Molecular dynamics simulation of interaction of the anti-cancer drug paclitaxel with the cell membrane: investigation of changes in van der Waals energy and center of mass

Abstract

Due to increasing of cancers and production of new anti-cancer drugs for its treatment, in this study, the interaction of new hydrophobic anti-cancer drug paclitaxel with the cell membrane has been discussed using computational tools. We have done molecular dynamics simulation using NAMD and also the initial structures that were achieved from the protein data bank have been modified using VMD package. Langevin algorithm was used for temperature control in 310 K, the human body temperature and the Brandson algorithm was utilized for pressure control in 1 bar. The simulation has been done during 10 ns. The simulation equations were based on Newton’s Motion Law and a Lenard−Jones potential. The anti-cancer drug paclitaxel interaction with the cell membrane has been investigated from the van der Waals energy and center of mass (COM) perspectives that show less stability and low absorption of the drug to the cell membrane. Computational results of this study confirm the validity of previously published computational and laboratory studies. According to the drug hydrophobicity, less stability, low absorption and also low efficacy has been shown in interaction with the cell membrane. As a result, administration of the anti-cancer drug can be very effective and efficient by using new drug delivery methods