Paper Citing NAMD - Abstract
Kang, Myungshim; Loverde, Sharon M.
Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11965-11972, OCT 16 2014
We report here the interactions between a hydrophobic drug and a model cellular membrane at the molecular level using all-atom molecular dynamics simulations of paclitaxel, a hydrophobic cancer drug. The calculated free energy of a single drug across the bilayer interface displays a minimum in the outer hydrophobic zone of the membrane. The transfer free energy shows excellent agreement with reported experimental data. In two sets of long-time simulations of high concentrations of drug in the membrane (12 and 11 mol %), the drugs display substantial clustering and rotation with significant directional preference in their diffusion. The main taxane ring partitions in the outer hydrophobic zone, while the three phenyl rings prefer to be closer to the hydrophobic core of the membrane. The clustering of the drug molecules, order parameters of the lipid tails, and water penetration suggest that the fluidity and permeability of the membrane are affected by the concentration of drugs that it contains. Furthermore, at the high-concentration limit, the free energy minimum shifts closer to the hydrophobic core and the central barrier to cross the membrane decreases. Moreover, the transfer free energy change substantially increases, suggesting that increasing concentration facilitates drug partitioning into the membrane.
