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

Abstract

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 K d = 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.

A hit expansion of 3‐benzamidopyrazine‐2‐carboxamide: Toward inhibitors of prolyl‐tRNA synthetase with antimycobacterial activity

“…[24] ). 1 3-Aminopyrazine-2-carboxamide (III): Into a 10 mL MW tube containing 1.0 mmol of 3-chloropyrazine-2-carboxamide (II), 5 mL (excess) of 7 N ammonia in anhyd. methanol (Merck) was added.…”

“…Natural alkaloid febrifugine (Figure 1a) and its derivatives, including halofuginone (HFG, Figure 1b), are ProRS inhibitors that occupy both L-Pro and tRNA binding sites of the enzyme. [1] They exhibit excellent properties against malaria, fibroproliferative diseases, or cancer. [2][3][4][5] However, both the antimalarial and antifibrotic activity of HFG are negatively affected by the accumulation of Pro due to the prolinecompetitive nature of the binding.…”

Transcriptome profile of halofuginone resistant and sensitive strains of Eimeria tenella

“…Halofuginone, a synthetic derivative of the natural product febrifugine, exhibits potent inhibitory activities against both protozoan parasites and numerous cancer cells ( Derbyshire et al, 2012 ; Zhang et al, 2012 ; McLaughlin et al, 2014 ; Herman et al, 2015 ; Bellini et al, 2020 ; Cheng et al, 2022 ). In Eimeria , it was shown that halofuginone inhibits the invasion of sporozoites into host cells at an early stage of the life cycle and later disrupts the development of schizonts ( Zhang et al, 2012 ).…”