Fragment-based discovery of nonpeptidic BACE-1 inhibitors using tethering.
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.
Yang
Wenjin
W
Department of Chemistry, Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard,South San Francisco, California 94080, USA. wyang@eigerbio.com
Fucini
Raymond V
RV
Fahr
Bruce T
BT
Randal
Mike
M
Lind
Kenneth E
KE
Lam
Melissa B
MB
Lu
Wanli
W
Lu
Yafan
Y
Cary
Douglas R
DR
Romanowski
Michael J
MJ
Colussi
Dennis
D
Pietrak
Beth
B
Allison
Timothy J
TJ
Munshi
Sanjeev K
SK
Penny
David M
DM
Pham
Phuongly
P
Sun
Jian
J
Thomas
Anila E
AE
Wilkinson
Jennifer M
JM
Jacobs
Jeffrey W
JW
McDowell
Robert S
RS
Ballinger
Marcus D
MD
D053829:Amyloid Precursor Protein Secretases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D055162:Biocatalysis; D020134:Catalytic Domain; D003545:Cysteine; D055808:Drug Discovery / Q000379:methods*; D004353:Drug Evaluation, Preclinical; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D010880:Piperidines / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship
D004791:Enzyme Inhibitors; D008024:Ligands; D010455:Peptides; D010880:Piperidines; D053829:Amyloid Precursor Protein Secretases; D003545:Cysteine