Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India.
J Cell Biochem. 2023 Jun;124(6):861-876. doi: 10.1002/jcb.30409. Epub 2023 Apr 26.
The spread of different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants underscores the need for insights into the structural properties of its structural and non-structural proteins. The highly conserved homo-dimeric chymotrypsin-like protease (3CL M ), belonging to the class of cysteine hydrolases, plays an indispensable role in processing viral polyproteins that are involved in viral replication and transcription. Studies have successfully demonstrated the role of M as an attractive drug target for designing antiviral treatments because of its importance in the viral life cycle. Herein, we report the structural dynamics of six experimentally solved structures of M (i.e., 6LU7, 6M03, 6WQF, 6Y2E, 6Y84, and 7BUY including both ligand-free and ligand-bound states) at different resolutions. We have employed a structure-based balanced forcefield, CHARMM36m through state-of-the-art all-atoms molecular dynamics simulations at µ-seconds scale at room temperature (303K) and pH 7.0 to explore their structure-function relationship. The helical domain-III responsible for dimerization mostly contributes to the altered conformational states and destabilization of M . A keen observation of the high degree of flexibility in the P5 binding pocket adjoining domain II-III highlights the reason for observation of conformational heterogeneity among the structural ensembles of M . We also observe a differential dynamics of the catalytic pocket residues His41, Cys145, and Asp187, which may lead to catalytic impairment of the monomeric proteases. Among the highly populated conformational states of the six systems, 6LU7 and 7M03 forms the most stable and compact M conformation with intact catalytic site and structural integrity. Altogether, our findings from this extensive study provides a benchmark to identify physiologically relevant structures of such promising drug targets for structure-based drug design and discovery of potent drug-like compounds having clinical potential.
不同严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）变体的传播凸显了深入了解其结构和非结构蛋白结构特性的必要性。高度保守的同源二聚体糜蛋白酶样蛋白酶（3CL M ）属于半胱氨酸水解酶类，在加工参与病毒复制和转录的病毒多蛋白方面发挥着不可或缺的作用。研究成功地证明了 M 作为设计抗病毒治疗药物的有吸引力的靶标，因为它在病毒生命周期中很重要。在此，我们报告了六种实验解决的 M 结构（即 6LU7、6M03、6WQF、6Y2E、6Y84 和 7BUY，包括无配体和配体结合状态）在不同分辨率下的结构动力学。我们采用基于结构的平衡力场 CHARMM36m，通过最先进的全原子分子动力学模拟，在室温（303K）和 pH 7.0 下进行微秒级的模拟，以探索其结构-功能关系。负责二聚化的螺旋域 III 主要导致构象状态的改变和 M 的不稳定性。对与 II-III 相邻的 P5 结合口袋的高度灵活性的敏锐观察突出了观察到 M 的结构集合之间的构象异质性的原因。我们还观察到催化口袋残基 His41、Cys145 和 Asp187 的差异动力学，这可能导致单体蛋白酶的催化失活。在六个系统的高占据构象状态中，6LU7 和 7M03 形成最稳定和紧凑的 M 构象，具有完整的催化位点和结构完整性。总之，我们从这项广泛研究中得出的发现为基于结构的药物设计和发现具有临床潜力的有效药物样化合物提供了一个基准，以识别此类有前途的药物靶标的生理相关结构。
