Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
Eur J Med Chem. 2020 Dec 1;207:112848. doi: 10.1016/j.ejmech.2020.112848. Epub 2020 Sep 19.
Aminoacyl-tRNA synthetases (aaRSs) are an attractive class of antibacterial drug targets due to their essential roles in protein translation. While most traditional aaRS inhibitors target the binding pockets of substrate amino acids and/or ATP, we recently developed a class of novel tRNA-amino acid dual-site inhibitors including inhibitor 3 ((2S,3R)-2-amino-N-((E)-4-(6,7-dichloro-4-oxoquinazolin-3(4H)-yl)but-2-en-1-yl)-3-hydroxybutanamide) against threonyl-tRNA synthetase (ThrRS). Here, the binding modes and structure-activity relationships (SARs) of these inhibitors were analyzed by the crystal structures of Salmonella enterica ThrRS (SeThrRS) in complex with three of them. Based on the cocrystal structures, twelve quinazolinone-threonine hybrids were designed and synthesized, and their affinities, enzymatic inhibitory activities, and cellular potencies were evaluated. The best derivative 8g achieved a K value of 0.40 μM, an IC value of 0.50 μM against SeThrRS and MIC values of 16-32 μg/mL against the tested bacterial strains. The cocrystal structure of the SeThrRS-8g complex revealed that 8g induced a bended conformation for Met332 by forming hydrophobic interactions, which better mimicked the binding of tRNA to ThrRS. Moreover, the inhibitory potency of 8g was less impaired than a reported ATP competitive inhibitor at high concentrations of ATP, supporting our hypothesis that tRNA site inhibitors are likely superior to ATP site inhibitors in vivo, where ATP typically reaches millimolar concentrations.
氨酰-tRNA 合成酶（aaRSs）是一类有吸引力的抗菌药物靶标，因为它们在蛋白质翻译中具有重要作用。虽然大多数传统的 aaRS 抑制剂靶向底物氨基酸和/或 ATP 的结合口袋，但我们最近开发了一类新型的 tRNA-氨基酸双位点抑制剂，包括抑制剂 3（((2S,3R)-2-氨基-N-((E)-4-(6,7-二氯-4-氧代喹唑啉-3(4H)-基)丁-2-烯-1-基)-3-羟基丁酰胺）针对苏氨酰-tRNA 合成酶（ThrRS）。在这里，通过与其中三种复合物的 Salmonella enterica ThrRS（SeThrRS）晶体结构分析了这些抑制剂的结合模式和结构-活性关系（SAR）。基于共晶结构，设计并合成了十二种喹唑啉酮-苏氨酸杂合体，并评估了它们的亲和力、酶抑制活性和细胞效力。最佳衍生物 8g 的 K 值为 0.40 μM，对 SeThrRS 的 IC 值为 0.50 μM，对测试的细菌菌株的 MIC 值为 16-32 μg/mL。SeThrRS-8g 复合物的共晶结构表明，8g 通过形成疏水相互作用诱导 Met332 弯曲构象，更好地模拟了 tRNA 与 ThrRS 的结合。此外，8g 的抑制效力在高浓度 ATP 下比报道的 ATP 竞争性抑制剂受损更小，这支持了我们的假设，即在体内，tRNA 位点抑制剂可能优于 ATP 位点抑制剂，因为体内的 ATP 通常达到毫摩尔浓度。
