Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
Identifieur interne : 001257 ( Main/Exploration ); précédent : 001256; suivant : 001258Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
Auteurs : Lily S. Cheng ; Rommie E. Amaro ; Dong Xu ; Wilfred W. Li ; Peter W. Arzberger ; J. Andrew MccammonSource :
- Journal of Medicinal Chemistry [ 0022-2623 ] ; 2008.
Abstract
Avian influenza virus subtype H5N1 is a potential pandemic threat with human-adapted strains resistant to antiviral drugs. Although virtual screening (VS) against a crystal or relaxed receptor structure is an established method to identify potential inhibitors, the more dynamic changes within binding sites are neglected. To accommodate full receptor flexibility, we use AutoDock4 to screen the NCI diversity set against representative receptor ensembles extracted from explicitly solvated molecular dynamics simulations of the neuraminidase system. The top hits are redocked to the entire nonredundant receptor ensemble and rescored using the relaxed complex scheme (RCS). Of the 27 top hits reported, half ranked very poorly if only crystal structures are used. These compounds target the catalytic cavity as well as the newly identified 150- and 430-cavities, which exhibit dynamic properties in electrostatic surface and geometric shape. This ensemble-based VS and RCS approach may offer improvement over existing strategies for structure-based drug discovery.
Url:
DOI: 10.1021/jm8001197
PubMed: 18558668
PubMed Central: 2652358
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase</title><author><name sortKey="Cheng, Lily S" sort="Cheng, Lily S" uniqKey="Cheng L" first="Lily S." last="Cheng">Lily S. Cheng</name></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name></author><author><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name></author><author><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name></author><author><name sortKey="Arzberger, Peter W" sort="Arzberger, Peter W" uniqKey="Arzberger P" first="Peter W." last="Arzberger">Peter W. Arzberger</name></author><author><name sortKey="Mccammon, J Andrew" sort="Mccammon, J Andrew" uniqKey="Mccammon J" first="J. Andrew" last="Mccammon">J. 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Cheng</name></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name></author><author><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name></author><author><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name></author><author><name sortKey="Arzberger, Peter W" sort="Arzberger, Peter W" uniqKey="Arzberger P" first="Peter W." last="Arzberger">Peter W. Arzberger</name></author><author><name sortKey="Mccammon, J Andrew" sort="Mccammon, J Andrew" uniqKey="Mccammon J" first="J. Andrew" last="Mccammon">J. Andrew Mccammon</name></author></analytic><series><title level="j">Journal of Medicinal Chemistry</title><idno type="ISSN">0022-2623</idno><idno type="eISSN">1520-4804</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p content-type="toc-graphic"><graphic xlink:href="jm-2008-001197_0009" id="tgr1"></graphic></p><p>Avian influenza virus subtype H5N1 is a potential pandemic threat with human-adapted strains resistant to antiviral drugs. Although virtual screening (VS) against a crystal or relaxed receptor structure is an established method to identify potential inhibitors, the more dynamic changes within binding sites are neglected. To accommodate full receptor flexibility, we use AutoDock4 to screen the NCI diversity set against representative receptor ensembles extracted from explicitly solvated molecular dynamics simulations of the neuraminidase system. The top hits are redocked to the entire nonredundant receptor ensemble and rescored using the relaxed complex scheme (RCS). Of the 27 top hits reported, half ranked very poorly if only crystal structures are used. These compounds target the catalytic cavity as well as the newly identified 150- and 430-cavities, which exhibit dynamic properties in electrostatic surface and geometric shape. This ensemble-based VS and RCS approach may offer improvement over existing strategies for structure-based drug discovery.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abdel Ghafar, A N" uniqKey="Abdel Ghafar A">A. N. 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Gubareva</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><name sortKey="Arzberger, Peter W" sort="Arzberger, Peter W" uniqKey="Arzberger P" first="Peter W." last="Arzberger">Peter W. Arzberger</name><name sortKey="Cheng, Lily S" sort="Cheng, Lily S" uniqKey="Cheng L" first="Lily S." last="Cheng">Lily S. Cheng</name><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name><name sortKey="Mccammon, J Andrew" sort="Mccammon, J Andrew" uniqKey="Mccammon J" first="J. Andrew" last="Mccammon">J. Andrew Mccammon</name><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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