Antiviral potential of natural compounds against influenza virus hemagglutinin.
Identifieur interne : 000026 ( PubMed/Corpus ); précédent : 000025; suivant : 000027Antiviral potential of natural compounds against influenza virus hemagglutinin.
Auteurs : S. Kannan ; P. KolandaivelSource :
- Computational biology and chemistry [ 1476-928X ] ; 2017.
English descriptors
- KwdEn :
- Antiviral Agents (chemistry), Antiviral Agents (pharmacology), Binding Sites (drug effects), Biological Products (chemistry), Biological Products (pharmacology), Hemagglutinin Glycoproteins, Influenza Virus (metabolism), Hydrogen Bonding, Molecular Dynamics Simulation, Orthomyxoviridae (chemistry), Orthomyxoviridae (drug effects).
- MESH :
- chemical , chemistry : Antiviral Agents, Biological Products.
- chemical , metabolism : Hemagglutinin Glycoproteins, Influenza Virus.
- chemical , pharmacology : Antiviral Agents, Biological Products.
- chemistry : Orthomyxoviridae.
- drug effects : Binding Sites, Orthomyxoviridae.
- Hydrogen Bonding, Molecular Dynamics Simulation.
Abstract
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared. The molecular mechanics Poission-Boltzmann surface area (MM-PBSA) method is used to compare the binding free energy, its different energy components and per residue binding contribution. The H1 subtype shows higher binding preference for all the curcumin derivatives than H2 and H3. The binding capability of protein subtypes with curcumin derivatives and the binding affinity of curcumin compounds are in the order H1>H2>H3 and CI>CII>CIII respectively. The two -O-CH3- groups present in the CI compound help to have strong binding with HA protein than CII and CIII. The van der Waals interaction energy plays a significant role for binding in all the complexes. The hydrogen bonding interactions were monitored throughout the MD simulation. The conserved region (153-155) and the helix region (193-194) of H1, H2, H3 protein subtypes are found to possess higher binding susceptibility for binding of the curcumin derivatives.
DOI: 10.1016/j.compbiolchem.2017.11.001
PubMed: 29149637
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pubmed:29149637Le document en format XML
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Electronic address: ponkvel@hotmail.com.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:29149637</idno><idno type="pmid">29149637</idno><idno type="doi">10.1016/j.compbiolchem.2017.11.001</idno><idno type="wicri:Area/PubMed/Corpus">000026</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000026</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Antiviral potential of natural compounds against influenza virus hemagglutinin.</title><author><name sortKey="Kannan, S" sort="Kannan, S" uniqKey="Kannan S" first="S" last="Kannan">S. Kannan</name><affiliation><nlm:affiliation>Department of Physics, Bharathiar University, Coimbatore, 641 046, India.</nlm:affiliation></affiliation></author><author><name sortKey="Kolandaivel, P" sort="Kolandaivel, P" uniqKey="Kolandaivel P" first="P" last="Kolandaivel">P. Kolandaivel</name><affiliation><nlm:affiliation>Department of Physics, Bharathiar University, Coimbatore, 641 046, India. Electronic address: ponkvel@hotmail.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Computational biology and chemistry</title><idno type="eISSN">1476-928X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Antiviral Agents (chemistry)</term><term>Antiviral Agents (pharmacology)</term><term>Binding Sites (drug effects)</term><term>Biological Products (chemistry)</term><term>Biological Products (pharmacology)</term><term>Hemagglutinin Glycoproteins, Influenza Virus (metabolism)</term><term>Hydrogen Bonding</term><term>Molecular Dynamics Simulation</term><term>Orthomyxoviridae (chemistry)</term><term>Orthomyxoviridae (drug effects)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Antiviral Agents</term><term>Biological Products</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Hemagglutinin Glycoproteins, Influenza Virus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term><term>Biological Products</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Orthomyxoviridae</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Binding Sites</term><term>Orthomyxoviridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Hydrogen Bonding</term><term>Molecular Dynamics Simulation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared. The molecular mechanics Poission-Boltzmann surface area (MM-PBSA) method is used to compare the binding free energy, its different energy components and per residue binding contribution. The H1 subtype shows higher binding preference for all the curcumin derivatives than H2 and H3. The binding capability of protein subtypes with curcumin derivatives and the binding affinity of curcumin compounds are in the order H1>H2>H3 and CI>CII>CIII respectively. The two -O-CH3- groups present in the CI compound help to have strong binding with HA protein than CII and CIII. The van der Waals interaction energy plays a significant role for binding in all the complexes. The hydrogen bonding interactions were monitored throughout the MD simulation. The conserved region (153-155) and the helix region (193-194) of H1, H2, H3 protein subtypes are found to possess higher binding susceptibility for binding of the curcumin derivatives.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29149637</PMID><DateCompleted><Year>2018</Year><Month>04</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>04</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1476-928X</ISSN><JournalIssue CitedMedium="Internet"><Volume>71</Volume><PubDate><Year>2017</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Computational biology and chemistry</Title><ISOAbbreviation>Comput Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Antiviral potential of natural compounds against influenza virus hemagglutinin.</ArticleTitle><Pagination><MedlinePgn>207-218</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1476-9271(17)30009-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.compbiolchem.2017.11.001</ELocationID><Abstract><AbstractText>Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared. The molecular mechanics Poission-Boltzmann surface area (MM-PBSA) method is used to compare the binding free energy, its different energy components and per residue binding contribution. The H1 subtype shows higher binding preference for all the curcumin derivatives than H2 and H3. The binding capability of protein subtypes with curcumin derivatives and the binding affinity of curcumin compounds are in the order H1>H2>H3 and CI>CII>CIII respectively. The two -O-CH3- groups present in the CI compound help to have strong binding with HA protein than CII and CIII. The van der Waals interaction energy plays a significant role for binding in all the complexes. The hydrogen bonding interactions were monitored throughout the MD simulation. The conserved region (153-155) and the helix region (193-194) of H1, H2, H3 protein subtypes are found to possess higher binding susceptibility for binding of the curcumin derivatives.</AbstractText><CopyrightInformation>Copyright © 2017 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kannan</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Physics, Bharathiar University, Coimbatore, 641 046, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kolandaivel</LastName><ForeName>P</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Physics, Bharathiar University, Coimbatore, 641 046, India. Electronic address: ponkvel@hotmail.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Comput Biol Chem</MedlineTA><NlmUniqueID>101157394</NlmUniqueID><ISSNLinking>1476-9271</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000998">Antiviral Agents</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D001688">Biological Products</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D019267">Hemagglutinin Glycoproteins, Influenza Virus</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000998" MajorTopicYN="N">Antiviral Agents</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001688" MajorTopicYN="N">Biological Products</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019267" MajorTopicYN="N">Hemagglutinin Glycoproteins, Influenza Virus</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056004" MajorTopicYN="N">Molecular Dynamics Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009975" MajorTopicYN="N">Orthomyxoviridae</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000187" MajorTopicYN="Y">drug effects</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Binding free energy</Keyword><Keyword MajorTopicYN="N">Density functional theory</Keyword><Keyword MajorTopicYN="N">Hemagglutinin</Keyword><Keyword MajorTopicYN="N">Molecular docking</Keyword><Keyword MajorTopicYN="N">Molecular dynamics simulation</Keyword><Keyword MajorTopicYN="N">Natural compounds</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>01</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>08</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>11</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>4</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29149637</ArticleId><ArticleId IdType="pii">S1476-9271(17)30009-9</ArticleId><ArticleId IdType="doi">10.1016/j.compbiolchem.2017.11.001</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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