Prediction of Urease Inhibitors as Antimicrobials for the Treatment of Pathogenic Enterobacter

Enterobacter is a bacterial genus that includes opportunistic pathogenic species associated with nosocomial infections, such as E. cloacae and E. hormaechei . Recognized for their resistance to multiple antibiotics, including carbapenems, these bacteria are considered a critical priority for new treatment development by the World Health Organization. Urease, an enzyme that hydrolyzes urea and produces ammonia, raising the intraphagosomal pH and allowing resistance to phagocytosis, is already a therapeutic target in other bacterial infections, such as Helicobacter pylori and Klebsiella aerogenes . This enzyme can be inhibited by drugs like acetohydroxamic acid (AHA) and N-acetylcysteine (NAC), which could potentially be repurposed for treating Enterobacter . To predict the potential repurposing of AHA and NAC as inhibitors of urease from Enterobacter through molecular docking. A total of 863 Enterobacter genomes from clinical human blood isolates were retrieved from the RefSeq database. The three-dimensional structures of their ureases were predicted using AlphaFold3. All models were compared using the RMSD metric calculated with PyMOL, and only one model was selected as the reference for docking. The 3D structures of AHA and NAC were obtained from the PubChem database. Molecular docking was performed using appropriate software. Most genomes retrieved belonged to E. hormaechei , but E. cloacae , E. roggenkampii , and E. kobei were also included. A total of 223 unique urease sequences were found. The predicted structures for these sequences were highly similar, with RMSDs below 0.2 Å. Thus, the structural model used for docking corresponded to the most frequent sequence among the genomes. Both compounds were predicted to interact with essential residues in the catalytic site of urease. AHA formed hydrogen bonds with histidines at positions 134, 136, 219, and 246, while NAC formed salt bridges with histidines 134, 136, 219, 246, and 272. Due to the high structural conservation observed among ureases from Enterobacter spp. isolated from bacteremia cases, molecular docking suggests that AHA and NAC have potential to interact with essential urease residues, acting as competitive inhibitors at the catalytic site and attenuating virulence.