SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective.
Identifieur interne : 001872 ( Main/Corpus ); précédent : 001871; suivant : 001873SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective.
Auteurs : Abdo A. ElfikySource :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2021.
Abstract
New treatment against SARS-CoV-2 now is a must. Nowadays, the world encounters a huge health crisis by the COVID-19 viral infection. Nucleotide inhibitors gave a lot of promising results in terms of its efficacy against different viral infections. In this work, molecular modeling, docking, and dynamics simulations are used to build a model for the viral protein RNA-dependent RNA polymerase (RdRp) and test its binding affinity to some clinically approved drugs and drug candidates. Molecular dynamics is used to equilibrate the system upon binding calculations to ensure the successful reproduction of previous results, to include the dynamics of the RdRp, and to understand how it affects the binding. The results show the effectiveness of Sofosbuvir, Ribavirin, Galidesivir, Remdesivir, Favipiravir, Cefuroxime, Tenofovir, and Hydroxychloroquine, in binding to SARS-CoV-2 RdRp. Additionally, Setrobuvir, YAK, and IDX-184, show better results, while four novel IDX-184 derivatives show promising results in attaching to the SARS-CoV-2 RdRp. There is an urgent need to specify drugs that can selectively bind and subsequently inhibit SARS-CoV-2 proteins. The availability of a punch of FDA-approved anti-viral drugs can help us in this mission, aiming to reduce the danger of COVID-19. The compounds 2 and 3 may tightly bind to the SARS-CoV-2 RdRp and so may be successful in the treatment of COVID-19.
DOI: 10.1080/07391102.2020.1761882
PubMed: 32338164
PubMed Central: PMC7222627
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pubmed:32338164Le document en format XML
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Elfiky</name><affiliation><nlm:affiliation>Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2021">2021</date><idno type="RBID">pubmed:32338164</idno><idno type="pmid">32338164</idno><idno type="doi">10.1080/07391102.2020.1761882</idno><idno type="pmc">PMC7222627</idno><idno type="wicri:Area/Main/Corpus">001872</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001872</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an <i>in silico</i> perspective.</title><author><name sortKey="Elfiky, Abdo A" sort="Elfiky, Abdo A" uniqKey="Elfiky A" first="Abdo A" last="Elfiky">Abdo A. Elfiky</name><affiliation><nlm:affiliation>Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of biomolecular structure & dynamics</title><idno type="eISSN">1538-0254</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">New treatment against SARS-CoV-2 now is a must. Nowadays, the world encounters a huge health crisis by the COVID-19 viral infection. Nucleotide inhibitors gave a lot of promising results in terms of its efficacy against different viral infections. In this work, molecular modeling, docking, and dynamics simulations are used to build a model for the viral protein RNA-dependent RNA polymerase (RdRp) and test its binding affinity to some clinically approved drugs and drug candidates. Molecular dynamics is used to equilibrate the system upon binding calculations to ensure the successful reproduction of previous results, to include the dynamics of the RdRp, and to understand how it affects the binding. The results show the effectiveness of Sofosbuvir, Ribavirin, Galidesivir, Remdesivir, Favipiravir, Cefuroxime, Tenofovir, and Hydroxychloroquine, in binding to SARS-CoV-2 RdRp. Additionally, Setrobuvir, YAK, and IDX-184, show better results, while four novel IDX-184 derivatives show promising results in attaching to the SARS-CoV-2 RdRp. There is an urgent need to specify drugs that can selectively bind and subsequently inhibit SARS-CoV-2 proteins. The availability of a punch of FDA-approved anti-viral drugs can help us in this mission, aiming to reduce the danger of COVID-19. The compounds 2 and 3 may tightly bind to the SARS-CoV-2 RdRp and so may be successful in the treatment of COVID-19.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32338164</PMID><DateRevised><Year>2021</Year><Month>05</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1538-0254</ISSN><JournalIssue CitedMedium="Internet"><Volume>39</Volume><Issue>9</Issue><PubDate><Year>2021</Year><Month>06</Month></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle>SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an <i>in silico</i> perspective.</ArticleTitle><Pagination><MedlinePgn>3204-3212</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2020.1761882</ELocationID><Abstract><AbstractText>New treatment against SARS-CoV-2 now is a must. Nowadays, the world encounters a huge health crisis by the COVID-19 viral infection. Nucleotide inhibitors gave a lot of promising results in terms of its efficacy against different viral infections. In this work, molecular modeling, docking, and dynamics simulations are used to build a model for the viral protein RNA-dependent RNA polymerase (RdRp) and test its binding affinity to some clinically approved drugs and drug candidates. Molecular dynamics is used to equilibrate the system upon binding calculations to ensure the successful reproduction of previous results, to include the dynamics of the RdRp, and to understand how it affects the binding. The results show the effectiveness of Sofosbuvir, Ribavirin, Galidesivir, Remdesivir, Favipiravir, Cefuroxime, Tenofovir, and Hydroxychloroquine, in binding to SARS-CoV-2 RdRp. Additionally, Setrobuvir, YAK, and IDX-184, show better results, while four novel IDX-184 derivatives show promising results in attaching to the SARS-CoV-2 RdRp. There is an urgent need to specify drugs that can selectively bind and subsequently inhibit SARS-CoV-2 proteins. The availability of a punch of FDA-approved anti-viral drugs can help us in this mission, aiming to reduce the danger of COVID-19. The compounds 2 and 3 may tightly bind to the SARS-CoV-2 RdRp and so may be successful in the treatment of COVID-19.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Elfiky</LastName><ForeName>Abdo A</ForeName><Initials>AA</Initials><Identifier Source="ORCID">0000-0003-4600-6240</Identifier><AffiliationInfo><Affiliation>Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Biomol Struct Dyn</MedlineTA><NlmUniqueID>8404176</NlmUniqueID><ISSNLinking>0739-1102</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">COVID-19</Keyword><Keyword MajorTopicYN="Y">RdRp</Keyword><Keyword MajorTopicYN="Y">SARS-CoV-2</Keyword><Keyword MajorTopicYN="Y">drug repurposing</Keyword><Keyword MajorTopicYN="Y">molecular docking</Keyword><Keyword MajorTopicYN="Y">molecular dynamics simulation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32338164</ArticleId><ArticleId IdType="doi">10.1080/07391102.2020.1761882</ArticleId><ArticleId IdType="pmc">PMC7222627</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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