Inhibition of prolyl-tRNA synthetase and efflux pumps as a dual-targeting strategy against multidrug-resistant bacteria

Aminoacyl-tRNA synthetases have been widely exploited as targets for antiparasitic and antifungal inhibitors; however, they have received little attention as targets in multidrug-resistant (MDR) bacteria. Here we describe the biochemical characterisation of Prolyl-tRNA synthetase from Klebsiella pneumoniae (KpProRS), highlighting its ligase and proofreading activities. Distinct classes of ProRS inhibitors were evaluated against KpProRS but only halofuginone (HF) strongly modulated KpProRS activity. A new HF analog (Cpd-6) was developed and exhibited superior inhibitory activity against KpProRS relative to HF but low efficacy against MDR K. pneumoniae, despite good antimicrobial activity against Escherichia coli and Staphylococcus aureus. Further studies revealed that Cpd-6 resistance in K. pneumonia is mainly mediated by AcrAB efflux pump activity, which could be counteracted by efflux pump inhibitors. These findings therefore reinforce KpProRS as a target for antimicrobial development and highlight the therapeutic potential of combining HF analogues with efflux pump inhibitors to fight Gram-negative MDR pathogens.