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  • Characterization of Natural Product Biological Imprints for Computer-aided Drug Design Applications

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    Sturm_2016_01Thesis.pdf (19.40Mb)
    Author(s)
    Sturm, Noe Joseph
    Primary Supervisor
    Quinn, Ronald
    Other Supervisors
    Kellenberger, Ester
    Year published
    2016
    Metadata
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    Abstract
    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 ...
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    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
    DOI
    https://doi.org/10.25904/1912/2674
    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
    Publication URI
    http://hdl.handle.net/10072/367893
    Collection
    • Theses - Higher Degree by Research

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