title: Mapping the Binding Site of BMS-708163 on γ-Secretase with Cleavable Photoprobes.
abstract: γ-Secretase, a four-subunit transmembrane aspartic proteinase, is a highly valued drug target in Alzheimer's disease and cancer. Despite significant progress in structural studies, the respective molecular mechanisms and binding modes of γ-secretase inhibitors (GSIs) and modulators (GSMs) remain uncertain. Here, we developed biotinylated cleavable-linker photoprobes based on the BMS-708163 GSI to study its interaction with γ-secretase. Comparison of four cleavable linkers indicated that the hydrazine-labile N-1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl (Dde) linker was cleaved most efficiently to release photolabeled and affinity-captured presenilin-1 (PS1), the catalytic subunit of γ-secretase. Peptide mapping showed that the BMS-708163-based probe photoinserted at L282 of PS1. This insertion site was consistent with the results of molecular dynamics simulations of the γ-secretase complex with inhibitor. Taken together, this work reveals the binding site of a GSI and offers insights into the mechanism of action of this class of inhibitors.
authors.affiliation: Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Biochemistry and Molecular Biology Program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.
authors.forename: Natalya
authors.initials: N
authors.lastname: Gertsik
authors.affiliation: Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Groton, CT 06340, USA.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Am Ende
authors.affiliation: Pfizer Worldwide Research and Development, Structural and Molecular Sciences, Groton, CT 06340, USA.
authors.forename: Kieran F
authors.initials: KF
authors.lastname: Geoghegan
authors.affiliation: Pfizer Worldwide Research and Development, Structural and Molecular Sciences, Groton, CT 06340, USA.
authors.forename: Chuong
authors.initials: C
authors.lastname: Nguyen
authors.affiliation: Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Groton, CT 06340, USA.
authors.forename: Paramita
authors.initials: P
authors.lastname: Mukherjee
authors.affiliation: Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry and Chemical Biology, Cambridge, MA 02139, USA.
authors.forename: Scot
authors.initials: S
authors.lastname: Mente
authors.affiliation: Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry and Chemical Biology, Cambridge, MA 02139, USA.
authors.forename: Uthpala
authors.initials: U
authors.lastname: Seneviratne
authors.affiliation: Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry and Chemical Biology, Cambridge, MA 02139, USA. Electronic address: doug.johnson@pfizer.com.
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Johnson
authors.affiliation: Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China. Electronic address: liy2@mskcc.org.
authors.forename: Yue-Ming
authors.initials: YM
authors.lastname: Li
mesh_terms: D053829:Amyloid Precursor Protein Secretases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D001665:Binding Sites / Q000187:drug effects; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D056004:Molecular Dynamics Simulation; D015335:Molecular Probes / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D015394:Molecular Structure; D010069:Oxadiazoles / Q000737:chemistry / Q000494:pharmacology*; D013449:Sulfonamides / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*
chemical_list: C554092:BMS 708163; D004791:Enzyme Inhibitors; D015335:Molecular Probes; D010069:Oxadiazoles; D013449:Sulfonamides; D053829:Amyloid Precursor Protein Secretases
keywords: Alzheimer's disease; cleavable linkers; molecular dynamics simulations; peptide mapping; photoaffinity labeling