Novel Benzimidazol-2-Acetamide Derivatives as Submicromolar Casein Kinase 1δ Inhibitors with Favourable Predicted Drug-like Properties

Background/Objective: Casein kinase 1δ (CK1δ) plays a central role in regulating circadian rhythms, DNA repair, apoptosis, and cell proliferation, and its dysregulation is associated with both cancer and neurodegenerative diseases, making CK1δ an attractive therapeutic target. This study aimed to develop novel CK1δ inhibitors with favourable drug-like properties through the synthesis and biological evaluation of benzimidazol-2-acetamide derivatives. Methods: A novel series of benzimidazol-2-acetamide derivatives was synthesized, incorporating different substituents on the benzimidazole core (5-chloro, 5,6-dichloro, 5-nitro, and 5-cyano) and various saturated cyclic amines on the acetamide moiety. Compounds were evaluated for CK1δ inhibitory activity, while molecular docking and molecular dynamics simulations were performed to investigate their binding mode. In silico ADME predictions assessed pharmacokinetic properties, and cytotoxicity was evaluated in SH-SY5Y neuroblastoma cells. Results: The 5,6-dichloro derivatives 20 and 24, bearing piperidin-4-ylmethanamine and morpholine moieties, respectively, displayed the highest CK1δ inhibitory activity (IC50 = 0.172 and 0.223 μM). The 5-cyano analogue 22 also exhibited a good potency (IC50 = 0.224 μM). Computational studies confirmed an ATP-competitive binding mode and highlighted the dynamic behaviour of the solvent-exposed substituents within the CK1δ binding site. Predicted pharmacokinetic properties suggested favourable oral absorption and blood–brain barrier penetration. Compounds 20, 22, and 24 showed no cytotoxicity in SH-SY5Y cells at concentrations up to 10 μM. Conclusions: The new benzimidazol-2-acetamide derivatives exhibited good inhibitor activity against CK1δ, favourable predicted ADME properties, and low cellular toxicity. The combined experimental and computational findings provide valuable insights for the further optimization of this scaffold toward the development of therapeutics for CK1δ-related diseases.