A road map to evaluate the proteome-wide selectivity of covalent kinase inhibitors

  • Nat Chem Biol. 2014 Sep;10(9):760-767. doi: 10.1038/nchembio.1582.
Bryan R Lanning   #  1 ,  Landon R Whitby   #  1 ,  Melissa M Dix  1 ,  John Douhan  2 ,  Adam M Gilbert  3 ,  Erik C Hett  2 ,  Theodore O Johnson  4 ,  Chris Joslyn  1 ,  John C Kath  4 ,  Sherry Niessen  4 ,  Lee R Roberts  2 ,  Mark E Schnute  2 ,  Chu Wang  1 ,  Jonathan J Hulce  1 ,  Baoxian Wei  5 ,  Laurence O Whiteley  3 ,  Matthew M Hayward  3 ,  Benjamin F Cravatt  1
Affiliations
  • 1. The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA, 92307.
  • 2. Pfizer Worldwide Research and Development, 200 Cambridge Park Drive, Cambridge, MA 02140.
  • 3. Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340.
  • 4. Pfizer Worldwide Research and Development, 10770 Science Park Drive, San Diego, CA 92121.
  • 5. Pfizer Worldwide Research and Development, 1 Burtt Rd, Andover, MA 01810.
  • # Contributed equally.
PMID: 25038787 DOI: 10.1038/nchembio.1582
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.

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