title: Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics.
abstract: The mechanism of inhibition of group VIA Ca(2+)-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. Empty pockets were identified during the 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.
authors.affiliation: Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0601, USA. howardhsu@thu.edu.tw
authors.forename: Yuan-Hao
authors.initials: YH
authors.lastname: Hsu
authors.forename: Denis
authors.initials: D
authors.lastname: Bucher
authors.forename: Jian
authors.initials: J
authors.lastname: Cao
authors.forename: Sheng
authors.initials: S
authors.lastname: Li
authors.forename: Sheng-Wei
authors.initials: SW
authors.lastname: Yang
authors.forename: George
authors.initials: G
authors.lastname: Kokotos
authors.forename: Virgil L
authors.initials: VL
authors.lastname: Woods
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Edward A
authors.initials: EA
authors.lastname: Dennis
mesh_terms: D001665:Binding Sites / Q000187:drug effects; D041961:Deuterium Exchange Measurement; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D054522:Group VI Phospholipases A2 / Q000037:antagonists & inhibitors* / Q000378:metabolism; D007659:Ketones / Q000737:chemistry / Q000494:pharmacology*; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure
chemical_list: D004791:Enzyme Inhibitors; D007659:Ketones; D008024:Ligands; D054522:Group VI Phospholipases A2