Development of potent inhibitors targeting bacterial prolyl-tRNA synthetase through fluorine scanning-directed activity tuning
- Eur J Med Chem. 2025 Jul 5:291:117647. doi: 10.1016/j.ejmech.2025.117647.
- 1. State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
- 2. State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
- 3. Department of Laboratory Medicine, The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, 511518, China. Electronic address: [email protected].
- 4. State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. Electronic address: [email protected].
As essential Enzymes encoded by single genes, aminoacyl-tRNA synthetases (aaRSs) have long been considered promising drug targets for combating microbial infections. In this study, we developed a novel class of amino acid-ATP dual-site inhibitors of prolyl-tRNA synthetase (ProRS) through the structural simplification of the intermediate product prolyl adenylate and its non-hydrolyzable mimic. The co-crystal structures of the compound PAA-5 bound to both Pseudomonas aeruginosa and human cytoplasmic ProRSs (PaProRS and HsPrors) were solved to high resolution. Utilizing the structural information gained, a fluorine scanning (F-scanning) strategy was applied to PAA-5, and the biochemical and biophysical assays demonstrated that fluorine substitutions at specific positions of PAA-5 selectively enhanced its activity against Bacterial ProRS. The dual-fluorinated derivative PAA-38 exhibited the highest Antibacterial potency, with a Kd value of 0.399 ± 0.074 nM and an IC50 value of 4.97 ± 0.98 nM against PaProRS and an MIC value of 4-8 μg mL-1 against tested Bacterial strains. Our study provides a novel lead compound for the development of aaRS-based Antibiotics and highlights F-scanning as a powerful strategy for lead optimization, particularly in pinpointing the subtle fluorophilic environments within the protein pocket to achieve better activity and selectivity.