Download MendeleyDevelopment of potent inhibitors targeting bacterial prolyl-tRNA synthetase through fluorine scanning-directed activity tuning.
Luo, Z., Qiu, H., Peng, X., Tan, Q., Chen, B., Gu, Q., Liu, H., Zhou, H.(2025) Eur J Med Chem 291: 117647-117647
- PubMed: 40253792
- DOI: https://doi.org/10.1016/j.ejmech.2025.117647
- Primary Citation of Related Structures:
8W8J, 8W8L, 8W9I, 8YTK - PubMed Abstract:
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 K d value of 0.399 ± 0.074 nM and an IC 50 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.
- 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.
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