Structural Insights into the Interactions of Belumosudil with Rho-Associated Coiled-Coil Containing Protein Kinases 1 and 2 Based on Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculations

Rho-associated coiled-coil containing protein kinases (ROCKs) are members of the cyclic adenosine monophosphate-dependent protein kinase/protein kinase G/protein kinase C family that participates in a variety of important physiological functions, including smooth muscle contraction, cell proliferation, cell adhesion, migration, and inflammatory responses. In this study, we focused on ROCK1 and ROCK2, which are targets of the Food and Drug Administration-approved inhibitor 2-(3-(4-((1H-Indazol-5-yl)amino)quinazolin-2-yl)phenoxy)-N-isopropylacetamide (belumosudil). We constructed four representative belumosudil/ROCK complex structures by molecular docking. The interactions between belumosudil and ROCK were then investigated via molecular dynamics simulations and binding free energy calculations. It was found that belumosudil showed a stronger binding affinity toward ROCK2 than toward ROCK1. Binding free energy calculations and free energy decompositions suggested that the modification of various regions of the belumosudil structure may enhance its binding affinity with ROCK, in addition to improving the selectivity between ROCK1 and ROCK2. This work therefore provides useful information to aid future drug design.