Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase

Aminoacyl-tRNA synthetases (aaRSs) are promising antimicrobial
targets due to their essential roles in protein translation, and expanding
their inhibitory mechanisms will provide new opportunities for drug
discovery. We report here that halofuginone (HF), an herb-derived
medicine, moderately inhibits prolyl-tRNA synthetases (ProRSs) from
various pathogenic bacteria. A cocrystal structure of Staphylococcus aureus ProRS (SaProRS)
with HF and an ATP analog was determined, which guided the design
of new HF analogs. Compound 3 potently inhibited SaProRS at IC50 = 0.18 μM and Kd = 30.3 nM and showed antibacterial activities with an
MIC of 1–4 μg/mL in vitro. The bacterial
drug resistance to 3 only developed at a rate similar
to or slower than those of clinically used antibiotics in
vitro. Our study indicates that the scaffold and ATP-aided
inhibitory mechanism of HF could apply to bacterial ProRS and also
provides a chemical validation for using bacterial ProRS as an antibacterial
target.