NMR study to identify a ligand-binding pocket in Ras.

Abstract

Despite decades of intense drug discovery efforts, to date no small molecules have been described that directly bind to Ras protein and effectively antagonize its function. In order to identify and characterize small-molecule binders to KRas, we carried out a fragment-based lead discovery effort. A ligand-detected primary nuclear magnetic resonance (NMR) screen identified 266 fragments from a library of 3285 diverse compounds. Protein-detected NMR using isotopically labeled KRas protein was applied for hit validation and binding site characterization. An area on the KRas surface emerged as a consensus site of fragment binding. X-ray crystallography studies on a subset of the hits elucidated atomic details of the ligand-protein interactions, and revealed that the consensus site comprises a shallow hydrophobic pocket. Comparison among the crystal structures indicated that the ligand-binding pocket is flexible and can be expanded upon ligand binding. The identified ligand-binding pocket is proximal to the protein-protein interface and therefore has the potential to mediate functional effects. Indeed, some ligands inhibited SOS1-dependent nucleotide exchange, although with weak potency. Several Ras ligands have been published in literature, the majority of which were discovered using NMR-based methods. Mapping of the ligand-binding sites revealed five areas on Ras with a high propensity for ligand binding and the potential of modulating Ras activity.