Design, synthesis, biological evaluation and computational investigation of Thiadiazole Benzimidazole derivatives bearing a Chlorophyrimidine pharmacophore as potent CLK2 inhibitors and anticancer agents.

Cdc2-like kinase 2 (CLK2) has emerged as an attractive anticancer therapeutic target because of its crucial role in pre-mRNA splicing and tumor growth. Here, we designed and synthesized a novel series of thiadiazole-based benzimidazole derivatives 15a-l incorporating chloropyrimidine pharmacophore and evaluated for CLK2 inhibition and antiproliferative activity against HCT116 cells. The synthesized derivatives exhibited CLK2 inhibition potential ranged from 0.2332 nM to >50 nM, with 15i displaying the highest potency with IC50 of 0.2332 nM, followed by 15 l (0.3342 nM), 15 k (0.5648 nM), and 15 g (0.6453 nM), as compared to standard T-025 (IC50 = 1.0 nM). In antiproliferative assay, 15 l exhibited the highest activity against HCT116 cells with IC50 23.52 nM, followed by compounds 15 h (28.54 nM), 15i (29.17 nM), and 15 g (33.43 nM), demonstrating higher cellular potency than T-025 (IC50 = 42 nM). Structure activity relationship (SAR) analysis indicated that fluorinated aromatic substituents and certain heteroaryl moieties linked to a thiadiazole ring favored CLK2 inhibition, although biochemical and cellular activities were not directly proportional. Molecular docking and molecular dynamics simulations provided a structural rationale consistent with experimental results by revealing the favorable and stable binding interactions within the CLK2 ATP-binding pocket. Density functional theory (DFT) calculations and in silico ADMET predictions further supported favorable electronic properties, drug-likeness and low predicted toxicity of the synthesized compounds.