Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase
Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase
复制标题
异香豆素衍生物抑制赖氨酰-tRNA 合成酶的原子分辨率分析。
DOI：
10.1021/acschembio.0c00032
复制
发表时间：
2020
影响因子：
4
通讯作者：
Pengfei Fang
中科院分区：
文献类型：
--
作者：
Jintong Zhou;Li Zheng;Zhoufei Hei;Wei Li;Jing Wang;Biao Yu;Pengfei Fang
氨酰-tRNA合成酶是蛋白质翻译的必需酶家族，是开发抗细菌、抗真菌和抗寄生虫药物以及治疗其他人类疾病的有吸引力的靶点。抗疟天然产物cladosporin是近年来发现的一种新的赖氨酰-tRNA合成酶（LysRS）特异性抑制剂。在这里，我们报告了一个彻底的分析cladosporin衍生物的化学合成，生物物理和生物化学实验。合成了一系列每个化合物只有一个非氢原子/键变化的异香豆素衍生物。这些变化包括甲基四氢吡喃部分被甲基环己烷或环己烷取代，内酯被内酰胺取代，羟基被甲氧基取代，以及C3处的手性中心被Δ3，4双键取代。我们通过热位移分析和酶促实验评估了这些化合物，并通过总共五个高分辨率晶体结构进一步研究了它们与恶性疟原虫LysRS的分子识别。我们的研究结果表明，甲基四氢吡喃部分的cladosporin可以取代一个更稳定的甲基环己烷，而不降低结合能力。从甲基环己烷部分去除甲基略微降低了与LysRS的相互作用。此外，骨架中的内酰胺基团或共轭Δ3，4双键的取代可能是优化化合物的两种选择。最后，两个酚羟基基团是化合物结合LysRS的关键。本研究在原子分辨率下的详细分析为进一步开发新的抗生素提供了基础。
Aminoacyl-tRNA synthetases, the essential enzyme family for protein translation, are attractive targets for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The antimalarial natural product cladosporin was discovered recently as a novel lysyl-tRNA synthetase (LysRS) specific inhibitor. Here, we report a thorough analysis of cladosporin derivatives using chemical synthesis, biophysical, and biochemical experiments. A series of isocoumarin derivatives with only one nonhydrogen atom/bond change per compound was synthesized. These changes include replacements of methyltetrahydropyran moiety by methylcyclohexane or cyclohexane, lactone by lactam, hydroxyl groups by methoxyl groups, and dismission of the chiral center at C3 with a Δ3,4double bond. We evaluated these compounds by thermal shift assays and enzymatic experiments and further studied their molecular recognition by thePlasmodium falciparumLysRS through total five high-resolution crystal structures. Our results showed that the methyltetrahydropyran moiety of cladosporin could be replaced by a more stable methylcyclohexane without reducing binding ability. Removing the methyl group from the methylcyclohexane moiety slightly decreased the interaction with LysRS. Besides, the replacement with a lactam group or a conjugated Δ3,4double bond within the scaffold could be two more options to optimize the compound. Lastly, the two phenolic hydroxyl groups were critical for the compounds to bind LysRS. The detailed analyses at atomic resolution in this study provide a foundation for the further development of new antibiotics from cladosporin derivatives.