Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus
Identifieur interne : 000048 ( Pmc/Checkpoint ); précédent : 000047; suivant : 000049Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus
Auteurs : Khanh Pb Le [Viêt Nam] ; Phuc-Chau Do [Viêt Nam] ; Rommie E. Amaro [États-Unis] ; Ly Le [Viêt Nam, États-Unis]Source :
- Evolutionary Bioinformatics Online [ 1176-9343 ] ; 2019.
Abstract
Influenza A has caused several deadly pandemics throughout human history. The virus is often resistant to developed treatments because of its genetic drift or shift property. Broad-spectrum antibodies show a promising potential to overcome the resistance of influenza viruses.
Url:
DOI: 10.1177/1176934319876938
PubMed: 31555044
PubMed Central: 6747855
Affiliations:
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Amaro</name><affiliation wicri:level="2"><nlm:aff id="aff2-1176934319876938">Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Le, Ly" sort="Le, Ly" uniqKey="Le L" first="Ly" last="Le">Ly Le</name><affiliation wicri:level="1"><nlm:aff id="aff1-1176934319876938">School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam</nlm:aff><country xml:lang="fr">Viêt Nam</country><wicri:regionArea>School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City</wicri:regionArea><wicri:noRegion>Ho Chi Minh City</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2-1176934319876938">Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31555044</idno><idno type="pmc">6747855</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747855</idno><idno type="RBID">PMC:6747855</idno><idno type="doi">10.1177/1176934319876938</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000961</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000961</idno><idno type="wicri:Area/Pmc/Curation">000961</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000961</idno><idno type="wicri:Area/Pmc/Checkpoint">000048</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000048</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus</title><author><name sortKey="Le, Khanh Pb" sort="Le, Khanh Pb" uniqKey="Le K" first="Khanh Pb" last="Le">Khanh Pb Le</name><affiliation wicri:level="1"><nlm:aff id="aff1-1176934319876938">School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam</nlm:aff><country xml:lang="fr">Viêt Nam</country><wicri:regionArea>School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City</wicri:regionArea><wicri:noRegion>Ho Chi Minh City</wicri:noRegion></affiliation></author><author><name sortKey="Do, Phuc Chau" sort="Do, Phuc Chau" uniqKey="Do P" first="Phuc-Chau" last="Do">Phuc-Chau Do</name><affiliation wicri:level="1"><nlm:aff id="aff1-1176934319876938">School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam</nlm:aff><country xml:lang="fr">Viêt Nam</country><wicri:regionArea>School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City</wicri:regionArea><wicri:noRegion>Ho Chi Minh City</wicri:noRegion></affiliation></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E" last="Amaro">Rommie E. Amaro</name><affiliation wicri:level="2"><nlm:aff id="aff2-1176934319876938">Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Le, Ly" sort="Le, Ly" uniqKey="Le L" first="Ly" last="Le">Ly Le</name><affiliation wicri:level="1"><nlm:aff id="aff1-1176934319876938">School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam</nlm:aff><country xml:lang="fr">Viêt Nam</country><wicri:regionArea>School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City</wicri:regionArea><wicri:noRegion>Ho Chi Minh City</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2-1176934319876938">Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of California, San Diego, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">Evolutionary Bioinformatics Online</title><idno type="eISSN">1176-9343</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Influenza A has caused several deadly pandemics throughout human history. The virus is often resistant to developed treatments because of its genetic drift or shift property. Broad-spectrum antibodies show a promising potential to overcome the resistance of influenza viruses. <italic>In silico</italic> studies on broad-reactive antibodies and their interactions with hemagglutinins might shed light on the rational design of a universal vaccine. In this study, 11 broad-spectrum antibodies (or antigen-binding fragments) and 14 hemagglutinins of H3N2 and H5N1 strains were docked and analyzed to provide information about the construction of the scaffold for using universal antibodies against the influenza A virus. Antigen-binding fragments that have high number of appearances in the top 3 within each H3 and H5 subtypes were chosen for protein-protein interaction analysis. The results show that while the hydrogen bond is important for Ab/Fab binding to H3, the H5-Ab/Fab system may need cation-pi interaction for a strong interaction.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Barry, Jm" uniqKey="Barry J">JM. Barry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bouvier, Nm" uniqKey="Bouvier N">NM Bouvier</name></author><author><name sortKey="Palese, P" uniqKey="Palese P">P. Palese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saunders Hastings, Pr" uniqKey="Saunders Hastings P">PR Saunders-Hastings</name></author><author><name sortKey="Krewski, D" uniqKey="Krewski D">D. Krewski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nguyen, D" uniqKey="Nguyen D">D. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Evol Bioinform Online</journal-id><journal-id journal-id-type="iso-abbrev">Evol. Bioinform. Online</journal-id><journal-id journal-id-type="publisher-id">EVB</journal-id><journal-id journal-id-type="hwp">spevb</journal-id><journal-title-group><journal-title>Evolutionary Bioinformatics Online</journal-title></journal-title-group><issn pub-type="epub">1176-9343</issn><publisher><publisher-name>SAGE Publications</publisher-name><publisher-loc>Sage UK: London, England</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31555044</article-id><article-id pub-id-type="pmc">6747855</article-id><article-id pub-id-type="doi">10.1177/1176934319876938</article-id><article-id pub-id-type="publisher-id">10.1177_1176934319876938</article-id><article-categories><subj-group subj-group-type="heading"><subject>Antimicrobial Resistance</subject><subj-group subj-group-type="heading"><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Le</surname><given-names>Khanh PB</given-names></name><xref ref-type="aff" rid="aff1-1176934319876938">1</xref><xref ref-type="author-notes" rid="fn1-1176934319876938">*</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">https://orcid.org/0000-0002-0280-0816</contrib-id><name><surname>Do</surname><given-names>Phuc-Chau</given-names></name><xref ref-type="aff" rid="aff1-1176934319876938">1</xref><xref ref-type="author-notes" rid="fn1-1176934319876938">*</xref></contrib><contrib contrib-type="author"><name><surname>Amaro</surname><given-names>Rommie E</given-names></name><xref ref-type="aff" rid="aff2-1176934319876938">2</xref></contrib><contrib contrib-type="author"><name><surname>Le</surname><given-names>Ly</given-names></name><xref ref-type="aff" rid="aff1-1176934319876938">1</xref><xref ref-type="aff" rid="aff2-1176934319876938">2</xref><xref ref-type="corresp" rid="corresp1-1176934319876938"></xref></contrib></contrib-group><aff id="aff1-1176934319876938"><label>1</label>School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam</aff><aff id="aff2-1176934319876938"><label>2</label>Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA</aff><author-notes><corresp id="corresp1-1176934319876938">Ly Le, School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam. Email: <email>ly.le@hcmiu.edu.vn</email></corresp><fn fn-type="equal" id="fn1-1176934319876938"><label>*</label><p>K.P.B.L. and P.-C.D. contributed equally to this article.</p></fn></author-notes><pub-date pub-type="epub"><day>16</day><month>9</month><year>2019</year></pub-date><pub-date pub-type="collection"><year>2019</year></pub-date><volume>15</volume><elocation-id>1176934319876938</elocation-id><history><date date-type="received"><day>21</day><month>8</month><year>2019</year></date><date date-type="accepted"><day>27</day><month>8</month><year>2019</year></date></history><permissions><copyright-statement>© The Author(s) 2019</copyright-statement><copyright-year>2019</copyright-year><copyright-holder content-type="sage">SAGE Publications Ltd unless otherwise noted. Manuscript content on this site is licensed under Creative Commons Licenses</copyright-holder><license license-type="creative-commons" xlink:href="http://www.creativecommons.org/licenses/by-nc/4.0/"><license-p>This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (<ext-link ext-link-type="uri" xlink:href="http://www.creativecommons.org/licenses/by-nc/4.0/">http://www.creativecommons.org/licenses/by-nc/4.0/</ext-link>) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (<ext-link ext-link-type="uri" xlink:href="https://us.sagepub.com/en-us/nam/open-access-at-sage">https://us.sagepub.com/en-us/nam/open-access-at-sage</ext-link>).</license-p></license></permissions><abstract><p>Influenza A has caused several deadly pandemics throughout human history. The virus is often resistant to developed treatments because of its genetic drift or shift property. Broad-spectrum antibodies show a promising potential to overcome the resistance of influenza viruses. <italic>In silico</italic> studies on broad-reactive antibodies and their interactions with hemagglutinins might shed light on the rational design of a universal vaccine. In this study, 11 broad-spectrum antibodies (or antigen-binding fragments) and 14 hemagglutinins of H3N2 and H5N1 strains were docked and analyzed to provide information about the construction of the scaffold for using universal antibodies against the influenza A virus. Antigen-binding fragments that have high number of appearances in the top 3 within each H3 and H5 subtypes were chosen for protein-protein interaction analysis. The results show that while the hydrogen bond is important for Ab/Fab binding to H3, the H5-Ab/Fab system may need cation-pi interaction for a strong interaction.</p></abstract><kwd-group><kwd>Hemagglutinin</kwd><kwd>broad-spectrum antibody</kwd><kwd>universal vaccine</kwd><kwd>MEGADOCK</kwd><kwd>protein-protein interaction</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>January-December 2019</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>Viêt Nam</li><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><country name="Viêt Nam"><noRegion><name sortKey="Le, Khanh Pb" sort="Le, Khanh Pb" uniqKey="Le K" first="Khanh Pb" last="Le">Khanh Pb Le</name></noRegion><name sortKey="Do, Phuc Chau" sort="Do, Phuc Chau" uniqKey="Do P" first="Phuc-Chau" last="Do">Phuc-Chau Do</name><name sortKey="Le, Ly" sort="Le, Ly" uniqKey="Le L" first="Ly" last="Le">Ly Le</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E" last="Amaro">Rommie E. Amaro</name></region><name sortKey="Le, Ly" sort="Le, Ly" uniqKey="Le L" first="Ly" last="Le">Ly Le</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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