nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of Moringa oleifera and hydroxychloroquine.
Identifieur interne : 001342 ( Main/Corpus ); précédent : 001341; suivant : 001343nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of Moringa oleifera and hydroxychloroquine.
Auteurs : Muhammad Hamza ; Ashaq Ali ; Suliman Khan ; Saeed Ahmed ; Zarlish Attique ; Saad Ur Rehman ; Ayesha Khan ; Hussain Ali ; Muhammad Rizwan ; Anum Munir ; Arshad Mehmood Khan ; Faiza Siddique ; Azhar Mehmood ; Faisal Nouroz ; Sajid KhanSource :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2020.
Abstract
An rare pandemic of viral pneumonia occurs in December 2019 in Wuhan, China, which is now recognized internationally as Corona Virus Disease 2019 (COVID-19), the etiological agent classified as Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). According to the World Health Organization (WHO), it has so far expanded to more than 213 countries/territories worldwide. Our study aims to find the viral peptides of SARS-COV-2 by peptide mass fingerprinting (PMF) in order to predict its novel structure and find an inhibitor for each viral peptide. For this reason, we calculated the mass of amino acid sequences translated from the SARS-CoV2 whole genome and identify the peptides that may be a target for inhibition. Molecular peptide docking with Moringa oleifera, phytochemicals (aqueous and ethanolic) leaf extracts of flavonoids (3.56 ± 0.03), (3.83 ± 0.02), anthraquinone (11.68 ± 0.04), (10.86 ± 0.06) and hydroxychloroquine present therapy of COVID-19 in Pakistan for comparative study. Results indicate that 15 peptides of SARS-CoV2 have been identified from PMF, which is then used as a selective inhibitor. The maximum energy obtained from AutoDock Vina for hydroxychloroquine is -5.1 kcal/mol, kaempferol (flavonoid) is -6.2 kcal/mol, and for anthraquinone -6 kcal/mol. Visualization of docking complex, important effects are observed regarding the binding of peptides to drug compounds. In conclusion, it is proposed that these compounds are effective antiviral agents against COVID-19 and can be used in clinical trials.Communicated by Ramaswamy H. Sarma.
DOI: 10.1080/07391102.2020.1778534
PubMed: 32567487
PubMed Central: PMC7332867
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of <i>Moringa oleifera</i> and hydroxychloroquine.</title><author><name sortKey="Hamza, Muhammad" sort="Hamza, Muhammad" uniqKey="Hamza M" first="Muhammad" last="Hamza">Muhammad Hamza</name><affiliation><nlm:affiliation>The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. 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Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Siddique, Faiza" sort="Siddique, Faiza" uniqKey="Siddique F" first="Faiza" last="Siddique">Faiza Siddique</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Mehmood, Azhar" sort="Mehmood, Azhar" uniqKey="Mehmood A" first="Azhar" last="Mehmood">Azhar Mehmood</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Nouroz, Faisal" sort="Nouroz, Faisal" uniqKey="Nouroz F" first="Faisal" last="Nouroz">Faisal Nouroz</name><affiliation><nlm:affiliation>Department of Bioinformatic, Hazara University Mansehra, Mansehra, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Khan, Sajid" sort="Khan, Sajid" uniqKey="Khan S" first="Sajid" last="Khan">Sajid Khan</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32567487</idno><idno type="pmid">32567487</idno><idno type="doi">10.1080/07391102.2020.1778534</idno><idno type="pmc">PMC7332867</idno><idno type="wicri:Area/Main/Corpus">001342</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001342</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of <i>Moringa oleifera</i> and hydroxychloroquine.</title><author><name sortKey="Hamza, Muhammad" sort="Hamza, Muhammad" uniqKey="Hamza M" first="Muhammad" last="Hamza">Muhammad Hamza</name><affiliation><nlm:affiliation>The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Ali, Ashaq" sort="Ali, Ashaq" uniqKey="Ali A" first="Ashaq" last="Ali">Ashaq Ali</name><affiliation><nlm:affiliation>Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>University of Chinese Academy of Sciences, Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Khan, Suliman" sort="Khan, Suliman" uniqKey="Khan S" first="Suliman" last="Khan">Suliman Khan</name><affiliation><nlm:affiliation>The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ahmed, Saeed" sort="Ahmed, Saeed" uniqKey="Ahmed S" first="Saeed" last="Ahmed">Saeed Ahmed</name><affiliation><nlm:affiliation>Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Attique, Zarlish" sort="Attique, Zarlish" uniqKey="Attique Z" first="Zarlish" last="Attique">Zarlish Attique</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Ur Rehman, Saad" sort="Ur Rehman, Saad" uniqKey="Ur Rehman S" first="Saad" last="Ur Rehman">Saad Ur Rehman</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Khan, Ayesha" sort="Khan, Ayesha" uniqKey="Khan A" first="Ayesha" last="Khan">Ayesha Khan</name><affiliation><nlm:affiliation>Department of Biotechnology, COMSATS Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Ali, Hussain" sort="Ali, Hussain" uniqKey="Ali H" first="Hussain" last="Ali">Hussain Ali</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Rizwan, Muhammad" sort="Rizwan, Muhammad" uniqKey="Rizwan M" first="Muhammad" last="Rizwan">Muhammad Rizwan</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Munir, Anum" sort="Munir, Anum" uniqKey="Munir A" first="Anum" last="Munir">Anum Munir</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Khan, Arshad Mehmood" sort="Khan, Arshad Mehmood" uniqKey="Khan A" first="Arshad Mehmood" last="Khan">Arshad Mehmood Khan</name><affiliation><nlm:affiliation>Department of Chemistry, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Siddique, Faiza" sort="Siddique, Faiza" uniqKey="Siddique F" first="Faiza" last="Siddique">Faiza Siddique</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Mehmood, Azhar" sort="Mehmood, Azhar" uniqKey="Mehmood A" first="Azhar" last="Mehmood">Azhar Mehmood</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Nouroz, Faisal" sort="Nouroz, Faisal" uniqKey="Nouroz F" first="Faisal" last="Nouroz">Faisal Nouroz</name><affiliation><nlm:affiliation>Department of Bioinformatic, Hazara University Mansehra, Mansehra, KPK, Pakistan.</nlm:affiliation></affiliation></author><author><name sortKey="Khan, Sajid" sort="Khan, Sajid" uniqKey="Khan S" first="Sajid" last="Khan">Sajid Khan</name><affiliation><nlm:affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</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">An rare pandemic of viral pneumonia occurs in December 2019 in Wuhan, China, which is now recognized internationally as Corona Virus Disease 2019 (COVID-19), the etiological agent classified as Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). According to the World Health Organization (WHO), it has so far expanded to more than 213 countries/territories worldwide. Our study aims to find the viral peptides of SARS-COV-2 by peptide mass fingerprinting (PMF) in order to predict its novel structure and find an inhibitor for each viral peptide. For this reason, we calculated the mass of amino acid sequences translated from the SARS-CoV2 whole genome and identify the peptides that may be a target for inhibition. Molecular peptide docking with <i>Moringa oleifera,</i> phytochemicals (aqueous and ethanolic) leaf extracts of flavonoids (3.56 ± 0.03), (3.83 ± 0.02), anthraquinone (11.68 ± 0.04), (10.86 ± 0.06) and hydroxychloroquine present therapy of COVID-19 in Pakistan for comparative study. Results indicate that 15 peptides of SARS-CoV2 have been identified from PMF, which is then used as a selective inhibitor. The maximum energy obtained from AutoDock Vina for hydroxychloroquine is -5.1 kcal/mol, kaempferol (flavonoid) is -6.2 kcal/mol, and for anthraquinone -6 kcal/mol. Visualization of docking complex, important effects are observed regarding the binding of peptides to drug compounds. In conclusion, it is proposed that these compounds are effective antiviral agents against COVID-19 and can be used in clinical trials.Communicated by Ramaswamy H. Sarma.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32567487</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1538-0254</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Jun</Month><Day>22</Day></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle>nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of <i>Moringa oleifera</i> and hydroxychloroquine.</ArticleTitle><Pagination><MedlinePgn>1-11</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2020.1778534</ELocationID><Abstract><AbstractText>An rare pandemic of viral pneumonia occurs in December 2019 in Wuhan, China, which is now recognized internationally as Corona Virus Disease 2019 (COVID-19), the etiological agent classified as Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). According to the World Health Organization (WHO), it has so far expanded to more than 213 countries/territories worldwide. Our study aims to find the viral peptides of SARS-COV-2 by peptide mass fingerprinting (PMF) in order to predict its novel structure and find an inhibitor for each viral peptide. For this reason, we calculated the mass of amino acid sequences translated from the SARS-CoV2 whole genome and identify the peptides that may be a target for inhibition. Molecular peptide docking with <i>Moringa oleifera,</i> phytochemicals (aqueous and ethanolic) leaf extracts of flavonoids (3.56 ± 0.03), (3.83 ± 0.02), anthraquinone (11.68 ± 0.04), (10.86 ± 0.06) and hydroxychloroquine present therapy of COVID-19 in Pakistan for comparative study. Results indicate that 15 peptides of SARS-CoV2 have been identified from PMF, which is then used as a selective inhibitor. The maximum energy obtained from AutoDock Vina for hydroxychloroquine is -5.1 kcal/mol, kaempferol (flavonoid) is -6.2 kcal/mol, and for anthraquinone -6 kcal/mol. Visualization of docking complex, important effects are observed regarding the binding of peptides to drug compounds. In conclusion, it is proposed that these compounds are effective antiviral agents against COVID-19 and can be used in clinical trials.Communicated by Ramaswamy H. Sarma.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hamza</LastName><ForeName>Muhammad</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ali</LastName><ForeName>Ashaq</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3224-2891</Identifier><AffiliationInfo><Affiliation>Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Suliman</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ahmed</LastName><ForeName>Saeed</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Attique</LastName><ForeName>Zarlish</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ur Rehman</LastName><ForeName>Saad</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Ayesha</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, COMSATS Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ali</LastName><ForeName>Hussain</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rizwan</LastName><ForeName>Muhammad</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Munir</LastName><ForeName>Anum</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Arshad Mehmood</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Siddique</LastName><ForeName>Faiza</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mehmood</LastName><ForeName>Azhar</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nouroz</LastName><ForeName>Faisal</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Bioinformatic, Hazara University Mansehra, Mansehra, KPK, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Sajid</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.</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>22</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">AutoDock Vina</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">anthraquinone</Keyword><Keyword MajorTopicYN="N">flavonoids</Keyword><Keyword MajorTopicYN="N">hydroxychloroquine</Keyword><Keyword MajorTopicYN="N">peptide mass 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