Design and discovery of 1,4-dihydropyrimidinone-based noncovalent DprE1 inhibitors with integrated biological and...

Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) is a key flavoenzyme required for mycobacterial cell wall biosynthesis and represents an important molecular target for antitubercular drug discovery. In this study, a novel set of 1,4-dihydropyrimidinone derivatives was rationally designed and synthesized as potential DprE1 inhibitors. The target compounds (3a-3d and 4a-4 k) were prepared through a concise multistep synthetic route involving O-alkylation, Biginelli-type cyclocondensation, and S-alkylation, and were fully characterized by spectroscopic and analytical methods. Several derivatives exhibited promising in vitro antimycobacterial activity against Mycobacterium tuberculosis in the low-micromolar range. Enzymatic assays indicated DprE1 inhibitory activity, with compounds 3a-3d displaying IC₅₀ values of 11.74-13.90 μM; compound 3d showed activity comparable to the reference inhibitor TCA-1. In addition, cytotoxicity evaluation against WI-38 human lung fibroblast cells suggested low cytotoxicity and favorable selectivity indices relative to whole-cell antimycobacterial activity, providing preliminary support for the safety profile of the synthesized compounds. Molecular docking, 100 ns molecular dynamics simulations, and MM-PBSA analysis provided supportive evidence for favorable accommodation within the catalytic site and favorable binding energetics. These findings suggest that the 1,4-dihydropyrimidinone scaffold represents a promising noncovalent framework for further structural optimization toward the development of novel DprE1-targeted antitubercular agents.