Discovery of a small-size imidazole-benzoindolium ligand for binding to KRAS promoter G-quadruplex that inhibits cancer growth with enhanced immunomodulation

KRAS overactivation is commonly present in a diversity of solid tumors. Recently, small-molecule inhibitors of KRAS G12C mutation are approved for clinical use, ending the long era of KRAS as an 'undruggable' target. However, new approaches to suppress a wide spectrum of KRAS abnormalities are still needed to be developed. G-quadruplex (G4) locates in the nuclease hypersensitive element (NHE) region of the promoter, and controls KRAS expression. Only a few KRAS G4 ligands have been discovered to date, which possess coplanar aromatic scaffolds, falling outside “drug-like” chemical space, and have no satisfactory selectivity between KRAS G4 and other DNAs. In this study, a series of drug-like, indolium-based analogs specifically targeting KRAS G4 were engineered, and BN1 was decided as the most potent ligand. BN1 effectively suppressed KRAS expression, thereby downregulating MEK-ERK pathway and PD-L1 expression in tumor cells. In vivo experiments displayed that BN1 was an effective agent to reduce tumor burden with immunostimulatory effects, including the increase of CD8+ IFN?+ cells, the decrease of CD4+ Foxp3+ cells and the regulation of cytokines. Collectively, it is the first time, to our knowledge, to report a KRAS G4-directed small-molecule ligand with antitumor efficacy related to enhanced immunomodulation. Overall design: To investigate the antitumor mechanisms of a small molecule G-quadruplex compound (BN1) against breast cancer cells, we treated MDA-MB-231 cells with BN1 for 24 h, and then performed gene expression profiling analysis obtained from RNA-seq of 3 duplicate cell samples.