Identification of KRAS mutants (G12C, G12D, and G12V) inhibitors

Aim: To identify and validate novel small-molecule inhibitors targeting KRAS G12C, G12D, and G12V mutants through a structure-based drug design and experimental approach.

Methods: We employed molecular docking, molecular dynamics (MD) simulations, MM-PBSA binding free energy calculations, and principal component analysis (PCA) to screen and evaluate potential inhibitors targeting the Switch-II pocket of KRAS mutants. Top-ranking compounds were experimentally validated using Bio-Layer Interferometry (BLI) for binding affinity and MTT assays to assess Anticancer activity in breast and lung Cancer cell lines.

Results: Compound C797-1505 showed strong binding to KRAS G12V (Dissociation constant (KD) = 141 µM), outperforming the reference Sotorasib (KD = 345 µM). C190-0346 displayed weak affinity toward KRAS G12C. MTT assays revealed that C797-1505 reduced breast Cancer cell viability (Half-maximal Inhibitory Concentration (IC50) = 43.51 µM), while both compounds demonstrated significant cytotoxicity against lung Cancer cells (IC50 = 18.78 µM and 22.93 µM, respectively).

Conclusion: Our integrated computational and experimental strategies successfully identified selective KRAS mutant inhibitors with promising Anticancer activity, particularly against G12V and G12C driven tumors. These findings support further development and preclinical evaluation of these compounds as targeted therapeutics.

KRAS; MAPK pathway; NSCLC; PDAC; colon cancer; molecular dynamics simulations; principle component analysis and free energy landscape; structure-based drug designing.