Water plays a major role in ligand binding and is attracting increasing attention in structure-based drug design. Water molecules can make large contributions to binding affinity by bridging protein–ligand interactions or by being displaced upon complex formation, but these phenomena are challenging to model at the molecular level. Herein, networks of ordered water molecules in protein binding sites were analyzed by clustering of molecular dynamics (MD) simulation trajectories. Locations of ordered waters (hydration sites) were first identified from simulations of high resolution crystal structures of 13 protein–ligand complexes. The MD-derived hydration sites reproduced 73% of the binding site water molecules observed in the crystal structures. If the simulations were repeated without the cocrystallized ligands, a majority (58%) of the crystal waters in the binding sites were still predicted. In addition, comparison of the hydration sites obtained from simulations carried out in the absence of ligands to those identified for the complexes revealed that the networks of ordered water molecules were preserved to a large extent, suggesting that the locations of waters in a protein–ligand interface are mainly dictated by the protein. Analysis of >1000 crystal structures showed that hydration sites bridged protein–ligand interactions in complexes with different ligands, and those with high MD-derived occupancies were more likely to correspond to experimentally observed ordered water molecules. The results demonstrate that ordered water molecules relevant for modeling of protein–ligand complexes can be identified from MD simulations. Our findings could contribute to development of improved methods for structure-based virtual screening and lead optimization.

中文翻译：

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从分子动力学模拟预测蛋白质结合位点中的有序水分子：配体结合对水合网络的影响

水在配体结合中起主要作用，并且在基于结构的药物设计中越来越引起人们的注意。水分子可以通过桥接蛋白质-配体相互作用或在复合物形成时被置换而对结合亲和力做出巨大贡献，但是这些现象对于在分子水平上进行建模具有挑战性。本文中，通过分子动力学（MD）模拟轨迹的聚类分析了蛋白质结合位点中的有序水分子网络。首先通过模拟13种蛋白质-配体复合物的高分辨率晶体结构来确定有序水的位置（水合位点）。MD衍生的水合位点重现了在晶体结构中观察到的结合位点水分子的73％。如果在没有共结晶配体的情况下重复进行模拟，结合位点中的大多数结晶水（58％）仍在预测中。此外，比较了在没有配体的情况下从模拟中获得的水合位点与为配合物鉴定的水合位点，结果表明，有序水分子的网络在很大程度上得以保留，这表明水在蛋白质-配体中的位置界面主要由蛋白质决定。对> 1000个晶体结构的分析表明，在具有不同配体的复合物中，水合位点桥接了蛋白质-配体之间的相互作用，而那些具有高MD衍生性的位点更可能与实验观察到的有序水分子相对应。结果表明，可以从MD模拟中识别与蛋白质-配体复合物建模相关的有序水分子。