title: Human factor Xa bound amidine inhibitor conformation by double rotational-echo double resonance nuclear magnetic resonance and molecular dynamics simulations.
abstract: Double rotational-echo double resonance (double REDOR) NMR was used to investigate the conformation of a (13)C-, (15)N-, and (19)F-labeled inhibitor (Berlex Biosciences compound no. ZK-806299) bound to human factor Xa. Conformationally dependent carbon-fluorine dipolar couplings were measured by (13)C[(19)F] REDOR. Natural abundance carbon signals in the full-echo spectra were removed by (13)C[(15)N] REDOR. Major and minor binding modes were suggested by the NMR data, but only the former had adequate signal to noise for distance determinations. Molecular dynamics simulations restrained by double-REDOR-determined intramolecular (13)C-(19)F distances revealed two models for the dominant binding mode that are consistent with the NMR data. We conclude that ZK-806299 binds similarly to both FXa. Moreover, it appears to bind to FXa in a fashion previously demonstrated for ZK-807834, a more selective FXa inhibitor.
authors.affiliation: Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130, USA. mcdowell@wuchem.wustl.edu
authors.forename: Lynda M
authors.initials: LM
authors.lastname: McDowell
authors.forename: Margaret A
authors.initials: MA
authors.lastname: McCarrick
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Studelska
authors.forename: Robert D
authors.initials: RD
authors.lastname: O'Connor
authors.forename: David R
authors.initials: DR
authors.lastname: Light
authors.forename: William J
authors.initials: WJ
authors.lastname: Guilford
authors.forename: Damian
authors.initials: D
authors.lastname: Arnaiz
authors.forename: Marc
authors.initials: M
authors.lastname: Adler
authors.forename: Jerry L
authors.initials: JL
authors.lastname: Dallas
authors.forename: Barbara
authors.initials: B
authors.lastname: Poliks
authors.forename: Jacob
authors.initials: J
authors.lastname: Schaefer
mesh_terms: D000578:Amidines / Q000737:chemistry*; D001665:Binding Sites; D015951:Factor Xa / Q000737:chemistry*; D065427:Factor Xa Inhibitors; D006801:Humans; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008968:Molecular Conformation; D011725:Pyridines / Q000737:chemistry*; D014357:Trypsin / Q000737:chemistry
chemical_list: D000578:Amidines; D065427:Factor Xa Inhibitors; D011725:Pyridines; C471166:ZK 806299; D014357:Trypsin; D015951:Factor Xa