1. Fragment-based discovery of nonpeptidic BACE-1 inhibitors using tethering
- Author
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Douglas R. Cary, Jennifer Wilkinson, Yafan Lu, Robert S. McDowell, Phuongly Pham, Jeffrey W. Jacobs, Wanli Lu, Melissa B Lam, Michael J. Romanowski, Beth Pietrak, Marcus Ballinger, Raymond V. Fucini, Jian Sun, David M Penny, Wenjin Yang, Timothy J. Allison, Mike Randal, Dennis Colussi, Anila E Thomas, Bruce T. Fahr, Kenneth E Lind, and Sanjeev Munshi
- Subjects
Models, Molecular ,Stereochemistry ,Drug Evaluation, Preclinical ,Molecular Conformation ,Ligands ,Biochemistry ,Structure-Activity Relationship ,Piperidines ,Catalytic Domain ,Drug Discovery ,Amyloid precursor protein ,Moiety ,Structure–activity relationship ,Humans ,Cysteine ,Enzyme Inhibitors ,chemistry.chemical_classification ,biology ,Chemistry ,Drug discovery ,Active site ,Small molecule ,Enzyme ,Mutation ,biology.protein ,Biocatalysis ,Amyloid Precursor Protein Secretases ,Peptides - Abstract
BACE-1 (beta-site amyloid precursor protein cleaving enzyme), a prominent target in Alzheimer's disease drug discovery efforts, was surveyed using Tethering technology to discover small molecule fragment ligands that bind to the enzyme active site. Screens of a library of >15000 thiol-containing fragments versus a panel of BACE-1 active site cysteine mutants under redox-controlled conditions revealed several novel amine-containing fragments that could be selectively captured by subsets of the tethering sites. For one such hit class, defined by a central aminobenzylpiperidine (ABP) moiety, X-ray crystal structures of BACE mutant-disulfide conjugates revealed that the fragment bound by engaging both catalytic aspartates with hydrogen bonds. The affinities of ABP fragments were improved by structure-guided chemistry, first for conjugation as thiol-containing fragments and then for stand-alone, noncovalent inhibition of wild-type (WT) BACE-1 activity. Crystallography confirmed that the inhibitors bound in exactly the same mode as the disulfide-conjugated fragments that were originally selected from the screen. The ABP ligands represent a new type of nonpeptidic BACE-1 inhibitor motif that has not been described in the aspartyl protease literature and may serve as a starting point for the development of BACE-1-directed Alzheimer's disease therapeutics.
- Published
- 2009