Structure-Based Identification and Synthesis of Benzimidazole Azo–Schiff Base Derivatives as Recommended CK2 and PIM-1 Inhibitors

Abstract

Casein Kinase-2 (CK2) and Proviral Integration site for Moloney murine leukemia virus-1 (PIM-1) are kinases that are continuously active and work together to promote oncogenesis, thus becoming an important target for anti-cancer drugs. This research highlights the design, synthesis, and in silico evaluation of a new class of azo–Schiff bases bearing benzimidazole moieties (A1–A7) as potential dual inhibitors of CK2/PIM-1 targets. The compounds were synthesized using diazotization/azocoupling reaction and Schiff's base condensation reactions, where structural elucidation was accomplished through FT-IR, 1H NMR, and 13C NMR analyses. The molecular docking process was performed using the GOLD docking program against ATP-binding sites on CK2 (PDB: 4DTK) and PIM-1 (PDB: 4KWP), followed by MD simulation for 100 ns using GROMACS software. Through computational screening, molecules A4 and A6 were found to be the most potent dual inhibitors. Compound A6 displayed the greatest affinity to CK2 with a PLP fitness value of 81.33, whereas compound A4 displayed the highest affinity to PIM-1 with a PLP fitness value of 86.80. The interesting thing is that both compounds revealed very good cross-reactivity to both enzymes and were superior to other compounds in the series concerning dual-target PLP fitness. The MD simulation results showed that A4 and A6 exhibit high stability in their interactions with minimal structural fluctuations, attributed to hydrogen bonds formed consistently within the active site regions. In contrast, A7 has been shown to be a PIM-1 selective inhibitor. The attachment of azo–Schiff base groups to the benzimidazole core results in an interesting structure with a potential for multi-kinase inhibitory activity. The current study has identified molecules A4 and A6 as potential leads that require further in vitro and in vivo validation.