Department of Chemistry, Rhodes University, Makhanda 6139, South Africa.
Viruses. 2023 Jun 29;15(7):1480. doi: 10.3390/v15071480.
The SARS-CoV-2 main protease (M) is essential for the life cycle of the COVID-19 virus. It cleaves the two polyproteins at 11 positions to generate mature proteins for virion formation. The cleavage site on these polyproteins is known to be Leu-Gln↓(Ser/Ala/Gly). A range of hexapeptides that follow the known sequence for recognition and cleavage was constructed using RDKit libraries and complexed with the crystal structure of M (PDB ID 6XHM) through extensive molecular docking calculations. A subset of 131 of these complexes underwent 20 ns molecular dynamics simulations. The analyses of the trajectories from molecular dynamics included principal component analysis (PCA), and a method to compare PCA plots from separate trajectories was developed in terms of encoding PCA progression during the simulations. The hexapeptides formed stable complexes as expected, with reproducible molecular docking of the substrates given the extensiveness of the procedure. Only Lys-Leu-Gln*** (KLQ***) sequence complexes were studied for molecular dynamics. In this subset of complexes, the PCA analysis identified four classifications of protein motions across these sequences. KLQ*** complexes illustrated the effect of changes in substrate on the active site, with implications for understanding the substrate recognition of M and informing the development of small molecule inhibitors.
新型冠状病毒 2 主蛋白酶（M）是 COVID-19 病毒生命周期所必需的。它在 11 个位置切割两个多蛋白，生成成熟的蛋白用于病毒形成。这些多蛋白上的切割位点已知为 Leu-Gln↓（Ser/Ala/Gly）。使用 RDKit 库构建了一系列紧随已知识别和切割序列的六肽，并通过广泛的分子对接计算与 M 的晶体结构（PDB ID 6XHM）复合。这些复合物的 131 个亚集中，有 131 个进行了 20ns 的分子动力学模拟。从分子动力学中轨迹的分析包括主成分分析（PCA），并且开发了一种方法来比较来自单独轨迹的 PCA 图，该方法是根据模拟过程中 PCA 进展情况进行编码的。六肽形成了预期的稳定复合物，由于该过程的广泛应用，底物的分子对接具有可重复性。仅研究了分子动力学中的 Lys-Leu-Gln***（KLQ***)序列复合物。在这组复合物中，PCA 分析确定了这些序列中蛋白质运动的四种分类。KLQ***复合物说明了底物变化对活性位点的影响，这对理解 M 的底物识别以及为小分子抑制剂的开发提供了信息。
