SI/II Pocket of Ras: An Opportunity for a Once "Undruggable" Target

Abstract

Mutations on the Ras-family of small GTPases are among the most common molecular oncogenic drivers, with the HRas isoform being primarily associated with head-and-neck and genito-urinary cancers. Although once considered "undruggable," recent efforts have identified a structurally conserved surface pocket in the Ras family, designated the SI/II pocket, situated near the binding site of the guanidine exchange factor (GEF) SOS1. The SI/II pocket may represent a potential target site for a pan-Ras drug. A crystal structure representing the native state of GDP-bound HRasG12V was generated to characterize the topology of the SI/II pocket. This native-state structure was employed, together with the published structure of GppNHp-bound HRasG12V in state 1 (PDB ID: 4EFM), as a base for further molecular dynamics simulations exploring the conformational dynamics of the SI/II pocket via four generated synthetic HRas model structures. Our results show that the SI/II pocket is natively inaccessible in GDP-bound HRas yet becomes accessible in state 1 GppNHp-bound HRas systems, an effect that seems to be more evident in the mutated enzyme. This points to the GTP-bound state as a most promising target for Ras inhibitors directed at the SI/II pocket. Occlusion of the SI/II pocket is dictated by the spatial position of the alpha 2 alpha helix in relation to the protein core, with alpha 2 residue Y71 acting as a "tyrosine toggle" capable of restricting the pocket access.</br