title: Studying epigenetic complexes and their inhibitors with the proteomics toolbox.
abstract: Some epigenetic modifier proteins have become validated clinical targets. With a few small molecule inhibitors already approved by national health administrations and many more in the pharmaceutical industry pipelines, there is a need for technologies that can promote full comprehension of the molecular action of these drugs. Proteomics, with its relatively unbiased nature, can contribute to a thorough understanding of the complexity of the megadalton complexes, which write, read and erase the histone code, and it can help study the on-target and off-target effect of the drugs designed to modulate their action. This review on the one hand gathers the published affinity probes able to decipher small molecule targets and off-targets in a close-to-native environment. These are small molecule analogues of epigenetic drugs conceived as protein target enrichment tools after they have engaged them in cells or lysates. Such probes, which have been designed for deacetylases, bromodomains, demethylases, and methyltransferases not only enrich their direct protein targets but also their stable interactors, which can be identified by mass spectrometry. Hence, they constitute a tool to study the epigenetic complexes together with other techniques also reviewed here: immunoaffinity purification with antibodies against native protein complex constituents or epitope tags, affinity matrices designed to bind recombinantly tagged protein, and enrichment of the complexes using histone tail peptides as baits. We expect that this toolbox will be adopted by more and more researchers willing to harness the spectacular advances in mass spectrometry to the epigenetic field.
authors.affiliation: Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany ; HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany.
authors.forename: David
authors.initials: D
authors.lastname: Weigt
authors.affiliation: Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany ; HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Hopf
authors.affiliation: Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany.
authors.forename: Guillaume
authors.identifier: 0000-0002-4782-4029
authors.initials: G
authors.lastname: Médard
mesh_terms: D000906:Antibodies / Q000494:pharmacology; D055808:Drug Discovery; D044127:Epigenesis, Genetic / Q000187:drug effects*; D000939:Epitopes / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D020543:Proteome / Q000037:antagonists & inhibitors* / Q000276:immunology; D040901:Proteomics / Q000379:methods*; D054852:Small Molecule Libraries / Q000494:pharmacology*
chemical_list: D000906:Antibodies; D000939:Epitopes; D006657:Histones; D020543:Proteome; D054852:Small Molecule Libraries
keywords: Affinity matrix; Affinity purification; Complex identification; Immunoaffinity purification; Photo-cross-linking; Target deconvolution