Anti-SARS drug screening by molecular docking.
Identifieur interne : 002296 ( PubMed/Checkpoint ); précédent : 002295; suivant : 002297Anti-SARS drug screening by molecular docking.
Auteurs : D-Q Wei [République populaire de Chine] ; R. Zhang ; Q-S Du ; W-N Gao ; Y. Li ; H. Gao ; S-Q Wang ; X. Zhang ; A-X Li ; S. Sirois ; K-C ChouSource :
- Amino acids [ 0939-4451 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Antiviral Agents.
- chemical , pharmacology : Antiviral Agents.
- drug effects : SARS Virus.
- Binding Sites, Drug Design, Hydrogen Bonding, Ligands, Microbial Sensitivity Tests, Models, Molecular, Protein Conformation, Structure-Activity Relationship.
Abstract
Starting from a collection of 1386 druggable compounds obtained from the 3D pharmacophore search, we performed a similarity search to narrow down the scope of docking studies. The template molecule is KZ7088 (Chou et al., 2003, Biochem Biophys Res Commun 308: 148-151). The MDL MACCS keys were used to fingerprint the molecules. The Tanimoto coefficient is taken as the metric to compare fingerprints. If the similarity threshold was 0.8, a set of 50 unique hits and 103 conformers were retrieved as a result of similarity search. The AutoDock 3.011 was used to carry out molecular docking of 50 ligands to their macromolecular protein receptors. Three compounds, i.e., C(28)H(34)O(4)N(7)Cl, C(21)H(36)O(5)N(6), and C(21)H(36)O(5)N(6), were found that may be promising candidates for further investigation. The main feature shared by these three potential inhibitors as well as the information of the involved side chains of SARS Cov Mpro may provide useful insights for the development of potent inhibitors against SARS enzyme.
DOI: 10.1007/s00726-006-0361-7
PubMed: 16715412
Affiliations:
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Zhang</name></author><author><name sortKey="Du, Q S" sort="Du, Q S" uniqKey="Du Q" first="Q-S" last="Du">Q-S Du</name></author><author><name sortKey="Gao, W N" sort="Gao, W N" uniqKey="Gao W" first="W-N" last="Gao">W-N Gao</name></author><author><name sortKey="Li, Y" sort="Li, Y" uniqKey="Li Y" first="Y" last="Li">Y. Li</name></author><author><name sortKey="Gao, H" sort="Gao, H" uniqKey="Gao H" first="H" last="Gao">H. Gao</name></author><author><name sortKey="Wang, S Q" sort="Wang, S Q" uniqKey="Wang S" first="S-Q" last="Wang">S-Q Wang</name></author><author><name sortKey="Zhang, X" sort="Zhang, X" uniqKey="Zhang X" first="X" last="Zhang">X. Zhang</name></author><author><name sortKey="Li, A X" sort="Li, A X" uniqKey="Li A" first="A-X" last="Li">A-X Li</name></author><author><name sortKey="Sirois, S" sort="Sirois, S" uniqKey="Sirois S" first="S" last="Sirois">S. Sirois</name></author><author><name sortKey="Chou, K C" sort="Chou, K C" uniqKey="Chou K" first="K-C" last="Chou">K-C Chou</name></author></analytic><series><title level="j">Amino acids</title><idno type="ISSN">0939-4451</idno><imprint><date when="2006" type="published">2006</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</term><term>Drug Design</term><term>Hydrogen Bonding</term><term>Ligands</term><term>Microbial Sensitivity Tests</term><term>Models, Molecular</term><term>Protein Conformation</term><term>SARS Virus (drug effects)</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Antiviraux ()</term><term>Antiviraux (pharmacologie)</term><term>Conception de médicament</term><term>Conformation des protéines</term><term>Liaison hydrogène</term><term>Ligands</term><term>Modèles moléculaires</term><term>Relation structure-activité</term><term>Sites de fixation</term><term>Tests de sensibilité microbienne</term><term>Virus du SRAS ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Antiviral Agents</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antiviraux</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Drug Design</term><term>Hydrogen Bonding</term><term>Ligands</term><term>Microbial Sensitivity Tests</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Antiviraux</term><term>Conception de médicament</term><term>Conformation des protéines</term><term>Liaison hydrogène</term><term>Ligands</term><term>Modèles moléculaires</term><term>Relation structure-activité</term><term>Sites de fixation</term><term>Tests de sensibilité microbienne</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Starting from a collection of 1386 druggable compounds obtained from the 3D pharmacophore search, we performed a similarity search to narrow down the scope of docking studies. The template molecule is KZ7088 (Chou et al., 2003, Biochem Biophys Res Commun 308: 148-151). The MDL MACCS keys were used to fingerprint the molecules. The Tanimoto coefficient is taken as the metric to compare fingerprints. If the similarity threshold was 0.8, a set of 50 unique hits and 103 conformers were retrieved as a result of similarity search. The AutoDock 3.011 was used to carry out molecular docking of 50 ligands to their macromolecular protein receptors. Three compounds, i.e., C(28)H(34)O(4)N(7)Cl, C(21)H(36)O(5)N(6), and C(21)H(36)O(5)N(6), were found that may be promising candidates for further investigation. The main feature shared by these three potential inhibitors as well as the information of the involved side chains of SARS Cov Mpro may provide useful insights for the development of potent inhibitors against SARS enzyme.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16715412</PMID><DateCompleted><Year>2007</Year><Month>02</Month><Day>05</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0939-4451</ISSN><JournalIssue CitedMedium="Print"><Volume>31</Volume><Issue>1</Issue><PubDate><Year>2006</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Amino acids</Title><ISOAbbreviation>Amino Acids</ISOAbbreviation></Journal><ArticleTitle>Anti-SARS drug screening by molecular docking.</ArticleTitle><Pagination><MedlinePgn>73-80</MedlinePgn></Pagination><Abstract><AbstractText>Starting from a collection of 1386 druggable compounds obtained from the 3D pharmacophore search, we performed a similarity search to narrow down the scope of docking studies. The template molecule is KZ7088 (Chou et al., 2003, Biochem Biophys Res Commun 308: 148-151). The MDL MACCS keys were used to fingerprint the molecules. The Tanimoto coefficient is taken as the metric to compare fingerprints. If the similarity threshold was 0.8, a set of 50 unique hits and 103 conformers were retrieved as a result of similarity search. The AutoDock 3.011 was used to carry out molecular docking of 50 ligands to their macromolecular protein receptors. Three compounds, i.e., C(28)H(34)O(4)N(7)Cl, C(21)H(36)O(5)N(6), and C(21)H(36)O(5)N(6), were found that may be promising candidates for further investigation. The main feature shared by these three potential inhibitors as well as the information of the involved side chains of SARS Cov Mpro may provide useful insights for the development of potent inhibitors against SARS enzyme.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>D-Q</ForeName><Initials>DQ</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Shanghai Jiaotong University, Shanghai, China. dqwei@sjtu.edu.cn</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Q-S</ForeName><Initials>QS</Initials></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>W-N</ForeName><Initials>WN</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>H</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>S-Q</ForeName><Initials>SQ</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>X</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>A-X</ForeName><Initials>AX</Initials></Author><Author ValidYN="Y"><LastName>Sirois</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Chou</LastName><ForeName>K-C</ForeName><Initials>KC</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>05</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>Austria</Country><MedlineTA>Amino 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