In Silico Identification of Novel and Potent Inhibitors Against Mutant BRAF (V600E), MD Simulations, Free Energy Calculations, and Experimental Determination of Binding Affinity.

Abstract

BRAF is a proto oncogene that functions as a key signal transducer in the MAPK-ERK pathway, which regulates cell growth, division, and survival. Mutations in BRAF, particularly the V600E substitution in its kinase domain, are major drivers in melanoma and several other metastatic cancers, including breast, colorectal, NSCLC, and gastrointestinal cancers. In this study, novel inhibitors targeting the BRAF(V600E) mutant using a structure-based drug design approach are identified. Four chemical libraries ChemDiv Kinase, ChemDiv Anticancer, NCI, and ChEMBL Kinase SARfari are screened. Compounds from the ChemDiv Anticancer database show better Glide scores comparable to the FDA-approved BRAF inhibitor Vemurafenib. The compounds P184-1419 and P184-1479 score -12.688 and -12.012 kcal/mol, respectively, versus -14.288 kcal/mol for Vemurafenib. Top hits are further validated using GOLD docking, X-score ranking, and interaction profiling via LigPlot. Molecular dynamics simulations, principal component analysis, and free energy calculations confirm the stability of protein-ligand complexes. Biolayer interferometry assays reveal P184-1419 exhibits stronger binding affinity (KD = 151 μM) than Vemurafenib (KD = 437 μM). These findings suggest P184-1419 is a promising lead compound against BRAF(V600E), offering potential for future development of more effective cancer therapies.