Natural products are made by nature through interacting with biosynthetic enzymes.  Natural products also exert their effect as drugs by interaction with proteins. We have explored the question does the recognition of the natural product by biosynthetic enzymes translate to recognition of the therapeutic target. Molecular modeling of flavonoid biosynthetic enzymes and protein kinases with a series of natural product kinase inhibitors led to the development of the concept of Protein Fold Topology (PFT).  PFT describes cavity recognition points unrelated to protein fold similarity. The topology or spatial properties are preserved even though there is deformation of the protein elements that participate in the protein-ligand interactions.  We observe helices or �-sheets as equivalent in providing the invariant topology for protein-ligand interaction and, as such, are seeking to find automated methods to interrogate these interactions.

Protein Fold Topology: Will it aid drug discovery or is it the reason natural products have drug properties?

241st National Meeting (2011)

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