Paper Citing NAMD - Abstract
Hsu, Yuan-Hao; Bucher, Denis; Cao, Jian; Li, Sheng; Yang, Sheng-Wei; Kokotos, George; Woods, Virgil L., Jr.; McCammon, J. Andrew; Dennis, Edward A.
Fluoroketone Inhibition of Ca2+-Independent Phospholipase A(2) through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:1330-1337, JAN 30 2013
The mechanism of inhibition of group VIA Ca2+-independent phospholipase A(2) (iPLA(2)) by fluoroketone (FK) ligands is examined by a combination of deuterium exchange mass spectrometry (DXMS) and molecular dynamics (MD). Models for iPLA(2) were built by homology with the known structure of patatin and equilibrated by extensive MD simulations and studied for their ability to accommodate FK inhibitors. Ligand docking techniques showed that the potent inhibitor 1,1,1,3-tetrafluoro-7-phenylheptan-2-one (PHFK) forms favorable interactions inside an active-site pocket, where it blocks the entrance of phospholipid substrates. The polar fluoroketone headgroup is stabilized by hydrogen bonds with residues Gly486, Gly487, and Ser519. The nonpolar aliphatic chain and aromatic group are stabilized by hydrophobic contacts with Met544, Val548, Phe549, Leu560, and Ala640. The binding mode is supported by DXMS experiments showing an important decrease of deuteration in the contact regions in the presence of the inhibitor. The discovery of the precise binding mode of FK ligands to the iPLA(2) should greatly improve our ability to design new inhibitors with higher potency and selectivity.
