title: Mapping the active site of factor Xa by selective inhibitors: an NMR and MD study.
abstract: The structure of two selective inhibitors, Ac-Tyr-Ile-Arg-Ile-Pro-NH2 and Ac-(4-Amino-Phe)-(Cyclohexyl-Gly)-Arg-NH2, in the active site of the blood clotting enzyme factor Xa was determined by using transferred nuclear Overhauser effect nuclear magnetic resonance (NMR) spectroscopy. They represent a family of peptidic inhibitors obtained by the screening of a vast combinatorial library. Each structure was first calculated by using standard computational procedures (distance geometry, simulated annealing, energy minimization) and then further refined by systematic search of the conformation of the inhibitor docked in the active site and repeating the simulated annealing and energy minimization. The final structure was optimized by molecular dynamics simulations of the inhibitor-complex in water. The NMR restraints were kept throughout the refinement. The inhibitors assume a compact, very well defined conformation, embedded into the substrate binding site not in the same way as a substrate, blocking thus the catalysis. The model allows to explain the mode of action, affinity, and specificity of the peptides and to map the active site.
authors.affiliation: Marion Merrell Research Institute, HMR, Strasbourg, France.
authors.forename: F
authors.initials: F
authors.lastname: Fraternali
authors.forename: Q T
authors.initials: QT
authors.lastname: Do
authors.forename: B T
authors.initials: BT
authors.lastname: Doan
authors.forename: R A
authors.initials: RA
authors.lastname: Atkinson
authors.forename: P
authors.initials: P
authors.lastname: Palmas
authors.forename: V
authors.initials: V
authors.lastname: Sklenar
authors.forename: P
authors.initials: P
authors.lastname: Safar
authors.forename: P
authors.initials: P
authors.lastname: Wildgoose
authors.forename: P
authors.initials: P
authors.lastname: Strop
authors.forename: V
authors.initials: V
authors.lastname: Saudek
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000502:physiology; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D015951:Factor Xa / Q000737:chemistry*; D065427:Factor Xa Inhibitors; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry / Q000494:pharmacology; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D004791:Enzyme Inhibitors; D065427:Factor Xa Inhibitors; D019151:Peptide Library; D010455:Peptides; D015951:Factor Xa