Structural analysis and molecular docking studies of thymogen

Abstract

Thymogen (L-Glutamyl-L-Tryptophan, H-Glu-Trp-OH), immunoactive dipeptide, was investigated by molecular modeling methods. The conformational profiles of this molecule were investigated by molecular mechanics method. Then obtained most stable conformations of this dipeptide were optimized using DFT/ B3LYP level of theory with 6-31+G(d,p) basis set. The structural characteristics, molecular electrostatic potential (MEP) map, highest occupied and lowest unoccupied molecular orbital energies, dipole moment (m), polarizability (a) and other parameters characterized the molecular properties of thymogen were calculated. It was found that the conformation with extended form of backbone is optimal for this molecule. Moreover, thymogen was docking onto the specific T-cell receptor using AutoDock Vina software. It was shown that the optimized structure of thymogen calculated by DFT/B3LYP/6-31+G(d,p) gives a binding affinity value –7.9 kcal/mol, which points out that it complements well a cleft on the surface of the receptor shown to be the attachment site. On the basis of the received results the model of pharmacophore of thymogen for its interaction with T-cell receptor was proposed.