COMPUTATIONAL TOOLS AND METHODS FOR THE IMPLEMENTATION AND ELABORATION OF MOLECULAR DOCKING FOR ENZYMES OF THE MEDICAL DESTINATION

At present biomedical research is based on joint fulfillment of theoretical and experimental investigations of various derivatives of potential therapeutic destination. Well-balanced combination of noted studies is provided for the high reliability of ensemble for obtained results. The implementation of molecular docking of high-molecule pharmacological compounds with different ligands of their natural microenvironment is notably important among such investigations. It should be noted the perspectives of such results for study of enzymes. The investigations of such kind are directed on ascertainment of mechanism of the action of these agents in biological systems and grounding of productive manners for obtaining of the high efftcacy of drug preparations of the enzyme nature. The implementation of molecular docking was conduced the lead-in of glycosaminoglycans (components of endothelial glycocalyx of the protective layer of the vessel wall) to circle of research interest. The implementation of molecular docking with elaboration of its data by methods of molecular dynamics became a productive approach for development of theoretical models of protein-glycosaminoglycan complexes. Algorithms of docking and scoring functions, conformational alterations of enzyme structure (on short /ps and ns/ more continual scale of time) were considered. The ponderable challenge of molecular docking progress was demonstrated as using of notion of the enzyme structure flexibility due to a mode of molecular dynamics with modeling of all freedom degrees in enzyme-ligand complex.

molecular docking, scoring function, tertiary enzyme structure, glycosaminoglycan ligands, design of novel drug derivative molecules