title: A road map to evaluate the proteome-wide selectivity of covalent kinase inhibitors.
abstract: Kinases are principal components of signal transduction pathways and the focus of intense basic and drug discovery research. Irreversible inhibitors that covalently modify non-catalytic cysteines in kinase active sites have emerged as valuable probes and approved drugs. Many protein classes, however, have functional cysteines, and therefore understanding the proteome-wide selectivity of covalent kinase inhibitors is imperative. Here, we accomplish this objective using activity-based protein profiling coupled with quantitative MS to globally map the targets, both specific and nonspecific, of covalent kinase inhibitors in human cells. Many of the specific off-targets represent nonkinase proteins that, notably, have conserved active site cysteines. We define windows of selectivity for covalent kinase inhibitors and show that, when these windows are exceeded, rampant proteome-wide reactivity and kinase target-independent cell death conjointly occur. Our findings, taken together, provide an experimental road map to illuminate opportunities and surmount challenges for the development of covalent kinase inhibitors.
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Lanning
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Landon R
authors.initials: LR
authors.lastname: Whitby
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Melissa M
authors.initials: MM
authors.lastname: Dix
authors.affiliation: Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140.
authors.forename: John
authors.initials: J
authors.lastname: Douhan
authors.affiliation: Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Gilbert
authors.affiliation: Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140.
authors.forename: Erik C
authors.initials: EC
authors.lastname: Hett
authors.affiliation: Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121.
authors.forename: Theodore O
authors.initials: TO
authors.lastname: Johnson
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Chris
authors.initials: C
authors.lastname: Joslyn
authors.affiliation: Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121.
authors.forename: John C
authors.initials: JC
authors.lastname: Kath
authors.affiliation: Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121.
authors.forename: Sherry
authors.initials: S
authors.lastname: Niessen
authors.affiliation: Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140.
authors.forename: Lee R
authors.initials: LR
authors.lastname: Roberts
authors.affiliation: Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Schnute
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Chu
authors.initials: C
authors.lastname: Wang
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Jonathan J
authors.initials: JJ
authors.lastname: Hulce
authors.affiliation: Pfizer Worldwide Research and Development, 1 Burtt Rd, Andover, MA 01810.
authors.forename: Baoxian
authors.initials: B
authors.lastname: Wei
authors.affiliation: Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340.
authors.forename: Laurence O
authors.initials: LO
authors.lastname: Whiteley
authors.affiliation: Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340.
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Hayward
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
authors.forename: Benjamin F
authors.initials: BF
authors.lastname: Cravatt
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives; D000077329:Agammaglobulinaemia Tyrosine Kinase; D045744:Cell Line, Tumor; D002470:Cell Survival / Q000187:drug effects; D003545:Cysteine / Q000737:chemistry; D018773:Genes, erbB-1 / Q000235:genetics; D006801:Humans; D007700:Kinetics; D010880:Piperidines; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D011494:Protein Kinases / Q000378:metabolism; D011505:Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors; D020543:Proteome / Q000235:genetics*; D011720:Pyrazoles / Q000494:pharmacology; D011743:Pyrimidines / Q000494:pharmacology; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics
chemical_list: D010880:Piperidines; D047428:Protein Kinase Inhibitors; D020543:Proteome; D011720:Pyrazoles; D011743:Pyrimidines; C551803:ibrutinib; D011494:Protein Kinases; D011505:Protein-Tyrosine Kinases; D000077329:Agammaglobulinaemia Tyrosine Kinase; D000225:Adenine; D003545:Cysteine