title: Molecular recognition at the active site of factor Xa: cation-π interactions, stacking on planar peptide surfaces, and replacement of structural water.
abstract: Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.
authors.affiliation: Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Salonen
authors.forename: Mareike C
authors.initials: MC
authors.lastname: Holland
authors.forename: Philip S J
authors.initials: PS
authors.lastname: Kaib
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Haap
authors.forename: Jörg
authors.initials: J
authors.lastname: Benz
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Mary
authors.forename: Olivier
authors.initials: O
authors.lastname: Kuster
authors.forename: W Bernd
authors.initials: WB
authors.lastname: Schweizer
authors.forename: David W
authors.initials: DW
authors.lastname: Banner
authors.forename: François
authors.initials: F
authors.lastname: Diederich
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D015951:Factor Xa / Q000737:chemistry / Q000235:genetics; D065427:Factor Xa Inhibitors; D006801:Humans; D007555:Isoxazoles / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D012697:Serine Endopeptidases / Q000378:metabolism; D013237:Stereoisomerism; D013816:Thermodynamics; D013876:Thiophenes / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D014443:Tyrosine / Q000235:genetics; D014867:Water / Q000737:chemistry*
chemical_list: D004791:Enzyme Inhibitors; D065427:Factor Xa Inhibitors; D007555:Isoxazoles; D010455:Peptides; D013876:Thiophenes; D014867:Water; D014443:Tyrosine; D012697:Serine Endopeptidases; D015951:Factor Xa