Targeting histidine biosynthesis in Acinetobacter baumannii: structure-based discovery of natural inhibitors of ATP-phosphoribosyltransferase.

The increasing threat of multidrug-resistant Acinetobacter baumannii infections demands the development of novel antimicrobials targeting unexplored bacterial pathways. ATP phosphoribosyltransferase (ATP-PRT), the first and rate-limiting enzyme in the bacterial histidine biosynthesis pathway, represents an excellent therapeutic target since it doesn't exist in the mammalian system and thus ensures excellent selectivity towards pathogenic bacteria. This study utilized a systematic computational-experimental methodology to identify natural inhibitors of the ATP-PRT enzyme. It utilized an all-inclusive structure-based virtual screening against ~ 20,000 natural compounds through the use of hierarchical docking methods to account for receptor flexibility. In order to evaluate complex stability under physiological conditions, top hits were further validated using 100 ns molecular dynamics simulations. Two natural molecules, Pentagalloylglucose (PGG) and Punicalagin, emerged as effective lead compounds with docking scores of -7.813 and -7.626 kcal/mol, respectively. Binding analysis of both compounds showed strong interaction with conserved active site residues (Arg29, Asp91, Glu160, Asp176, Thr177, and Thr180). In-vitro broth microdilution assays confirmed potent antimicrobial activity, with minimum inhibitory concentrations (MICs) of 7.82 µg/mL for both compounds against multidrug-resistant A. baumannii. Time-kill kinetics demonstrated concentration-dependent bactericidal action, with > 95% bacterial reduction within 12 h at MIC, indicating rapid antimicrobial onset. Intracellular histidine quantification further verified pathway inhibition in PGG- and Punicalagin-treated cells compared to controls. Surface plasmon resonance (SPR) analysis confirmed direct binding to ATP-PRT, with equilibrium dissociation constants (KD) of 7.7 nM for PGG and 7.2 µM for Punicalagin. Collectively, these findings highlight the therapeutic potential of PGG and Punicalagin as natural ATP-PRT inhibitors, effectively targeting histidine biosynthesis in A. baumannii.