Study of the interactions between asteropsin_A and paclitaxel by the use of molecular dynamics simulation and MM-PBSA

In this paper, the interactions between paclitaxel molecule and asteropsin_A protein in the aqueous media have been studied by molecular dynamics simulation and MM-PBSA method. The binding energies between paclitaxel and asteropsin_A have been evaluated by the help of MM-PBSA in these systems after equilibration and simulation. The main goal of this study is investigated the active sites to create effective interactions between drug nanoparticles and proteins and also to form a framework for drug by proteins, for this purpose used one, two, three, four and five asteropsin_A. The results of molecular dynamics simulations, such as radius of gyration, radial distribution functions and hydrogen bonding, have been discussed. The results were analyzed by the comparing their values in the systems with and without Paclitaxel. The results show that by increasing the number of asteropsin_A in the systems, the solubility of paclitaxel in water increases. Also, the results show that the residues Gly2, Leu21, Cys3, Phe14 and PGa1 have maximum interactions with paclitaxel in the systems containing one, two, three, four and five asteropsin_A proteins, respectively. The results represent that increasing the number of asteropsin A, lead to increasing the binding affinity of drug to proteins.