Paper Citing NAMD - Abstract
Soriano-Ursua, Marvin A.; Trujillo-Ferrara, Jose G.; Correa-Basurto, Jose
Homology modeling and flex-ligand docking studies on the guinea pig beta(2) adrenoceptor: structural and experimental similarities differences with the human beta(2)
JOURNAL OF MOLECULAR MODELING, 15:1203-1211, OCT 2009
The trachea of a guinea pig is widely used in drug development assays focused on the treatment of pulmonary diseases. Some of these drugs relax the airways by binding to the guinea pig beta(2)-adrenoceptor (G beta(2)AR). In this work, the amino acid sequence of the G beta(2)AR was searched to carry out homology modeling, using the Swiss-Model server, with the human beta(2)AR as the parent template. The G beta(2)AR 3-D structure was structurally and energetically optimized in vacuo using NAMD 2.6 program. The refined 3-D model obtained was used for further study. Molecular docking simulations were performed by testing a set of well-known beta(2)AR ligands using the AutoDock 3.0.5 program. The results show that the homology model of G beta(2)AR has a 3-D structure very similar to the crystal structure of recently studied human beta(2)AR. This was also corroborated by identity (94.23%), Ramachandran map, and docking results. The theoretical simulation showed that the ligands bind at sites that are similar to those reported for the human beta(2)AR. The R-enantiomer ligands showed correlation with in vitro data. We have obtained a G beta(2)AR 3-D model which can be used to carry out computational screening as a complementary tool during the drug design and experimental tests under guinea pig models.
