State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China.
ACS Chem Biol. 2020 Apr 17;15(4):1016-1025. doi: 10.1021/acschembio.0c00032. Epub 2020 Mar 26.
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 Δ double bond. We evaluated these compounds by thermal shift assays and enzymatic experiments and further studied their molecular recognition by the LysRS 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 Δ double 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.
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。最近发现抗疟天然产物克拉多菌素是一种新型赖氨酸-tRNA 合成酶 (LysRS) 特异性抑制剂。在这里，我们通过化学合成、生物物理和生化实验对克拉多菌素衍生物进行了全面分析。合成了一系列异噁唑啉衍生物，每个化合物只有一个非氢原子/键变化。这些变化包括用甲基环己烷或环己烷替代甲基四氢吡喃部分、内酯替代内酰胺、羟基替代甲氧基以及在 C3 处消除手性中心形成 Δ双键。我们通过热位移测定和酶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 LysRS 的分子识别。结果表明，克拉多菌素的甲基四氢吡喃部分可以用更稳定的甲基环己烷替代而不降低结合能力。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，在支架内用内酰胺基团或共轭 Δ双键替代也可以是优化化合物的另外两个选择。最后，两个酚羟基对于化合物与 LysRS 结合至关重要。本研究在原子分辨率的详细分析为从克拉多菌素衍生物进一步开发新型抗生素提供了基础。
