title: Protein-Templated Formation of an Inhibitor of the Blood Coagulation Factor Xa through a Background-Free Amidation Reaction.
abstract: Protein-templated reactions enable the target-guided formation of protein ligands from reactive fragments, ideally with no background reaction. Herein, we investigate the templated formation of amides. A nucleophilic fragment that binds to the coagulation factor Xa was incubated with the protein and thirteen differentially activated dipeptides. The protein induced a non-catalytic templated reaction for the phenyl and trifluoroethyl esters; the latter was shown to be a completely background-free reaction. Starting from two fragments with millimolar affinity, a 29 nm superadditive inhibitor of factor Xa was obtained. The fragment ligation reaction was detected with high sensitivity by an enzyme activity assay and by mass spectrometry. The reaction progress and autoinhibition of the templated reaction by the formed ligation product were determined, and the structure of the protein-inhibitor complex was elucidated.
authors.affiliation: Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195, Berlin, Germany.
authors.forename: Mike
authors.initials: M
authors.lastname: Jaegle
authors.affiliation: Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35037, Marburg, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Steinmetzer
authors.affiliation: Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195, Berlin, Germany.
authors.forename: Jörg
authors.identifier: 0000-0001-6678-3165
authors.initials: J
authors.lastname: Rademann
mesh_terms: D000577:Amides / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D001550:Benzamidines / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology; D060326:Chemistry Techniques, Synthetic / Q000379:methods; D004151:Dipeptides / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D055808:Drug Discovery; D004951:Esterification; D015951:Factor Xa / Q000737:chemistry* / Q000378:metabolism; D065427:Factor Xa Inhibitors / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation
chemical_list: D000577:Amides; D001550:Benzamidines; D004151:Dipeptides; D065427:Factor Xa Inhibitors; D008024:Ligands; C096003:N-methylbenzamidine; D015951:Factor Xa
keywords: amide bond formation; enzyme inhibitors; fragment-based drug discovery; peptide bond formation; protein-templated reactions