Novel pyrimido[1,2- <i>a</i> ]imidazole derivatives as potent Pks13-TE inhibitors: structure-based virtual screening and rational design

Tuberculosis (TB) remains a major global health threat, exacerbated by the emergence of drug-resistant strains. The mycobacterial enzyme Pks13 has emerged as a promising drug target for novel anti-TB agents. We herein report the design, synthesis, and biological evaluation of a series of pyrimido[1,2-<i>a</i>]imidazole derivatives as potent Pks13-TE inhibitors. An integrated virtual and biological screening of 10.5 million commercially available compounds identified TJA-31 as a hit compound, which showed moderate Pks13-TE inhibitory activity (IC₅₀ = 1.34 μM). The systematic optimization of TJA-31 based on its physicochemical properties, docking scores, and MM/GBSA binding free energy estimates led to the synthesis of 50 analogues, among which 20 compounds exhibited submicromolar inhibition. The most promising derivative, compound 34, demonstrated significantly enhanced potency with an IC₅₀ value of 0.23 μM, representing a sixfold improvement over the hit. Molecular docking studies indicated that the high activity of compound 34 could be attributed to a halogen bond between its bromine substituent and the nitrogen atom of residue His1664, a water-mediated hydrogen bond between the Ala1564 nitrogen and the 3-methoxy oxygen, and π-π stacking interactions with residues within the Pks13-TE binding pocket. These results underscore the pyrimido[1,2-<i>a</i>]imidazole scaffold as a promising lead series for the development of Pks13-TE inhibitors.