Zhang Chao, Li Jia-Bin, Zhang Yi-Wen, Tang Yun-Sang, Yu Xiao-Fei, Zhang Qing-Guang, Jin Zhe, Hou Shi-Cheng, Shaw Pang-Chui, Hu Chun
Key Laboratory of Structure-based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang, 110016, China.
School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China.
Eur J Med Chem. 2025 Sep 5;293:117681. doi: 10.1016/j.ejmech.2025.117681. Epub 2025 May 2.
In this study, a series of benzamide derivatives with an indole moiety as dual-target inhibitors were designed, synthesized and evaluated against the RNA-dependent RNA polymerase (RdRp) complex of influenza viruses. The target compounds can simultaneously disrupt two key molecular interactions: the PA terminal domain and the nucleoprotein (NP) oligomerization. Through efficient synthesis and structure-activity relationship (SAR) analysis, compounds 8e and 8f as highly potent inhibitors were identified. Both compounds (8e and 8f) exhibited submicromolar EC values (1.64 ± 0.05 μM and 1.41 ± 0.27 μM) against influenza A virus (H1N1, A/WSN/33) and broad-spectrum activity against other influenza strains, including influenza B virus and multiple subtypes of influenza A. Notably, their cytotoxicity was significantly reduced compared to previous benzofurazan derivatives, with CC values exceeding 100 μM. Surface plasmon resonance (SPR) experiments confirmed that 8e and 8f bound strongly to the PA C-terminal domain (KD = 8.90 μM and 4.82 μM) and NP (KD = 52.5 μM and 3.13 μM). Computational modeling approaches, including molecular docking, molecular dynamics (MD) simulations, and dynamical cross-correlation matrix (DCCM) analysis, principal component analysis (PCA) analysis and density functional theory (DFT) calculations, were employed to elucidate the putative binding modes and delineate critical interaction sites between the ligands and target proteins. These insights not only modulated subsequent structure-based lead optimization but also strengthened our understanding of the molecular determinants governing antiviral activity. This research provides a promising scaffold for developing dual-target antiviral agents with enhanced potency and safety, offering new strategies to combat influenza viruses.
在本研究中，设计、合成了一系列带有吲哚部分的苯甲酰胺衍生物作为双靶点抑制剂，并针对流感病毒的RNA依赖性RNA聚合酶（RdRp）复合物进行了评估。目标化合物可同时破坏两种关键的分子相互作用：PA末端结构域和核蛋白（NP）寡聚化。通过高效合成和构效关系（SAR）分析，确定了化合物8e和8f为高效抑制剂。这两种化合物（8e和8f）对甲型流感病毒（H1N1，A/WSN/33）表现出亚微摩尔级的EC值（1.64±0.05μM和1.41±0.27μM），并对包括乙型流感病毒和多种甲型流感亚型在内的其他流感毒株具有广谱活性。值得注意的是，与先前的苯并呋喃嗪衍生物相比，它们的细胞毒性显著降低，CC值超过100μM。表面等离子体共振（SPR）实验证实，8e和8f与PA C末端结构域（KD = 8.90μM和4.82μM）和NP（KD = 52.5μM和3.13μM）紧密结合。采用了包括分子对接、分子动力学（MD）模拟、动态交叉相关矩阵（DCCM）分析、主成分分析（PCA）和密度泛函理论（DFT）计算在内的计算建模方法，以阐明假定的结合模式，并描绘配体与靶蛋白之间的关键相互作用位点。这些见解不仅调节了后续基于结构的先导化合物优化，还加深了我们对控制抗病毒活性的分子决定因素的理解。这项研究为开发具有更高效力和安全性的双靶点抗病毒药物提供了一个有前景的骨架，为对抗流感病毒提供了新策略。
