MTK5R6E: A Novel Natural Inhibitor of P-loop Residues of Thymidylate Monophosphate Kinase from Mycobacterium tuberculosis

Introduction Tuberculosis (TB) remains a leading cause of global morbidity and mortality. Novel therapeutic agents are urgently required, particularly from natural sources. Mycobacterium tuberculosis thymidylate monophosphate kinase (TMPKmt), which catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP), is a promising target for the development of new antibiotics. Objective This study aimed to identify natural inhibitors of TMPKmt from 120 natural compounds. Methods All 120 compounds were screened for IC₅₀ against TMPKmt. Compounds exhibiting IC₅₀ values Results MTK5R6E (IC50: 1.2 μg) exhibited lead likeness and good binding affinity within the catalytic pocket of TMPKmt. It also formed hydrogen bonds with Asp9, Asp163, and Glu166, as well as hydrophobic contacts with Phe36, Pro37, Phe70, Arg95, Tyr103, and Tyr165. Protein backbone RMSD values (3.5-4.5 Å) and ligand RMSD values (~4.5-6.0 Å) indicated moderate fluctuations, while the ligand remained associated with the active site throughout the trajectory, suggesting stable binding despite conformational flexibility. Free energy calculations further supported a favorable binding affinity. The per-residue energy decomposition profile illustrated stabilizing contributions from Asp9 (-6.2 kcal/mol) and Tyr103. Discussion The RMSD data suggest that MTK5R6E exhibits stable binding despite conformational flexibility. Free energy calculations further support favorable binding affinity. Conclusion MTK5R6E demonstrates favorable interactions within the active site of TMPKmt, highlighting its potential for anti-TB drug development.