes with respect to time vividly indicates that drug molecule has a profound impact on the binding sites as well as overall geometry of the protease moiety. On the whole, hydroxyxhloroquine confers good inhibitory response to COVID-19 main protease. We hope the present study should help workers in the field to develop potential vaccines and therapeutics against the novel coronavirus.</AbstractText><CopyrightInformation>© 2020 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Baildya</LastName><ForeName>Nabajyoti</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Kalyani, Kalyani, 741235, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ghosh</LastName><ForeName>Narendra Nath</ForeName><Initials>NN</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Gour Banga, Mokdumpur, Malda, 732103, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chattopadhyay</LastName><ForeName>Asoke P</ForeName><Initials>AP</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Kalyani, Kalyani, 741235, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Mol Struct</MedlineTA><NlmUniqueID>0141747</NlmUniqueID><ISSNLinking>0022-2860</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">COVID-19 main chain protease</Keyword><Keyword MajorTopicYN="N">Hydroxychloroquine</Keyword><Keyword MajorTopicYN="N">MD-Simulation</Keyword><Keyword MajorTopicYN="N">Molecular docking</Keyword></KeywordList><CoiStatement>The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>05</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32834108</ArticleId><ArticleId IdType="doi">10.1016/j.molstruc.2020.128595</ArticleId><ArticleId IdType="pii">S0022-2860(20)30920-0</ArticleId><ArticleId IdType="pii">128595</ArticleId><ArticleId IdType="pmc">PMC7266611</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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