WaterMap calculations

WaterMap calculations were used to assess the thermodynamic parameters of waters in the binding site. These parameters can be used for ligand design by examining how ligands displace/replace these hydration sites. It is based on a small molecular dynamics simulation of explicit solvent followed by clustering and generation thermodynamic properties of hydration sites. It classifies water hydration sites into two categories, namely stable water and unstable waters based on the thermodynamic properties like entropy (-TΔS), enthalpy (-ΔH), free energy (ΔG) (Abel et al., 2011; Riniker et al., 2012).

WaterMap calculations for the prepared protein structure were performed using default simulation parameters (TIP4P solvent model at 300 K, 1 atmospheric pressure and 2 ns of simulation time) and treating existing waters as a part of explicit solvent (Release 2019-1: WaterMap, Schrödinger, LLC, New York, NY, 2020). The binding site was defined using the coordinates of the co-crystallized ligand. The truncate protein option was left unchecked for this study. The generated hydration sites were examined according to their enthalpy, entropy and free energy values.

The WM/MM scoring approach was employed to score the ligands which uses a combination of MMGBSA and WaterMap data to assess the best binding pose. The scoring was performed using VSGB solvation model and defining residues within the vicinity of the ligand as non-flexible.