Computational design, synthesis, and biological evaluation of small molecule anti-cancer therapeutics

It’s estimated that as many as 80% of the existing potential cancer targets are considered to be ‘undruggable’. The vast majority of these targets engage in protein-protein interactions (PPIs). Within this class are the RAS GTPases (HRAS, KRAS (4A and 4B), NRAS), which are the most frequently mutated oncoproteins in human cancer- present in 30% of all malignancies. Despite efforts to target the RAS proteins spanning over 30 years, there still exists no direct therapeutic agent. The focus of this work has been using in silico tools to develop general approaches for designing inhibitors of PPIs and applying them to the RAS family of GTPases. Two parallel approaches are described. The first uses pharmacophore screening with a model derived from the residues on the proteins interacting with RAS that have been established through mutagenesis studies to be functionally important for binding. The second is a process we have termed PAINT- Process for Assembling ligands for Intractable Targets. This approach first entails the docking of fragments into multiple sites on a target engaging in protein-protein interactions. The fragment docking results are analyzed for enriched molecular architectures and are then used for the basis of combinatorial in silico libraries. A library is designed in one site and then the top scoring compounds are selected and used to extend into adjacent sites in an iterative docking and design process. This work describes the synthesis, biochemical, cell-based, and in vivo evaluations of inhibitors designed using this approach.