title: Design and development of histone deacetylase (HDAC) chemical probes for cell-based profiling.
abstract: Histone deacetylases (HDACs) contribute to regulation of gene expression by mediating higher-order chromatin structures. They assemble into large multiprotein complexes that regulate activity and specificity. We report the development of small molecule probes with class IIa and pan-HDAC activity that contain photoreactive crosslinking groups and either a biotin reporter, or a terminal alkyne handle for subsequent bioorthogonal ligation. The probes retained inhibitory activity against recombinant HDAC proteins and caused an accumulation of acetylated histone and tubulin following cell treatment. The versatility of the probes has been demonstrated by their ability to photoaffinity modify HDAC targets in vitro. An affinity enrichment probe was used in conjunction with mass spectrometry proteomics to isolate HDACs and their interacting proteins in a native proteome. The performance of the probes in recombinant versus cell-based systems highlights issues for the development of chemoproteomic technologies targeting class IIa HDACs in particular.
authors.affiliation: Pfizer Ltd, The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, UK.
authors.forename: Victoria E
authors.initials: VE
authors.lastname: Albrow
authors.affiliation: Pfizer Ltd, The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, UK.
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Grimley
authors.affiliation: Department of Chemistry and Institute of Chemical Biology, Imperial College London, London, SW7 2AZ, UK.
authors.forename: James
authors.initials: J
authors.lastname: Clulow
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, USA.
authors.forename: Colin R
authors.initials: CR
authors.lastname: Rose
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, USA.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Sun
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, USA.
authors.forename: Joseph S
authors.initials: JS
authors.lastname: Warmus
authors.affiliation: Department of Chemistry and Institute of Chemical Biology, Imperial College London, London, SW7 2AZ, UK.
authors.forename: Edward W
authors.initials: EW
authors.lastname: Tate
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Inc., 610 Main Street, Cambridge, MA 02139, USA.
authors.forename: Lyn H
authors.initials: LH
authors.lastname: Jones
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer Ltd, The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, UK. ian.storer@pfizer.com.
authors.forename: R Ian
authors.initials: RI
authors.lastname: Storer
mesh_terms: D000107:Acetylation; D002463:Cell Membrane Permeability / Q000187:drug effects; D055808:Drug Discovery; D004789:Enzyme Activation / Q000187:drug effects; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006655:Histone Deacetylases / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry; D015335:Molecular Probes / Q000737:chemistry* / Q000494:pharmacology; D015394:Molecular Structure; D020543:Proteome; D040901:Proteomics / Q000379:methods; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D013194:Staining and Labeling
chemical_list: D056572:Histone Deacetylase Inhibitors; D015335:Molecular Probes; D020543:Proteome; D011994:Recombinant Proteins; D006655:Histone Deacetylases