UC Riverside

Computer-aided drug design (CADD) represents computational methods and resources that are used to facilitate the design and discovery of new therapeutic solutions. It has been applied at almost all stages in the drug discovery pipeline. CADD has the advantage of reducing the cost and time for the expensive and extensive laboratory-based experiment. In CADD, protein flexibility has long been recognized as a complicating factor. Proteins are in constant motions in their physiological environment and their conformational dynamics play important roles in various biological functions and regulating ligand binding. My research focuses on modeling of protein flexibility and inter-molecular interactions and their applications to CADD. Detailed projects include method development for analyzing protein conformational changes using Perl and applications of various computing tools to study protein dynamics and protein-ligand interactions. In addition, ligand-specific molecular model was constructed on cannabinoid CB1 receptor, a G-protein coupled receptor, with protein flexibility considered. To discover novel antimicrobial agents against tryptophan synthase, another project was carried out using structure-based virtual screening method. Recently, nanoparticles have been applied to therapeutic use. To promote safer implementation of nanotechnology and reduce nanotoxicity for drug delivery, dynamics and interactions between human serum albumin and nanoparticles were studied.