Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
Int J Mol Sci. 2023 Jul 22;24(14):11784. doi: 10.3390/ijms241411784.
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
水是自然界各种过程的关键因素，因此，分子工程必须考虑水合的结构和能量后果。虽然本综述的重点是药物设计中的靶标-配体相互作用，主要针对生物分子，但这些方法和应用可以很容易地应用于分子配合物的分子工程的其他领域，包括固体水合物。本综述首先讨论了确定水结构的问题和解决方案。总结了实验方法和理论计算，包括概念分类。介绍了水模型的实现和应用，用于计算结合热力学和计算配体对接。结论是，理论方法不仅可以再现或补充实验水结构，还可以提供关于单个水分子贡献的关键信息，是分子工程中不可或缺的工具。
