Decoding ROCK1 inhibition: A comprehensive computational analysis of key binding determinants for rational design of...

Rho-Associated coiled-coil kinase 1 (ROCK1) is a potential drug target against neurological disorders. In this work, we deployed molecular docking, free energy calculations, and steered molecular dynamics (SMD) to identify crucial amino acids that could act as anchor points for effective inhibitor binding at the ROCK1 active site. Molecular docking studies followed by detailed interaction analysis were conducted on previously reported ROCK1 inhibitors, including standard approved ROCK1 drugs, Netrasudil and Fasudil. The interacting amino acids were confirmed by quantifying their sole energetic contributions toward the total binding energy through free energy analysis. The stability of the protein-ligand complexes under simulation conditions was further evaluated by performing molecular dynamics simulations in triplicates. SMD simulations were used to understand the magnitude of interactions between the ROCK1. Detailed interaction analysis and free energy mapping highlighted the crucial role of G83, V90, A103, K105, M153, E154, M156, D202, L205, A215, and D216 in efficacious inhibitor binding. These amino acids significantly influenced the ROCK1-inhibitor complexes' overall binding free energy, indicating their importance in optimal inhibitor binding. The present work makes use of classical molecular mechanics-based and steered molecular dynamics simulations to provide a thorough understanding of the mechanisms underlying ROCK1 inhibition, which can be of significance in the discovery and design of potential drugs.