Estudi del procés d’unió entre la benzamidina i la tripsina mitjançant docking molecular i simulacions de dinàmica molecular

Abstract

Understanding the process of protein-ligand binding is of capital importance to design a new drug. However, elucidating the nature of this process is complex because of the intrinsically dynamic character of proteins. In this study, we investigate the effect of protein conformational changes on the ligand-binding energies using computational methods. The system analysed is the trypsin-benzamidine enzyme-inhibitor complex. Molecular dynamics (MD) simulations have been successfully combined with molecular docking to obtain the interaction energy of each protein conformation. Here, molecular dynamics simulations in the apo (trypsin) and holo (trypsin and benzamidina) protein states have been performed to obtain a total of 100,000,000 conformations which are equivalent to 200 ns of simulation time. The trypsin conformations obtained for the apo molecular dynamics simulations can be classified in three groups: open, semi-open and close structures, depending on the interaction of benzamidine with the amino acids of active site. In addition, the conformational changes of tryptophan 193 and glutamine 174 are fundamental to determine the different conformations of trypsin. To simplify the amount of information obatined, clustering methods are used to get the most representatives structures of each simulation, by grouping the structures based on their similarity. The most representative structures were used to calculate the most favorable orientation of the benzamidine ligand and the interaction energy for the different protein conformations using molecular docking techniques. If the most favorable orientation predicted by docking does not target the active site, then less favorable orientations are checked to estimate the interaction energy with the active site. When the active site is found in the close conformation benzamidine does not fit in the active site and the binding event is not observed. Moreover, the crystallographic structure of trypsin (PDB: 3PTB) has been used as a benchmark for docking benzamidine and 10 molecules that contain the benzamidine group in their structure. Finally, the ligand is placed in the solvent at a certain distance from the target protein to reproduce the binding pathway of benzamidine to trypsin