Identifying small-molecule inhibitors of protein interactions has traditionally presented a challenge for modern screening methods, despite interest stemming from the fact that such interactions comprise the underlying mechanisms for cell proliferation, differentiation, and survival. The objective of this application is to employ insights from computational methodology we have recently developed to address the distinct challenges associated with finding inhibitors of different classes of protein surface. Our central hypothesis is that exploring protein fluctuations leading to formation of surface pockets is criticl for understanding the regions of chemical space in which suitable inhibitory compounds may be found. We propose to meet our objective by pursuit of the following three specific aims: 1) Apply pocket optimization for selecting and characterizing protein targets. 2) Employ protein-ligand complementarity to build libraries enriched in protein interface inhibitors. 3) Extend these tools to allosteric inhibitors of protein interfaces. The proposed research is innovative in its ue of insight from protein fluctuations to identify binding pockets. By first confirming the ability o a target protein to form a suitable pocket and second assembling a complementary library, we collectively address the two main hurdles outlined above that have hitherto hindered identification of small molecules that directly inhibit protein-protein interactions. By combining this approach with in vitro biochemical screening, we expect to identify novel inhibitors of protei interactions involving each of three well-validated cancer targets: Bcl-xL, survivin, and b- TrCP.
This research is expected to have an important positive impact because it will provide new insights and tools to address the distinct challenges associated with finding small-molecule inhibitors of protein interactions. This contribution is significant because protein interactions have traditionally represented challenging targets for modern screening methods, despite interest stemming from the fact that such interactions comprise the underlying mechanisms for cell proliferation, differentiation, and survival.
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|Khar, Karen R; Goldschmidt, Lukasz; Karanicolas, John (2013) Fast docking on graphics processing units via Ray-Casting. PLoS One 8:e70661|