Mutations in the Kirsten rat sarcoma virus (KRAS) protein occur in nearly 30% of all tumors and are a hallmark of several aggressive cancers. Despite the development of inhibitors that selectively target certain KRAS mutants, a single point mutation can substantially reduce their effectiveness, underscoring the urgent need for alternative therapeutic strategies. One promising avenue is to target G-quadruplexes (GQs), noncanonical nucleic acid structures stabilized by guanine tetrads. GQs are found throughout the genome but are particularly enriched in promoter regions, where they modulate transcriptional regulation. Increasingly, GQs are being explored as therapeutic targets to tune gene expression in a sequence- and context-specific manner. Two different GQs have been identified in the KRAS promoter, one being a 32-nucleotide (nt) structure and the other being a 22-nt GQ that can form in the presence of GQ-stabilizing ligands. Studies have shown that these GQs modulate KRAS expression, therefore stabilizing one or both structures is a potentially novel therapeutic strategy. Effective computer-aided drug design efforts require an atomistic understanding of KRAS GQ structures and dynamics. To assess their conformational landscapes, we performed Drude polarizable molecular dynamics (MD) simulations on both the wild-type and mutant 22-nt KRAS GQs and two conformations of the 32-nt GQ. Our simulations revealed extensive loop flexibility and transient stacking rearrangements, suggesting a dynamic ensemble rather than a single dominant fold. Characteristic structures were identified using k-means-based clustering methods. To further connect structural dynamics with ligand design, we applied the site identification by ligand competitive saturation (SILCS) method to these GQ variants. This approach enables a direct comparison of small-molecule affinity patterns as a function of mutation or conformational state. Together, this integrated framework establishes how the KRAS GQ topology impacts ligand-binding opportunities, advancing strategies for therapeutic intervention in KRAS-driven cancers.
Hosahalli et al. (Sun,) studied this question.