Development of highly potent and selective oncogenic KRASG12D PROTAC degraders

Abstract

As a key driver of tumorigenesis and cancer development, the KRAS^G12D mutation is ubiquitous existed in KRAS-associated malignancies, highlighting the urgent clinical need for effective KRAS^G12D targeting drugs. In this study, through rational design and multiple cell type-based antiproliferative evaluation, we identified a novel KRAS^G12D inhibitor, Y-I-1, which demonstrated remarkable anti-cancer activity. Subsequent computational analyses including molecular dynamics (MD) simulations, binding free energy calculations, umbrella sampling, and protein-ligand docking revealed its excellent binding characteristics, rationalizing the observed potency. Building upon the structure of Y-I-1, we constructed proteolysis-targeting chimera (PROTAC) by conjugating it with different linker moieties and VH032. Among them, degrader Y-D-2 potently and selectively exhibited nanomolar inhibitory IC₅₀, degradation DC₅₀ values, and more than 95 % maximum degradation (D_max) in KRAS^G12D-mutant cancer cells via ubiquitin proteasome-involving pathway, accompanied by nanomolar IC₅₀ efficiency for phosphorylated ERK (pERK) inhibition. Mechanistically, Y-D-2 significantly induced cell apoptosis, G1 cell cycle arrest and inhibited cell migration and invasion. Notably, Y-D-2 led to significant tumor growth inhibition in the GP2D xenograft model with well-tolerated dose-schedules with favorable PK properties. This study not only provides an important theoretical basis for the optimal design of KRAS^G12D degraders, but also highlights its potential for the treatment of KRAS^G12D-driven cancers.