Similarity between Flavonoid Biosynthetic Enzymes and Flavonoid Protein Targets Captured by Three-Dimensional Computing Approach.
Identifieur interne : 002833 ( Main/Curation ); précédent : 002832; suivant : 002834Similarity between Flavonoid Biosynthetic Enzymes and Flavonoid Protein Targets Captured by Three-Dimensional Computing Approach.
Auteurs : Noé Sturm [Australie] ; Ronald J. Quinn [Australie] ; Esther Kellenberger [France]Source :
- Planta medica [ 1439-0221 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- biosynthèse : Flavonoïdes.
- métabolisme : Enzymes, Flavonoïdes, Protéines.
- Bases de données de protéines, Conformation des protéines, Enzymes, Protéines, Sites de fixation.
English descriptors
- KwdEn :
- MESH :
- chemical , biosynthesis : Flavonoids.
- chemical , chemistry : Enzymes, Proteins.
- chemical , metabolism : Enzymes, Flavonoids, Proteins.
- Binding Sites, Databases, Protein, Protein Conformation.
Abstract
Natural products are made by nature through interaction with biosynthetic enzymes. They also exert their effect as drugs by interaction with proteins. To address the question "Do biosynthetic enzymes and therapeutic targets share common mechanisms for the molecular recognition of natural products?", we compared the active site of five flavonoid biosynthetic enzymes to 8077 ligandable binding sites in the Protein Data Bank using two three-dimensional-based methods (SiteAlign and Shaper). Virtual screenings efficiently retrieved known flavonoid targets, in particular protein kinases. A consistent performance obtained for variable site descriptions (presence/absence of water, variable boundaries, or small structural changes) indicated that the methods are robust and thus well suited for the identification of potential target proteins of natural products. Finally, our results suggested that flavonoid binding is not primarily driven by shape, but rather by the recognition of common anchoring points.
DOI: 10.1055/s-0035-1545697
PubMed: 25719942
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pubmed:25719942Le document en format XML
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Quinn</name><affiliation wicri:level="1"><nlm:affiliation>Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Eskitis Institute for Drug Discovery, Griffith University, Brisbane</wicri:regionArea><wicri:noRegion>Brisbane</wicri:noRegion></affiliation></author><author><name sortKey="Kellenberger, Esther" sort="Kellenberger, Esther" uniqKey="Kellenberger E" first="Esther" last="Kellenberger">Esther Kellenberger</name><affiliation wicri:level="4"><nlm:affiliation>Laboratory of Therapeutic Innovation, Medalis Drug Discovery Center, Université de Strasbourg, Illkirch, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratory of Therapeutic Innovation, Medalis Drug Discovery Center, Université de Strasbourg, Illkirch</wicri:regionArea><wicri:noRegion>Illkirch</wicri:noRegion><orgName type="university">Université de Strasbourg</orgName><placeName><settlement type="city">Strasbourg</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Alsace (région administrative)</region></placeName></affiliation></author></analytic><series><title level="j">Planta medica</title><idno type="eISSN">1439-0221</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Databases, Protein</term><term>Enzymes (chemistry)</term><term>Enzymes (metabolism)</term><term>Flavonoids (biosynthesis)</term><term>Flavonoids (metabolism)</term><term>Protein Conformation</term><term>Proteins (chemistry)</term><term>Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données de protéines</term><term>Conformation des protéines</term><term>Enzymes ()</term><term>Enzymes (métabolisme)</term><term>Flavonoïdes (biosynthèse)</term><term>Flavonoïdes (métabolisme)</term><term>Protéines ()</term><term>Protéines (métabolisme)</term><term>Sites de fixation</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Flavonoids</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Enzymes</term><term>Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Enzymes</term><term>Flavonoids</term><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Flavonoïdes</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Enzymes</term><term>Flavonoïdes</term><term>Protéines</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Databases, Protein</term><term>Protein Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données de protéines</term><term>Conformation des protéines</term><term>Enzymes</term><term>Protéines</term><term>Sites de fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Natural products are made by nature through interaction with biosynthetic enzymes. They also exert their effect as drugs by interaction with proteins. To address the question "Do biosynthetic enzymes and therapeutic targets share common mechanisms for the molecular recognition of natural products?", we compared the active site of five flavonoid biosynthetic enzymes to 8077 ligandable binding sites in the Protein Data Bank using two three-dimensional-based methods (SiteAlign and Shaper). Virtual screenings efficiently retrieved known flavonoid targets, in particular protein kinases. A consistent performance obtained for variable site descriptions (presence/absence of water, variable boundaries, or small structural changes) indicated that the methods are robust and thus well suited for the identification of potential target proteins of natural products. Finally, our results suggested that flavonoid binding is not primarily driven by shape, but rather by the recognition of common anchoring points.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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