We propose to compare the effectiveness of the conventional high-throughput screening (HTS) approach with a new integrated ligand design strategy using computational modeling, biophysical NMR studies and biochemical assays. We will compare the effectiveness of these two approaches against two targets-a conventional kinase (B-Raf) and a challenging protein-protein interaction between K-Ras and B-Raf. K-Ras is an oncoprotein of paramount importance of cancer biology. The Ras oncoproteins (K-Ras, H-Ras, N-Ras) were discovered over 30 years ago, but have been resistant to direct targeting with small molecule drugs. Thus, despite the fact that the KRAS gene is mutated in ~20% of all tumors, and >60% of pancreatic cancers, there is no therapy for treating mutant KRAS tumors. K-Ras activation of effector proteins (Raf proteins, PI3K proteins, and Ral-GDS, among others) is mediated through the switch I region on K-Ras, which forms an extended beta sheet with the Ras-binding domain of B- Raf and other effector proteins. An antibody that disrupts this protein-protein interaction reverses Ras-induced tumor formation in animals. Thus, a small molecule inhibitor of this interaction is likely to be a useful therapeutic for tumors containing mutant KRAS. If we demonstrate increased effectiveness of this new design approach compared to standard HTS, it will have a profound effect on the likelihood of small molecule inhibitor discovery against currently undruggable target proteins. This project could thus lead to the first small molecule therapeutics for targeting tumors with mutant K-Ras and may open up a large number of undruggable targets to small molecule inhibition.
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