Human factor Xa bound amidine inhibitor conformation by double rotational-echo double resonance nuclear magnetic resonance and molecular dynamics simulations.
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.
McDowell
Lynda M
LM
Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130, USA. mcdowell@wuchem.wustl.edu
McCarrick
Margaret A
MA
Studelska
Daniel R
DR
O'Connor
Robert D
RD
Light
David R
DR
Guilford
William J
WJ
Arnaiz
Damian
D
Adler
Marc
M
Dallas
Jerry L
JL
Poliks
Barbara
B
Schaefer
Jacob
J
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
D000578:Amidines; D065427:Factor Xa Inhibitors; D011725:Pyridines; C471166:ZK 806299; D014357:Trypsin; D015951:Factor Xa