Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach.
Identifieur interne : 000F39 ( Main/Exploration ); précédent : 000F38; suivant : 000F40Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach.
Auteurs : Joyce Oloaigbe Ogidigo [Nigeria] ; Emmanuel A. Iwuchukwu [Afrique du Sud] ; Collins U. Ibeji [Afrique du Sud, Nigeria] ; Okiemute Okpalefe [Nigeria] ; Mahmoud E S. Soliman [Afrique du Sud]Source :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2020.
Abstract
At present, there is no cure or vaccine for the devastating new highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has affected people globally. Herein, we identified potent phytocompounds from two antiviral plants Momordica charantia L. and Azadirachta indica used locally for the treatment of viral and parasitic infections. Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (Mpro) SARS-CoV-2. A total of 86 compounds from M. charantia L. and A. indica were identified. The top six phytocompounds; momordicine, deacetylnimninene, margolonone, momordiciode F2, nimbandiol, 17-hydroxyazadiradione were examined and when compared with three FDA reference drugs (remdesivir, hydroxychloroquine and ribavirin). The top six ranked compounds and FDA drugs were then subjected to MD simulation and pharmacokinetic studies. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; -41.1 and -43.4 kcal/mol) against the Mpro of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Per-residue analysis, root mean square deviation and solvent-accessible surface area revealed that compounds interacted with key amino acid residues at the active site of the enzyme and showed good system stability. The results obtained in this study show that these phytocompounds could emerge as promising therapeutic inhibitors for the Mpro of SARS-CoV-2. However, urgent trials should be conducted to validate this outcome. Communicated by Ramaswamy H. Sarma.
DOI: 10.1080/07391102.2020.1837681
PubMed: 33103616
PubMed Central: PMC7596894
Affiliations:
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Iwuchukwu</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu Natal, Durban</wicri:regionArea><wicri:noRegion>Durban</wicri:noRegion></affiliation></author><author><name sortKey="Ibeji, Collins U" sort="Ibeji, Collins U" uniqKey="Ibeji C" first="Collins U" last="Ibeji">Collins U. Ibeji</name><affiliation wicri:level="1"><nlm:affiliation>Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban</wicri:regionArea><wicri:noRegion>Durban</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Enugu State</wicri:regionArea><wicri:noRegion>Enugu State</wicri:noRegion></affiliation></author><author><name sortKey="Okpalefe, Okiemute" sort="Okpalefe, Okiemute" uniqKey="Okpalefe O" first="Okiemute" last="Okpalefe">Okiemute Okpalefe</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu</wicri:regionArea><wicri:noRegion>Enugu</wicri:noRegion></affiliation></author><author><name sortKey="Soliman, Mahmoud E S" sort="Soliman, Mahmoud E S" uniqKey="Soliman M" first="Mahmoud E S" last="Soliman">Mahmoud E S. Soliman</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu Natal, Durban</wicri:regionArea><wicri:noRegion>Durban</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">At present, there is no cure or vaccine for the devastating new highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has affected people globally. Herein, we identified potent phytocompounds from two antiviral plants <i>Momordica charantia</i> L. and <i>Azadirachta indica</i> used locally for the treatment of viral and parasitic infections. Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (M<sup>pro</sup>) SARS-CoV-2. A total of 86 compounds from <i>M. charantia</i> L. and <i>A. indica</i> were identified. The top six phytocompounds; momordicine, deacetylnimninene, margolonone, momordiciode F2, nimbandiol, 17-hydroxyazadiradione were examined and when compared with three FDA reference drugs (remdesivir, hydroxychloroquine and ribavirin). The top six ranked compounds and FDA drugs were then subjected to MD simulation and pharmacokinetic studies. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; -41.1 and -43.4 kcal/mol) against the M<sup>pro</sup> of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Per-residue analysis, root mean square deviation and solvent-accessible surface area revealed that compounds interacted with key amino acid residues at the active site of the enzyme and showed good system stability. The results obtained in this study show that these phytocompounds could emerge as promising therapeutic inhibitors for the M<sup>pro</sup> of SARS-CoV-2. However, urgent trials should be conducted to validate this outcome. Communicated by Ramaswamy H. Sarma.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33103616</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>Oct</Month><Day>25</Day></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle>Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach.</ArticleTitle><Pagination><MedlinePgn>1-18</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2020.1837681</ELocationID><Abstract><AbstractText>At present, there is no cure or vaccine for the devastating new highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has affected people globally. Herein, we identified potent phytocompounds from two antiviral plants <i>Momordica charantia</i> L. and <i>Azadirachta indica</i> used locally for the treatment of viral and parasitic infections. Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (M<sup>pro</sup>) SARS-CoV-2. A total of 86 compounds from <i>M. charantia</i> L. and <i>A. indica</i> were identified. The top six phytocompounds; momordicine, deacetylnimninene, margolonone, momordiciode F2, nimbandiol, 17-hydroxyazadiradione were examined and when compared with three FDA reference drugs (remdesivir, hydroxychloroquine and ribavirin). The top six ranked compounds and FDA drugs were then subjected to MD simulation and pharmacokinetic studies. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; -41.1 and -43.4 kcal/mol) against the M<sup>pro</sup> of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Per-residue analysis, root mean square deviation and solvent-accessible surface area revealed that compounds interacted with key amino acid residues at the active site of the enzyme and showed good system stability. The results obtained in this study show that these phytocompounds could emerge as promising therapeutic inhibitors for the M<sup>pro</sup> of SARS-CoV-2. However, urgent trials should be conducted to validate this outcome. Communicated by Ramaswamy H. Sarma.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ogidigo</LastName><ForeName>Joyce Oloaigbe</ForeName><Initials>JO</Initials><AffiliationInfo><Affiliation>Bio-resources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Genetics, Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iwuchukwu</LastName><ForeName>Emmanuel A</ForeName><Initials>EA</Initials><AffiliationInfo><Affiliation>Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ibeji</LastName><ForeName>Collins U</ForeName><Initials>CU</Initials><AffiliationInfo><Affiliation>Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Okpalefe</LastName><ForeName>Okiemute</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soliman</LastName><ForeName>Mahmoud E S</ForeName><Initials>MES</Initials><AffiliationInfo><Affiliation>Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>25</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">MMGBA</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">molecular dynamics simulations</Keyword><Keyword MajorTopicYN="N">natural phytocompounds</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>10</Month><Day>26</Day><Hour>8</Hour><Minute>42</Minute></PubMedPubDate><PubMedPubDate 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Ibeji</name><name sortKey="Ogidigo, Joyce Oloaigbe" sort="Ogidigo, Joyce Oloaigbe" uniqKey="Ogidigo J" first="Joyce Oloaigbe" last="Ogidigo">Joyce Oloaigbe Ogidigo</name><name sortKey="Ogidigo, Joyce Oloaigbe" sort="Ogidigo, Joyce Oloaigbe" uniqKey="Ogidigo J" first="Joyce Oloaigbe" last="Ogidigo">Joyce Oloaigbe Ogidigo</name><name sortKey="Okpalefe, Okiemute" sort="Okpalefe, Okiemute" uniqKey="Okpalefe O" first="Okiemute" last="Okpalefe">Okiemute Okpalefe</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Iwuchukwu, Emmanuel A" sort="Iwuchukwu, Emmanuel A" uniqKey="Iwuchukwu E" first="Emmanuel A" last="Iwuchukwu">Emmanuel A. Iwuchukwu</name></noRegion><name sortKey="Ibeji, Collins U" sort="Ibeji, Collins U" uniqKey="Ibeji C" first="Collins U" last="Ibeji">Collins U. Ibeji</name><name sortKey="Soliman, Mahmoud E S" sort="Soliman, Mahmoud E S" uniqKey="Soliman M" first="Mahmoud E S" last="Soliman">Mahmoud E S. 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