State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China.
Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.
J Med Chem. 2024 Sep 26;67(18):16556-16575. doi: 10.1021/acs.jmedchem.4c01386. Epub 2024 Aug 28.
Bacterial RNA polymerase (RNAP), the core enzyme responsible for bacterial transcription, requires the NusG factor for efficient transcription elongation and termination. As the primary binding site for NusG, the RNAP clamp-helix (CH) domain represents a potential protein-protein interaction (PPI) target for novel antimicrobial agent design and discovery. In this study, we designed a pharmacophore model based on the essential amino acids of the CH for binding to NusG, such as R270, R278, and R281 ( numbering), and identified a hit compound with mild antimicrobial activity. Subsequent rational design and synthesis of this hit compound led to improved antimicrobial activity against , with the minimum inhibitory concentration (MIC) reduced from 128 to 1 μg/mL. Additional characterization of the antimicrobial activity, inhibitory activity against RNAP-NusG interaction, and cell-based transcription and fluorescent assays of the optimized compounds demonstrated their potential for further lead optimization.
细菌 RNA 聚合酶（RNAP）是负责细菌转录的核心酶，需要 NusG 因子才能实现有效的转录延伸和终止。作为 NusG 的主要结合位点，RNAP 夹钳螺旋（CH）结构域代表了新型抗菌剂设计和发现的潜在蛋白-蛋白相互作用（PPI）靶标。在这项研究中，我们设计了一个基于 CH 与 NusG 结合的必需氨基酸（如 R270、R278 和 R281[编号]）的药效团模型，鉴定出一种具有温和抗菌活性的先导化合物。随后对该先导化合物进行合理设计和合成，提高了对 的抗菌活性，最低抑菌浓度（MIC）从 128 降低到 1μg/mL。对优化化合物的抗菌活性、对 RNAP-NusG 相互作用的抑制活性以及基于细胞的转录和荧光测定的进一步表征，证明了它们进一步优化先导化合物的潜力。
