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  • Similarity between flavonoid biosynthetic enzymes and flavonoid protein targets captured by three-dimensional computing approach

    Author(s)
    Sturm, Noe
    Quinn, Ronald J
    Kellenberger, Esther
    Griffith University Author(s)
    Quinn, Ronald J.
    Year published
    2015
    Metadata
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    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 ...
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    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.
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    Journal Title
    Planta Medica
    Volume
    81
    Issue
    6
    DOI
    https://doi.org/10.1055/s-0035-1545697
    Subject
    Plant biology
    Plant biology not elsewhere classified
    Traditional, complementary and integrative medicine
    Pharmacology and pharmaceutical sciences
    Publication URI
    http://hdl.handle.net/10072/101204
    Collection
    • Journal articles

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