新型冠状病毒 3CL 蛋白酶与其抑制剂吡脲炔酯手性异构体的结合机制研究

Study on the binding mechanism between SARS-CoV-2 3CL protease and chiral isomers of its inhibitor pyridyl-urea diyne ester

摘要

新型冠状病毒 3CL 蛋白酶是病毒复制与转录过程中的关键蛋白酶，因其结构高度保守且在宿主中缺乏同源蛋白，被认为是广谱抗冠状病毒药物的重要靶点。文中系统比较了含双手性碳的吡脲炔酯 (PyDU) 分子的 4 种手性异构体在 3CL 蛋白酶活性口袋中的结合模式与动力学机制。通过分子对接、MD (molecular dynamic) 模拟、MM/GBSA 结合自由能计算及动态交叉相关矩阵 (DCCM, dynamic cross-correlation matrices) 分析，发现 PyDU 主要依靠大量疏水作用与口袋稳定结合。其中，(R, S) 构型在对接打分、结合自由能分解和关键残基作用的综合表现最优；(R, S) 与 (S, R) 构型增加了结合口袋附近区域的协同运动，(R, S) 构型对结构域Ⅲ摆动有调控作用，或将影响 3CL 蛋白酶二聚体聚合；(S, S) 构型由于缺少有效疏水面结合情况较差。本研究创新地结合手性差异、结合能贡献及蛋白协同运动特征，揭示了小分子立体化学结构在调控蛋白结合亲和力与动力学行为中的双重作用，为基于手性设计的抗冠状病毒的小分子抑制剂开发提供了理论依据。

Abstract

3CL protease (3CLpro) of SARS-CoV-2 is a pivotal enzyme required in coronavirus replication and transcription. Its highly conserved structure and the absence of homologous proteins in the host make it an ideal target for broad-spectrum anti-coronavirus drug development. In this work, we systematically investigated and compared the binding modes and dynamic properties of the four stereoisomers of a pyridyl-urea diyne ester (PyDU) molecule with two chiral centers within the 3CLpro active site. Through molecular docking, MD simulations, MM/GBSA binding free-energy calculations, and DCCM analysis, all four stereoisomers were stabilized primarily by hydrophobic packing. Among them, the (R,S) isomer exhibited the best overall performance, including docking score, binding free-energy components, and key residue interactions. The (R,S) and (S,R) isomers also enhanced the cooperative motions around the binding pocket, while the (R,S) isomer further modulated the flexibility of domain III, which may influence 3CLpro dimerization. Conversely, the (S,S) isomer exhibited the weakest affinity due to insufficient hydrophobic contact. By innovatively integrating chirality, binding energy and protein dynamical features, we revealed the dual role of chirality in modulating affinity and dynamic responses, which provides a theoretical basis for the chiral-guided design of coronavirus inhibitors.

关键词

3CL 蛋白酶 / 手性异构体 / 分子动力学模拟 / 疏水作用 / MM/GBSA 计算

Key words

3CL protease / stereoisomer / molecular dynamics simulation / hydrophobic interaction / MM/GBSA calculation

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基金资助

国家自然科学基金项目(22373065)

国家重点研发计划项目(2023YFF1204903)