The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI-DII interface. Twenty-one conserved water molecules (W4–W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI-DII interface. Grid-based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water-mediated H-bond with catalytic His41 via the interaction Thr25(OG)---W13---W---His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.

中文翻译：

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Mpro native 中守恒水分子的结构和热力学性质：MD 模拟和网格非均匀溶剂化理论的组合方法

严重急性呼吸综合征冠状病毒-2 (SARS-CoV-2) 的新病毒株不断增加，毒力和传播力不断增强。因此，开发新型抗病毒药物至关重要。由于其在 SARS-CoV-2 病毒生命周期中的重要作用，主要蛋白酶 (Mpro) 是抗病毒药物设计的主要目标。Mpro单体由结构域DI、DII和DI-DII界面组成。根据多重晶体结构分析，这些区域占据了二十一个保守水分子（W4-W24）。晶体和 MD 结构揭示了 DI、DII 域中以及 DI-DII 界面中剩余的八个保守水位点的存在。基于网格的非均质流体溶剂化理论 (GIST) 用于 Mpro native 的 MD 结构，以预测每个保守水位点的结构和热力学性质，以便重点识别可轻松被拟议配体取代的特定保守水分子。最后，MD water W13 因其平均相互作用能低、与蛋白质的松散结合特性以及通过 Thr25 相互作用参与水介导的与催化 His41 的氢键结合而成为水模拟药物设计的有前途的候选者。 OG)---W13---W---His41(NE2)。在这种情况下，W13 的水占有率、相对相互作用能、熵和拓扑在热力学上对于水置换方法是可接受的。因此，通过设计具有适当定向化学基团的新配体来模拟其结构、电子和热力学特性，可以战略性地利用W13在DI域中的几何位置来开发针对COVID疾病的药物。