Paper Citing NAMD - Abstract
Arsawang, Uthumporn; Saengsawang, Oraphan; Rungrotmongkol, Thanyada; Sornmee, Purinchaya; Wittayanarakul, Kitiyaporn; Remsungnen, Tawun; Hannongbua, Supot
How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system?
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:591-596, FEB 2011
Aiming at understanding the molecular properties of the encapsulation of the anticancer drug gemcitabine in the single-walled carbon nanotube (SWCNT), molecular dynamics (MD) simulations were applied to the two scenarios; that of gemcitabine filling inside the SWCNT, and that of the drug in the free state. Inside the SWCNT, the cytosine ring of gemcitabine was found to form a pi-pi stacking conformation with the SWCNT surface, and this movement is not along the centerline of the tube from one end to the other of the tube where the distance from the center of gravity of the molecule to the surface is 4.7 angstrom. A tilted angle of 19 degrees was detected between the cytosine ring of gemcitabine and the inner surface of SWCNT. In comparison to its conformation in the free form, no significant difference was observed on the torsion angle between the five- (ribose) and the six- (cytosine) membered rings. However, gemcitabine inside the SWCNT was found to have a lower number of solvating water molecules but with a stronger net solvation than the drug in the free state. This is due to the collaborative interactions between gemcitabine and the surface of the SWCNT. In addition, the steered molecular dynamics simulation (SMD) approach was employed to investigate the binding free energy for gemcitabine moving from one end to another end throughout the SWCNT. In excellent agreement with that yielded from the classical MD, the SMD energy profile confirms that the drug molecule prefers to locate inside the SWCNT. (C) 2010 Elsevier Inc. All rights reserved.
