title: Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of β-Secretase.
abstract: Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods. Here, we demonstrate the utility and power of (19)F-based fragment screening by detailing the identification of a second-site fragment through (19)F NMR screening that binds to a specific pocket of the aspartic acid protease, β-secretase (BACE-1). The identification of this second-site fragment allowed the undertaking of a fragment-linking approach, which ultimately yielded a molecule exhibiting a more than 360-fold increase in potency while maintaining reasonable ligand efficiency and gaining much improved selectivity over cathepsin-D (CatD). X-ray crystallographic studies of the molecules demonstrated that the linked fragments exhibited binding modes consistent with those predicted from the targeted screening approach, through-space NMR data, and molecular modeling.
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: John B
authors.initials: JB
authors.lastname: Jordan
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Whittington
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Bartberger
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: E Allen
authors.initials: EA
authors.lastname: Sickmier
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: Kui
authors.initials: K
authors.lastname: Chen
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.
authors.forename: Ted
authors.initials: T
authors.lastname: Judd
mesh_terms: D053829:Amyloid Precursor Protein Secretases / Q000037:antagonists & inhibitors*; D018360:Crystallography, X-Ray; D055808:Drug Discovery; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D005461:Fluorine; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D020349:Surface Plasmon Resonance
chemical_list: D004791:Enzyme Inhibitors; D005461:Fluorine; D053829:Amyloid Precursor Protein Secretases