Novel 5,6-dichlorobenzimidazole derivatives as dual BRAFWT and BRAFV600E inhibitors: design, synthesis, anti-cancer activity and molecular dynamics simulations

A new series of 1-substiuted-5,6-dichloro-2-(4-methoxyphenyl)-1H-benzo[d]imidazoles 10a-p was designed and synthesized to target both BRAF_WT and BRAF_V600E. The design strategy ensures that these derivatives would effectively occupy the ATP binding pocket of BRAF_WT/V600E kinase domains and extend over the gate area interacting through hydrogen bonding with the surrounding key amino acids Glu500 and Asp593 and to finally occupy the allosteric hydrophobic back pocket. Some synthesized derivatives demonstrated impressive potency against BRAF_WT with % inhibition approaching 91% at a concentration of 10 µM. The most potent candidate 10h demonstrated IC₅₀ values of 1.72 and 2.76 µM on BRAF_WT and BRAF_V600E, respectively. At the same time, the synthesized benzimidazoles 10a-p were examined for their growth inhibitory activity on NCI-60 cancer cell lines. Again, compound 10h revealed a potent GI₅₀ across a range of cancer cell lines. Moreover, it arrested cell cycle progression in HT29 colon cancer cell line at G2/M phase and induced apoptosis in the same cell line. Molecular dynamics simulations supported the validity of the design assumption, simultaneously, ADME prediction study displayed that the designed benzimidazoles exhibit promising physiochemical and drug-likeness properties as anticancer agents.