Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors
Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors
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一类喹唑啉酮-苏氨酸杂化物作为抗菌 ThrRS 抑制剂的结构引导优化和机理研究
DOI：
10.1016/j.ejmech.2020.112848
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发表时间：
2020-12-01
影响因子：
6.7
通讯作者：
Zhou, Huihao
中科院分区：
文献类型：
--
作者：
Guo, Junsong;Chen, Bingyi;Zhou, Huihao
氨酰基-tRNA 合成酶 (aaRS) 因其在蛋白质翻译中的重要作用而成为一类颇具吸引力的抗菌药物靶点。虽然大多数传统的 aaRS 抑制剂靶向底物氨基酸和/或 ATP 的结合袋，但我们最近开发了一类新型 tRNA-氨基酸双位点抑制剂，包括抑制剂 3 ((2S,3R)-2-amino-N-((E)-4-(6,7-二氯-4-oxoquinazolin-3(4H)-yl)but-2-en-1-yl)-3-羟基丁酰胺）苏氨酰-tRNA 合成酶 (ThrRS)。在这里，通过肠沙门氏菌 ThrRS (SeThrRS) 与其中三种抑制剂复合物的晶体结构分析了这些抑制剂的结合模式和构效关系 (SAR)。基于共晶结构，设计并合成了十二种喹唑啉酮-苏氨酸杂化物，并评估了它们的亲和力、酶抑制活性和细胞效力。最好的衍生物8g对SeThrRS的Kd值为0.40μM，IC50值为0.50μM，对测试菌株的MIC值为16-32μg/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，从而更好地模拟 tRNAThr 与 ThrRS 的结合。此外，在高浓度 ATP 下，8g 的抑制效力比报道的 ATP 竞争性抑制剂受到的损害更小，这支持了我们的假设，即 tRNA 位点抑制剂可能优于体内 ATP 位点抑制剂，体内 ATP 通常达到毫摩尔浓度。(C) 2020 Elsevier Masson SAS。版权所有。
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 Kd value of 0.40 mu M, an IC50 value of 0.50 mu M against SeThrRS and MIC values of 16-32 mu g/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 tRNAThr 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.(C) 2020 Elsevier Masson SAS. All rights reserved.