Comprehensive 3D-RISM Analysis of the Hydration of Small Molecule Binding Sites in Ligand-Free Protein Structures

Abstract

Ligand binding to proteins involves displacing water molecules at the binding site and rearranging water molecules close to the ligand. The hydration state of ligand binding sites is important for the stability of the ligand-protein complex. Using the three-dimensional reference interaction site model (3D-RISM) theory, here we calculated the three-dimensional distribution function of the water oxygen site, gO(r), for 3,706 ligand-free protein structures of small molecule-protein complexes [1]. The 3D-RISM theory allowed the first comprehensive analysis of the hydration state for a large number of protein structures, a difficult subject for existing methods based on molecular dynamics simulations. The probability distribution of gO(r) at the positions of approximately 620,000 crystallographic waters (CWs) was calculated and analyzed. The gO(r) for CWs close to the ligand revealed that several CWs were stabilized by interaction networks formed between the ligand, CW, and protein. Analysis of gO(r) at the position of ligand heavy atoms indicated that, in the crystallographic binding poses (correct poses) of the ligand, hydrogen bond interactions are dominant in the highly hydrated regions whereas weak interactions such as CH-O are dominant in the moderately hydrated regions. Further, polar heteroatoms of the ligand tend to occupy highly hydrated regions in the correct poses and less hydrated regions in the wrongly docked poses, suggesting a way to distinguish these two poses. [1] T. Yoshidome, M. Ikeguchi, and M. Ohta, J. Comp. Chem., 41, 2406 (2020).