Unraveling the mechanistic details of rho-associated coiled-coil kinase1 (ROCK1) inhibition: Implications from pharmacophore mapping and free energy analysis

Rho-associated coiled-coil kinases (ROCKs) are essential for various cellular processes and play a crucial role in neurological and inflammatory disorders. The two ROCK isoforms (ROCK1 and ROCK2) are involved in the pathogenesis of multiple diseases. Increased levels of ROCK1 are observed in patients with Alzheimer's disease (AD), making it a promising drug target. This work presents the mechanism of inhibitor binding at the ROCK1 active site using a combination of ligand and structure-based drug design techniques. Ligand-based pharmaco-phore studies were performed on previously reported ROCK1 inhibitors to unravel the 3D steric and electronic features essential for ROCK1 inhibition. Molecular docking and molecular dynamics-based free energy analysis studies were performed to recognize the amino acids assisting in inhibitor binding by stabilizing the identified pharmacophore features. The crucial 3D pharmacophore features of ROCK1 inhibitors included hydrophobic (HYD), hydrogen-bond acceptor (HBA), and hydrogen-bond donor (HBD) characteristics. These features were oriented next to the complementary amino acids in the ROCK1 active site, as evident from the detailed inter-action analysis. The free energy calculations provided a quantifiable estimate of the favorable energetic contribution of Gly83, Val90, Lys105, Asp160, Leu205, and Asp216 to the total binding energy. These amino acids significantly contributed to the ROCK1-inhibitor complexes' overall binding free energy, indicating their importance in inhibitor binding.