Novel Allosteric Sites on Ras for Lead Generation

TLDR

Aberrant Ras activity underlies many cancers and developmental diseases, yet conventional small‑molecule inhibitors have largely failed. The study aims to develop a multi‑level computational strategy to identify inhibitors targeting previously uncharacterized allosteric sites on Ras. The method integrates bioinformatics, advanced molecular dynamics, ensemble docking of ZINC and NCI libraries, and preliminary experimental testing to identify candidate binders. Molecular dynamics and bioinformatics revealed conserved allosteric coupling and novel transient pockets near the switch region, and cell‑based assays confirmed that selected binders inhibit Ras signaling, supporting these sites as viable drug targets.

Abstract

Aberrant Ras activity is a hallmark of diverse cancers and developmental diseases. Unfortunately, conventional efforts to develop effective small molecule Ras inhibitors have met with limited success. We have developed a novel multi-level computational approach to discover potential inhibitors of previously uncharacterized allosteric sites. Our approach couples bioinformatics analysis, advanced molecular simulations, ensemble docking and initial experimental testing of potential inhibitors. Molecular dynamics simulation highlighted conserved allosteric coupling of the nucleotide-binding switch region with distal regions, including loop 7 and helix 5. Bioinformatics methods identified novel transient small molecule binding pockets close to these regions and in the vicinity of the conformationally responsive switch region. Candidate binders for these pockets were selected through ensemble docking of ZINC and NCI compound libraries. Finally, cell-based assays confirmed our hypothesis that the chosen binders can inhibit the downstream signaling activity of Ras. We thus propose that the predicted allosteric sites are viable targets for the development and optimization of new drugs.