Wagle Swapnil, Bayly Christopher I, Mobley David L
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.
OpenEye Scientific, Cadence Molecular Sciences, 9 Bisbee Ct Suite D, Santa Fe, New Mexico 87508, United States.
J Chem Theory Comput. 2025 Aug 12;21(15):7593-7604. doi: 10.1021/acs.jctc.5c00758. Epub 2025 Jul 30.
The formation of protein-ligand complexes involves displacement of water molecules that were previously occupying the protein's binding site. In some cases, however, some water molecules may not be displaced by the ligand's binding, and they can stabilize the complex by mediating the interactions between the ligand and the protein. A relative binding free energy (RBFE) calculation between two ligands, one of which binds to the protein with an intermediate water while the other displaces the water, can yield wrong results if the water fails to rearrange itself within the simulation timescale. Enhanced sampling methods have previously been used to address the sampling of such "trapped" waters, inserting or deleting waters in the protein's binding site during ligand transformation. While sometimes effective, the enhanced sampling methods typically require long simulation times to converge and may lead to differences in RBFE estimates (i.e., hysteresis) based on initial water placement. In this study, we present a non-equilibrium switching (NES) method to calculate RBFEs in systems with trapped waters. Our approach requires the knowledge of the positions of the trapped waters prior to performing the free energy calculation for ligand transformation and then uses this information to efficiently calculate the RBFE between the ligands. In our simulation protocol, we perform ligand transformation in the binding site of the target protein by using three consecutive NES switches. The three NES switches implement restraints, transform the ligand, and then remove the restraints. We demonstrate that our NES simulation-based method results in RBFE estimates within 1.1 kcal mol of experimental RBFEs, with associated statistical errors under 0.4 kcal mol, for eight systems involving trapped water displacement. Our method provides a computationally inexpensive alternative for estimating RBFEs for systems involving trapped waters by leveraging distributed computational resources.
蛋白质-配体复合物的形成涉及到先前占据蛋白质结合位点的水分子的置换。然而，在某些情况下，一些水分子可能不会因配体的结合而被置换，它们可以通过介导配体与蛋白质之间的相互作用来稳定复合物。如果在模拟时间尺度内水未能重新排列自身，那么在两个配体之间进行相对结合自由能（RBFE）计算时，其中一个配体与蛋白质结合时带有中间水分子而另一个配体将水置换，可能会产生错误的结果。以前曾使用增强采样方法来处理此类“被困”水的采样问题，即在配体转化过程中在蛋白质结合位点插入或删除水分子。虽然有时有效，但增强采样方法通常需要很长的模拟时间才能收敛，并且可能会因初始水的放置而导致RBFE估计值出现差异（即滞后现象）。在本研究中，我们提出了一种非平衡切换（NES）方法来计算存在被困水的系统中的RBFE。我们的方法在对配体转化进行自由能计算之前需要知道被困水的位置，然后利用这些信息有效地计算配体之间的RBFE。在我们的模拟方案中，我们通过使用三个连续的NES切换在目标蛋白质的结合位点进行配体转化。这三个NES切换实施约束、转化配体，然后去除约束。我们证明，对于八个涉及被困水置换的系统，我们基于NES模拟的方法得出的RBFE估计值与实验RBFE值相差在1.1 kcal/mol以内，相关统计误差在0.4 kcal/mol以下。我们的方法通过利用分布式计算资源，为估计涉及被困水的系统的RBFE提供了一种计算成本较低的替代方法。
