Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies.
Identifieur interne : 001114 ( Main/Exploration ); précédent : 001113; suivant : 001115Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies.
Auteurs : Kalirajan Rajagopal [Inde] ; Potlapati Varakumar [Inde] ; Baliwada Aparna [Inde] ; Gowramma Byran [Inde] ; Srikanth Jupudi [Inde]Source :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2020.
Abstract
Coronavirus disease (COVID-19), a life-threatening disease, is caused by SARS-CoV-2. The targeted therapeutics of small molecules helps the scientific community to fight against SARS-CoV-2. In this article, some oxazine substituted 9-anilinoacridines (A1-A48) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands A1-A48 against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, in silico ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Compound A38 has the highest G-score (-7.83) when compared to all the standard compounds which are proposed for COVID-19 treatment such as ritonavir (-7.48), lopinavir (-6.94), nelfinavir (-5.93), hydroxychloroquine (-5.47) and mataquine (-5.37). Compounds A13, A23, A18, A7, A48, A46, A32, A20, A1 and A47 are significantly active against SARS-CoV-2 main protease when compared with hydroxychloroquine and mataquine. The residues GLN19, THR24, THR25, THR26, LEU27, HIE41, SER46, MET49, ASN119, ASN142, HIE164, MET165, ASP187, ARG188 and GLN189 of SARS-CoV-2 main protease play a crucial role in binding with ligands. The in silico ADMET properties of the molecules are within the recommended values. The binding free energy was calculated using PRIME MM-GB/SA studies. From the ligands A38, A13, A23, A18, A7, A48 and A46 with significant Glide scores may produce significant COVID-19 activity for further development. Compound A38 was subjected to MD simulation at 100 ns to study the dynamic behaviour of protein-ligand complex. Communicated by Ramaswamy H. Sarma.
DOI: 10.1080/07391102.2020.1798285
PubMed: 32720578
PubMed Central: PMC7441781
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Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu</wicri:regionArea><wicri:noRegion>Tamilnadu</wicri:noRegion></affiliation></author><author><name sortKey="Varakumar, Potlapati" sort="Varakumar, Potlapati" uniqKey="Varakumar P" first="Potlapati" last="Varakumar">Potlapati Varakumar</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu</wicri:regionArea><wicri:noRegion>Tamilnadu</wicri:noRegion></affiliation></author><author><name sortKey="Aparna, Baliwada" sort="Aparna, Baliwada" uniqKey="Aparna B" first="Baliwada" last="Aparna">Baliwada Aparna</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu</wicri:regionArea><wicri:noRegion>Tamilnadu</wicri:noRegion></affiliation></author><author><name sortKey="Byran, Gowramma" sort="Byran, Gowramma" uniqKey="Byran G" first="Gowramma" last="Byran">Gowramma Byran</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu</wicri:regionArea><wicri:noRegion>Tamilnadu</wicri:noRegion></affiliation></author><author><name sortKey="Jupudi, Srikanth" sort="Jupudi, Srikanth" uniqKey="Jupudi S" first="Srikanth" last="Jupudi">Srikanth Jupudi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu</wicri:regionArea><wicri:noRegion>Tamilnadu</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of biomolecular structure & dynamics</title><idno type="eISSN">1538-0254</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">Coronavirus disease (COVID-19), a life-threatening disease, is caused by SARS-CoV-2. The targeted therapeutics of small molecules helps the scientific community to fight against SARS-CoV-2. In this article, some oxazine substituted 9-anilinoacridines (<b>A1-A48</b>) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands <b>A1-A48</b> against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, <i>in silico</i> ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Compound <b>A38</b> has the highest G-score (-7.83) when compared to all the standard compounds which are proposed for COVID-19 treatment such as ritonavir (-7.48), lopinavir (-6.94), nelfinavir (-5.93), hydroxychloroquine (-5.47) and mataquine (-5.37). Compounds <b>A13</b>, <b>A23</b>, <b>A18</b>, <b>A7</b>, <b>A48</b>, <b>A46</b>, <b>A32</b>, <b>A20</b>, <b>A1</b> and <b>A47</b> are significantly active against SARS-CoV-2 main protease when compared with hydroxychloroquine and mataquine. The residues GLN19, THR24, THR25, THR26, LEU27, HIE41, SER46, MET49, ASN119, ASN142, HIE164, MET165, ASP187, ARG188 and GLN189 of SARS-CoV-2 main protease play a crucial role in binding with ligands. The <i>in silico</i> ADMET properties of the molecules are within the recommended values. The binding free energy was calculated using PRIME MM-GB/SA studies. From the ligands <b>A38</b>, <b>A13</b>, <b>A23</b>, <b>A18</b>, <b>A7</b>, <b>A48</b> and <b>A46</b> with significant Glide scores may produce significant COVID-19 activity for further development. Compound <b>A38</b> was subjected to MD simulation at 100 ns to study the dynamic behaviour of protein-ligand complex. Communicated by Ramaswamy H. Sarma.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32720578</PMID><DateRevised><Year>2021</Year><Month>05</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1538-0254</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Jul</Month><Day>28</Day></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle>Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies.</ArticleTitle><Pagination><MedlinePgn>1-12</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2020.1798285</ELocationID><Abstract><AbstractText>Coronavirus disease (COVID-19), a life-threatening disease, is caused by SARS-CoV-2. The targeted therapeutics of small molecules helps the scientific community to fight against SARS-CoV-2. In this article, some oxazine substituted 9-anilinoacridines (<b>A1-A48</b>) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands <b>A1-A48</b> against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, <i>in silico</i> ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Compound <b>A38</b> has the highest G-score (-7.83) when compared to all the standard compounds which are proposed for COVID-19 treatment such as ritonavir (-7.48), lopinavir (-6.94), nelfinavir (-5.93), hydroxychloroquine (-5.47) and mataquine (-5.37). Compounds <b>A13</b>, <b>A23</b>, <b>A18</b>, <b>A7</b>, <b>A48</b>, <b>A46</b>, <b>A32</b>, <b>A20</b>, <b>A1</b> and <b>A47</b> are significantly active against SARS-CoV-2 main protease when compared with hydroxychloroquine and mataquine. The residues GLN19, THR24, THR25, THR26, LEU27, HIE41, SER46, MET49, ASN119, ASN142, HIE164, MET165, ASP187, ARG188 and GLN189 of SARS-CoV-2 main protease play a crucial role in binding with ligands. The <i>in silico</i> ADMET properties of the molecules are within the recommended values. The binding free energy was calculated using PRIME MM-GB/SA studies. From the ligands <b>A38</b>, <b>A13</b>, <b>A23</b>, <b>A18</b>, <b>A7</b>, <b>A48</b> and <b>A46</b> with significant Glide scores may produce significant COVID-19 activity for further development. Compound <b>A38</b> was subjected to MD simulation at 100 ns to study the dynamic behaviour of protein-ligand complex. Communicated by Ramaswamy H. Sarma.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rajagopal</LastName><ForeName>Kalirajan</ForeName><Initials>K</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-3382-4316</Identifier><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Varakumar</LastName><ForeName>Potlapati</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aparna</LastName><ForeName>Baliwada</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Byran</LastName><ForeName>Gowramma</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jupudi</LastName><ForeName>Srikanth</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, JSS College of Pharmacy [A Constituent College of JSS Academy of Higher Education & Research-(Deemed to be University)], Ooty, Tamilnadu, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType 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