Characterization of Natural Product Biological Imprints for Computer-aided Drug Design Applications
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Author(s)
Primary Supervisor
Quinn, Ronald
Other Supervisors
Kellenberger, Ester
Year published
2016
Metadata
Show full item recordAbstract
Can computational binding site similarity tools verify the hypothesis: “Biosynthetic moldings give potent biological activities to natural products”? To answer this question, we designed a tool modeling binding site properties according to solvent exposure. The method showed interesting characteristics but suffers from sensitivity to atomic coordinates.
However, existing methods have delivered evidence that the hypothesis was valid for the flavonoid chemical class. In order to extend the study, we designed an automated pipeline capable of searching natural product biosynthetic enzyme structures embedding ligandable catalytic ...
View more >Can computational binding site similarity tools verify the hypothesis: “Biosynthetic moldings give potent biological activities to natural products”? To answer this question, we designed a tool modeling binding site properties according to solvent exposure. The method showed interesting characteristics but suffers from sensitivity to atomic coordinates. However, existing methods have delivered evidence that the hypothesis was valid for the flavonoid chemical class. In order to extend the study, we designed an automated pipeline capable of searching natural product biosynthetic enzyme structures embedding ligandable catalytic sites. We collected structures of 117 biosynthetic enzymes. Finally, according to structural investigations of biosynthetic enzymes, we characterized diverse substrate-enzyme binding-modes, suggesting that natural product biological imprints usually do not agree with the “key-lock” model.
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View more >Can computational binding site similarity tools verify the hypothesis: “Biosynthetic moldings give potent biological activities to natural products”? To answer this question, we designed a tool modeling binding site properties according to solvent exposure. The method showed interesting characteristics but suffers from sensitivity to atomic coordinates. However, existing methods have delivered evidence that the hypothesis was valid for the flavonoid chemical class. In order to extend the study, we designed an automated pipeline capable of searching natural product biosynthetic enzyme structures embedding ligandable catalytic sites. We collected structures of 117 biosynthetic enzymes. Finally, according to structural investigations of biosynthetic enzymes, we characterized diverse substrate-enzyme binding-modes, suggesting that natural product biological imprints usually do not agree with the “key-lock” model.
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Thesis Type
Thesis (PhD Doctorate)
Degree Program
Doctor of Philosophy (PhD)
School
School of Natural Sciences
Copyright Statement
The author owns the copyright in this thesis, unless stated otherwise.
Item Access Status
Public
Subject
Drug design
Natural products
Biosynthetic moldings
Substrate-enzyme binding-modes