In silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro.
Identifieur interne : 000817 ( Main/Corpus ); précédent : 000816; suivant : 000818In silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro.
Auteurs : Mala Rajendran ; Sudeep Roy ; Keerthana Ravichandran ; Bagdevi Mishra ; Deepak K. Gupta ; Subash Nagarajan ; Ruby Celsia Arul Selvaraj ; Ivo ProvaznikSource :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2020.
Abstract
SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodock Vina. Phytochemicals with binding energy ≥ -8.0 kcal/mol were selected to understand their interaction with MPro. Virtual screening was further validated by performing molecular docking to generate favorable docked poses and the participation of important amino acid residues. Molecular dynamics simulation for the docked poses was performed to study thermodynamic properties of the protein, ligand and protein-ligand complexes. The finding shows that cinnamtannin B2 and cyanin showed favorable binding affinity values with SARS-CoV-2 MPro. The results are comparable in terms of docked poses, important amino acid participation and thermodynamic properties with the standard control drugs remdesivir, benazepril and hydroxychloroquine diphosphate. Prime MM-GBSA was employed for end-point binding energy calculation. Binding to domain I and II of MPro were mediated through the OH, SH, NH2 and non-polar side chain of amino acids. Cinnamtannin B2 and cyanin binds to MPro with many sub sites within the active site with RMSD and RMSF within 4 Å. The results computed using Prime MM-GBSA show that cinnamtannin B2 (-68.54940214 kcal/mol) and cyanin (-62.1902835 kcal/mol) have better binding affinity in comparison to hydroxychloroquine diphosphate (-54.00912412 kcal/mol) and benazepril (-53.70242369 kcal/mol). The results provide a basis for exploiting cinnamtannin B2 and cyanin as a starting point potential candidate for the development of drug against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
DOI: 10.1080/07391102.2020.1845980
PubMed: 33200680
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><i>In silico</i> screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 M<sup>Pro</sup>.</title><author><name sortKey="Rajendran, Mala" sort="Rajendran, Mala" uniqKey="Rajendran M" first="Mala" last="Rajendran">Mala Rajendran</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Roy, Sudeep" sort="Roy, Sudeep" uniqKey="Roy S" first="Sudeep" last="Roy">Sudeep Roy</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.</nlm:affiliation></affiliation></author><author><name sortKey="Ravichandran, Keerthana" sort="Ravichandran, Keerthana" uniqKey="Ravichandran K" first="Keerthana" last="Ravichandran">Keerthana Ravichandran</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Mishra, Bagdevi" sort="Mishra, Bagdevi" uniqKey="Mishra B" first="Bagdevi" last="Mishra">Bagdevi Mishra</name><affiliation><nlm:affiliation>Neogen Informatics, A121, Vikas Marg, New Delhi, India.</nlm:affiliation></affiliation></author><author><name sortKey="Gupta, Deepak K" sort="Gupta, Deepak K" uniqKey="Gupta D" first="Deepak K" last="Gupta">Deepak K. Gupta</name><affiliation><nlm:affiliation>Neogen Informatics, A121, Vikas Marg, New Delhi, India.</nlm:affiliation></affiliation></author><author><name sortKey="Nagarajan, Subash" sort="Nagarajan, Subash" uniqKey="Nagarajan S" first="Subash" last="Nagarajan">Subash Nagarajan</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Arul Selvaraj, Ruby Celsia" sort="Arul Selvaraj, Ruby Celsia" uniqKey="Arul Selvaraj R" first="Ruby Celsia" last="Arul Selvaraj">Ruby Celsia Arul Selvaraj</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Provaznik, Ivo" sort="Provaznik, Ivo" uniqKey="Provaznik I" first="Ivo" last="Provaznik">Ivo Provaznik</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:33200680</idno><idno type="pmid">33200680</idno><idno type="doi">10.1080/07391102.2020.1845980</idno><idno type="wicri:Area/Main/Corpus">000817</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000817</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en"><i>In silico</i> screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 M<sup>Pro</sup>.</title><author><name sortKey="Rajendran, Mala" sort="Rajendran, Mala" uniqKey="Rajendran M" first="Mala" last="Rajendran">Mala Rajendran</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Roy, Sudeep" sort="Roy, Sudeep" uniqKey="Roy S" first="Sudeep" last="Roy">Sudeep Roy</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.</nlm:affiliation></affiliation></author><author><name sortKey="Ravichandran, Keerthana" sort="Ravichandran, Keerthana" uniqKey="Ravichandran K" first="Keerthana" last="Ravichandran">Keerthana Ravichandran</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Mishra, Bagdevi" sort="Mishra, Bagdevi" uniqKey="Mishra B" first="Bagdevi" last="Mishra">Bagdevi Mishra</name><affiliation><nlm:affiliation>Neogen Informatics, A121, Vikas Marg, New Delhi, India.</nlm:affiliation></affiliation></author><author><name sortKey="Gupta, Deepak K" sort="Gupta, Deepak K" uniqKey="Gupta D" first="Deepak K" last="Gupta">Deepak K. Gupta</name><affiliation><nlm:affiliation>Neogen Informatics, A121, Vikas Marg, New Delhi, India.</nlm:affiliation></affiliation></author><author><name sortKey="Nagarajan, Subash" sort="Nagarajan, Subash" uniqKey="Nagarajan S" first="Subash" last="Nagarajan">Subash Nagarajan</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Arul Selvaraj, Ruby Celsia" sort="Arul Selvaraj, Ruby Celsia" uniqKey="Arul Selvaraj R" first="Ruby Celsia" last="Arul Selvaraj">Ruby Celsia Arul Selvaraj</name><affiliation><nlm:affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</nlm:affiliation></affiliation></author><author><name sortKey="Provaznik, Ivo" sort="Provaznik, Ivo" uniqKey="Provaznik I" first="Ivo" last="Provaznik">Ivo Provaznik</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.</nlm:affiliation></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">SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 M<sup>Pro</sup>. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodock Vina. Phytochemicals with binding energy ≥ -8.0 kcal/mol were selected to understand their interaction with M<sup>Pro</sup>. Virtual screening was further validated by performing molecular docking to generate favorable docked poses and the participation of important amino acid residues. Molecular dynamics simulation for the docked poses was performed to study thermodynamic properties of the protein, ligand and protein-ligand complexes. The finding shows that cinnamtannin B2 and cyanin showed favorable binding affinity values with SARS-CoV-2 M<sup>Pro</sup>. The results are comparable in terms of docked poses, important amino acid participation and thermodynamic properties with the standard control drugs remdesivir, benazepril and hydroxychloroquine diphosphate. Prime MM-GBSA was employed for end-point binding energy calculation. Binding to domain I and II of M<sup>Pro</sup> were mediated through the OH, SH, NH<sub>2</sub> and non-polar side chain of amino acids. Cinnamtannin B2 and cyanin binds to M<sup>Pro</sup> with many sub sites within the active site with RMSD and RMSF within 4 Å. The results computed using Prime MM-GBSA show that cinnamtannin B2 (-68.54940214 kcal/mol) and cyanin (-62.1902835 kcal/mol) have better binding affinity in comparison to hydroxychloroquine diphosphate (-54.00912412 kcal/mol) and benazepril (-53.70242369 kcal/mol). The results provide a basis for exploiting cinnamtannin B2 and cyanin as a starting point potential candidate for the development of drug against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33200680</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1538-0254</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Nov</Month><Day>17</Day></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle><i>In silico</i> screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 M<sup>Pro</sup>.</ArticleTitle><Pagination><MedlinePgn>1-15</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2020.1845980</ELocationID><Abstract><AbstractText>SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 M<sup>Pro</sup>. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodock Vina. Phytochemicals with binding energy ≥ -8.0 kcal/mol were selected to understand their interaction with M<sup>Pro</sup>. Virtual screening was further validated by performing molecular docking to generate favorable docked poses and the participation of important amino acid residues. Molecular dynamics simulation for the docked poses was performed to study thermodynamic properties of the protein, ligand and protein-ligand complexes. The finding shows that cinnamtannin B2 and cyanin showed favorable binding affinity values with SARS-CoV-2 M<sup>Pro</sup>. The results are comparable in terms of docked poses, important amino acid participation and thermodynamic properties with the standard control drugs remdesivir, benazepril and hydroxychloroquine diphosphate. Prime MM-GBSA was employed for end-point binding energy calculation. Binding to domain I and II of M<sup>Pro</sup> were mediated through the OH, SH, NH<sub>2</sub> and non-polar side chain of amino acids. Cinnamtannin B2 and cyanin binds to M<sup>Pro</sup> with many sub sites within the active site with RMSD and RMSF within 4 Å. The results computed using Prime MM-GBSA show that cinnamtannin B2 (-68.54940214 kcal/mol) and cyanin (-62.1902835 kcal/mol) have better binding affinity in comparison to hydroxychloroquine diphosphate (-54.00912412 kcal/mol) and benazepril (-53.70242369 kcal/mol). The results provide a basis for exploiting cinnamtannin B2 and cyanin as a starting point potential candidate for the development of drug against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rajendran</LastName><ForeName>Mala</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Roy</LastName><ForeName>Sudeep</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ravichandran</LastName><ForeName>Keerthana</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mishra</LastName><ForeName>Bagdevi</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Neogen Informatics, A121, Vikas Marg, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gupta</LastName><ForeName>Deepak K</ForeName><Initials>DK</Initials><AffiliationInfo><Affiliation>Neogen Informatics, A121, Vikas Marg, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nagarajan</LastName><ForeName>Subash</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Arul Selvaraj</LastName><ForeName>Ruby Celsia</ForeName><Initials>RC</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Provaznik</LastName><ForeName>Ivo</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>11</Month><Day>17</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="N">cinnamon</Keyword><Keyword MajorTopicYN="N">cinnamtannin</Keyword><Keyword MajorTopicYN="N">cyanin</Keyword><Keyword MajorTopicYN="N">hydroxychloroquine diphosphate</Keyword><Keyword MajorTopicYN="N">remdesivir and spices</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>11</Month><Day>17</Day><Hour>8</Hour><Minute>39</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33200680</ArticleId><ArticleId IdType="doi">10.1080/07391102.2020.1845980</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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