Structural Searching of Biosynthetic Enzymes to Predict Protein Targets of Natural Products.
Identifieur interne : 000330 ( PubMed/Checkpoint ); précédent : 000329; suivant : 000331Structural Searching of Biosynthetic Enzymes to Predict Protein Targets of Natural Products.
Auteurs : Noé Sturm [France] ; Ronald J. Quinn [Australie] ; Esther Kellenberger [France]Source :
- Planta medica [ 1439-0221 ] ; 2017.
Abstract
Recently, we have demonstrated that site comparison methodology using flavonoid biosynthetic enzymes as the query could automatically identify structural features common to different flavonoid-binding proteins, allowing for the identification of flavonoid targets such as protein kinases. With the aim of further validating the hypothesis that biosynthetic enzymes and therapeutic targets can contain a similar natural product imprint, we collected a set of 159 crystallographic structures representing 38 natural product biosynthetic enzymes by searching the Protein Databank. Each enzyme structure was used as a query to screen a repository of approximately 10 000 ligandable sites by active site similarity. We report a full analysis of the screening results and highlight three retrospective examples where the natural product validates the method, thereby revealing novel structural relationships between natural product biosynthetic enzymes and putative protein targets of the natural product. From a prospective perspective, our work provides a list of up to 64 potential novel targets for 25 well-characterized natural products.
DOI: 10.1055/s-0043-121992
PubMed: 29100267
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Quinn</name><affiliation wicri:level="1"><nlm:affiliation>Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Griffith 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="1"><nlm:affiliation>Laboratory of Therapeutic Innovation, Medalis Drug Discovery Center, University of Strasbourg, Illkirch, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratory of Therapeutic Innovation, Medalis Drug Discovery Center, University of Strasbourg, Illkirch</wicri:regionArea><wicri:noRegion>Illkirch</wicri:noRegion><wicri:noRegion>Illkirch</wicri:noRegion></affiliation></author></analytic><series><title level="j">Planta medica</title><idno type="eISSN">1439-0221</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recently, we have demonstrated that site comparison methodology using flavonoid biosynthetic enzymes as the query could automatically identify structural features common to different flavonoid-binding proteins, allowing for the identification of flavonoid targets such as protein kinases. With the aim of further validating the hypothesis that biosynthetic enzymes and therapeutic targets can contain a similar natural product imprint, we collected a set of 159 crystallographic structures representing 38 natural product biosynthetic enzymes by searching the Protein Databank. Each enzyme structure was used as a query to screen a repository of approximately 10 000 ligandable sites by active site similarity. We report a full analysis of the screening results and highlight three retrospective examples where the natural product validates the method, thereby revealing novel structural relationships between natural product biosynthetic enzymes and putative protein targets of the natural product. From a prospective perspective, our work provides a list of up to 64 potential novel targets for 25 well-characterized natural products.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">29100267</PMID><DateCreated><Year>2017</Year><Month>11</Month><Day>03</Day></DateCreated><DateRevised><Year>2017</Year><Month>11</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1439-0221</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2017</Year><Month>Nov</Month><Day>03</Day></PubDate></JournalIssue><Title>Planta medica</Title><ISOAbbreviation>Planta Med.</ISOAbbreviation></Journal><ArticleTitle>Structural Searching of Biosynthetic Enzymes to Predict Protein Targets of Natural Products.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1055/s-0043-121992</ELocationID><Abstract><AbstractText>Recently, we have demonstrated that site comparison methodology using flavonoid biosynthetic enzymes as the query could automatically identify structural features common to different flavonoid-binding proteins, allowing for the identification of flavonoid targets such as protein kinases. With the aim of further validating the hypothesis that biosynthetic enzymes and therapeutic targets can contain a similar natural product imprint, we collected a set of 159 crystallographic structures representing 38 natural product biosynthetic enzymes by searching the Protein Databank. Each enzyme structure was used as a query to screen a repository of approximately 10 000 ligandable sites by active site similarity. We report a full analysis of the screening results and highlight three retrospective examples where the natural product validates the method, thereby revealing novel structural relationships between natural product biosynthetic enzymes and putative protein targets of the natural product. From a prospective perspective, our work provides a list of up to 64 potential novel targets for 25 well-characterized natural products.</AbstractText><CopyrightInformation>Georg Thieme Verlag KG Stuttgart · New York.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sturm</LastName><ForeName>Noé</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Laboratory of Therapeutic Innovation, Medalis Drug Discovery Center, University of Strasbourg, Illkirch, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Quinn</LastName><ForeName>Ronald J</ForeName><Initials>RJ</Initials><AffiliationInfo><Affiliation>Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kellenberger</LastName><ForeName>Esther</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Laboratory of Therapeutic Innovation, Medalis Drug Discovery Center, University of Strasbourg, Illkirch, France.</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>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Planta Med</MedlineTA><NlmUniqueID>0066751</NlmUniqueID><ISSNLinking>0032-0943</ISSNLinking></MedlineJournalInfo><CoiStatement>Conflict of Interest: The authors declare no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>11</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29100267</ArticleId><ArticleId IdType="doi">10.1055/s-0043-121992</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>France</li></country></list><tree><country name="France"><noRegion><name sortKey="Sturm, Noe" sort="Sturm, Noe" uniqKey="Sturm N" first="Noé" last="Sturm">Noé Sturm</name></noRegion><name sortKey="Kellenberger, Esther" sort="Kellenberger, Esther" uniqKey="Kellenberger E" first="Esther" last="Kellenberger">Esther Kellenberger</name></country><country name="Australie"><noRegion><name sortKey="Quinn, Ronald J" sort="Quinn, Ronald J" uniqKey="Quinn R" first="Ronald J" last="Quinn">Ronald J. 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