title: Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors.
abstract: We describe a chemical proteomics approach to profile the interaction of small molecules with hundreds of endogenously expressed protein kinases and purine-binding proteins. This subproteome is captured by immobilized nonselective kinase inhibitors (kinobeads), and the bound proteins are quantified in parallel by mass spectrometry using isobaric tags for relative and absolute quantification (iTRAQ). By measuring the competition with the affinity matrix, we assess the binding of drugs to their targets in cell lysates and in cells. By mapping drug-induced changes in the phosphorylation state of the captured proteome, we also analyze signaling pathways downstream of target kinases. Quantitative profiling of the drugs imatinib (Gleevec), dasatinib (Sprycel) and bosutinib in K562 cells confirms known targets including ABL and SRC family kinases and identifies the receptor tyrosine kinase DDR1 and the oxidoreductase NQO2 as novel targets of imatinib. The data suggest that our approach is a valuable tool for drug discovery.
authors.affiliation: Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Bantscheff
authors.forename: Dirk
authors.initials: D
authors.lastname: Eberhard
authors.forename: Yann
authors.initials: Y
authors.lastname: Abraham
authors.forename: Sonja
authors.initials: S
authors.lastname: Bastuck
authors.forename: Markus
authors.initials: M
authors.lastname: Boesche
authors.forename: Scott
authors.initials: S
authors.lastname: Hobson
authors.forename: Toby
authors.initials: T
authors.lastname: Mathieson
authors.forename: Jessica
authors.initials: J
authors.lastname: Perrin
authors.forename: Manfred
authors.initials: M
authors.lastname: Raida
authors.forename: Christina
authors.initials: C
authors.lastname: Rau
authors.forename: Valérie
authors.initials: V
authors.lastname: Reader
authors.forename: Gavain
authors.initials: G
authors.lastname: Sweetman
authors.forename: Andreas
authors.initials: A
authors.lastname: Bauer
authors.forename: Tewis
authors.initials: T
authors.lastname: Bouwmeester
authors.forename: Carsten
authors.initials: C
authors.lastname: Hopf
authors.forename: Ulrich
authors.initials: U
authors.lastname: Kruse
authors.forename: Gitte
authors.initials: G
authors.lastname: Neubauer
authors.forename: Nigel
authors.initials: N
authors.lastname: Ramsden
authors.forename: Jens
authors.initials: J
authors.lastname: Rick
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kuster
authors.forename: Gerard
authors.initials: G
authors.lastname: Drewes
mesh_terms: D001549:Benzamides; D002457:Cell Extracts; D002846:Chromatography, Affinity; D000070819:Discoidin Domain Receptor 1; D004800:Enzymes, Immobilized / Q000037:antagonists & inhibitors; D006367:HeLa Cells; D006801:Humans; D000068877:Imatinib Mesylate; D020128:Inhibitory Concentration 50; D020014:K562 Cells; D004364:Pharmaceutical Preparations; D010766:Phosphorylation / Q000187:drug effects; D010879:Piperazines / Q000494:pharmacology; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D040901:Proteomics / Q000379:methods*; D016315:Proto-Oncogene Proteins c-abl / Q000037:antagonists & inhibitors*; D011743:Pyrimidines / Q000494:pharmacology; D011808:Quinone Reductases / Q000037:antagonists & inhibitors; D020794:Receptor Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors; D015398:Signal Transduction / Q000187:drug effects
chemical_list: D001549:Benzamides; D002457:Cell Extracts; D004800:Enzymes, Immobilized; D004364:Pharmaceutical Preparations; D010879:Piperazines; D047428:Protein Kinase Inhibitors; D011743:Pyrimidines; D000068877:Imatinib Mesylate; C419642:NRH - quinone oxidoreductase2; D011808:Quinone Reductases; C092030:DDR1 protein, human; D000070819:Discoidin Domain Receptor 1; D020794:Receptor Protein-Tyrosine Kinases; D016315:Proto-Oncogene Proteins c-abl