Development of SILCS kinetics methodology for the determination of ligand dissociation pathways and free energy barriers

Abstract

The fast and accurate assessment of unbinding kinetics of ligands from proteins remains challenging due to high computational requirements and the lack of the information about the molecular transition states due to limited conformational sampling. Therefore, in the present study we investigate the extension of the site-identification by ligand competitive saturation (SILCS) methodology towards estimation of ligand unbinding kinetics. The proposed SILCS-kinetics (SILCS-KIN) method is implemented to sample the free-energy landscape of drug dissociation pathways. SILCS-KIN methodology will be expected as a potential tool for the discovery and design of drug-like compounds with optimized ligand dissociation properties