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  • Review Article
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Non-kinase targets of protein kinase inhibitors

Key Points

  • Kinase targets and overall toxicity-related off-targets of kinase inhibitors are usually identified in the early stages of drug development. The kinase selectivity profiles are well documented in the literature.

  • Non-kinase targets of kinase inhibitors often remain undiscovered, as the cytotoxicity of the kinase inhibitor is attributed to the inhibition of the targeted kinase. This can lead to misinterpretation of data and faulty links between the pathway and disease pathology.

  • The phenomenon that kinase inhibitors exert their anticancer effect through unintended non-kinase targets is increasingly being appreciated, and it implies that the mechanism of action of kinase inhibitors should be investigated beyond the kinome.

  • Tubulin and bromodomain and extra-terminal domain (BET) proteins have so far been the most frequent non-kinase targets identified for a relatively large number of kinase inhibitors.

  • Detailed orthogonal approaches to drug–target validation using orthogonal inhibitors are needed for pharmacological investigations, in particular when working with kinase inhibitors. These approaches will generate more reliable and reproducible data.

  • It is anticipated that future research will uncover more novel non-kinase targets of kinase inhibitors, which will enable new discoveries and better-validated drug targets.

Abstract

Kinome-wide profiling platforms have comprehensively identified the relevant kinases that are targeted by numerous protein kinase inhibitors. However, recent projects have begun to discover non-kinase targets of kinase inhibitors. These non-kinase targets can contribute to the desired or undesired activities of inhibitors, or act as silent bystanders. As a full awareness of a drug's mechanism of action is crucial for the interpretation of results and for successful preclinical and clinical drug development, these discoveries highlight the importance of understanding the pharmacology of kinase inhibitors beyond the kinome. In this Review, I discuss kinase inhibitors for which non-kinase targets have been identified and the application of emerging techniques to validate drug–target engagement in intact cells.

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Figure 1: Identification of tivantinib as a tubulin-targeting drug.
Figure 2: Kinase and scaffolding functions of EGFR.
Figure 3: Kinase and scaffolding functions of RIPK1 and RIPK3.

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References

  1. Wu, P., Nielsen, T. E. & Clausen, M. H. Small-molecule kinase inhibitors: an analysis of FDA-approved drugs. Drug Discov. Today 21, 5–10 (2016).

    Article  CAS  PubMed  Google Scholar 

  2. Dar, A. C. & Shokat, K. M. The evolution of protein kinase inhibitors from antagonists to agonists of cellular signaling. Ann. Rev. Biochem. 80, 769–795 (2011).

    Article  CAS  PubMed  Google Scholar 

  3. Davis, M. et al. Comprehensive analysis of kinase inhibitor selectivity. Nat. Biotechnol. 29, 1046–1051 (2011).

    Article  CAS  PubMed  Google Scholar 

  4. Miduturu, C. V. et al. High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors. Chem. Biol. 18, 868–879 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Fedorov, O. et al. A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc. Natl Acad. Sci. USA 104, 20523–20528 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Jacoby, E. et al. Extending kinome coverage by analysis of kinase inhibitor broad profiling data. Drug Discov. Today 20, 652–658 (2015).

    Article  CAS  PubMed  Google Scholar 

  7. Bowes, J. et al. Reducing safety-related drug attrition: the use of in vitro pharmacological profiling. Nat. Rev. Drug Discov. 11, 909–922 (2012).

    Article  CAS  PubMed  Google Scholar 

  8. Komlodi-Pasztor, E., Sackett, D., Wilkerson, J. & Fojo, T. Mitosis is not a key target of microtubule agents in patient tumors. Nat. Rev. Clin. Oncol. 8, 244–250 (2011).

    Article  CAS  PubMed  Google Scholar 

  9. Mccarroll, J., Parker, A. & Kavallaris, M. Microtubules and their role in cellular stress in cancer. Front. Oncol. 4, 153 (2014).

    PubMed  PubMed Central  Google Scholar 

  10. Dumontet, C. & Jordan, M. A. Microtubule-binding agents: a dynamic field of cancer therapeutics. Nat. Rev. Drug Discov. 9, 790–803 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Munshi, N. et al. ARQ 197, a novel and selective inhibitor of the human c-Met receptor tyrosine kinase with antitumor activity. Mol. Cancer Ther. 9, 1544–1553 (2010).

    Article  CAS  PubMed  Google Scholar 

  12. Eathiraj, S. et al. Discovery of a novel mode of protein kinase inhibition characterized by the mechanism of inhibition of human mesenchymal-epithelial transition factor (c-Met) protein autophosphorylation by ARQ 197. J. Biol. Chem. 286, 20666–20676 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Basilico, C. et al. Tivantinib (ARQ197) displays cytotoxic activity that is independent of its ability to bind MET. Clin. Cancer Res. 19, 2381–2392 (2013).

    Article  CAS  PubMed  Google Scholar 

  14. Katayama, R. et al. Cytotoxic activity of tivantinib (ARQ 197) is not due solely to c-MET inhibition. Cancer Res. 73, 3087–3096 (2013). References 13 and 14 revealed in parallel that the MET inhibitor tivantinib exerts its anticancer activity independently of MET inhibition and showed that tivantinib is a tubulin-targeting drug.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Aoyama, A. et al. Tivantinib (ARQ 197) exhibits antitumor activity by directly interacting with tubulin and overcomes ABC transporter–mediated drug resistance. Mol. Cancer Ther. 13, 2978–2990 (2014).

    Article  CAS  PubMed  Google Scholar 

  16. Wang, Y. et al. Structures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery. FEBS J. 283, 102–111 (2016).

    Article  CAS  PubMed  Google Scholar 

  17. Mashhoon, N. et al. Crystal structure of a conformation-selective casein kinase-1 inhibitor. J. Biol. Chem. 275, 20052–20060 (2000).

    Article  CAS  PubMed  Google Scholar 

  18. Davidson, W. et al. Discovery and characterization of a substrate selective p38α inhibitor. Biochemistry 43, 11658–11671 (2004).

    Article  CAS  PubMed  Google Scholar 

  19. Brockschmidt, C. et al. Anti-apoptotic and growth-stimulatory functions of CK1δ and ɛ in ductal adenocarcinoma of the pancreas are inhibited by IC261 in vitro and in vivo. Gut 57, 799–806 (2008).

    Article  CAS  PubMed  Google Scholar 

  20. Behrend, L. et al. IC261, a specific inhibitor of the protein kinase casein kinase1-δ and -ɛ, triggers mitotic checkpoint and induces p53-dependent postmitotic affects. Oncogene 19, 5303–5313 (2000).

    Article  CAS  PubMed  Google Scholar 

  21. Cheong, J. K. et al. IC261 induces cell cycle arrest and apoptosis of human cancer cells via CK1δ/ɛ and Wnt/β-catenin independent inhibition of mitotic spindle formation. Oncogene 30, 2558–2569 (2011). The kinase inhibitor IC261 was identified as an inhibitor of tubulin polymerization, which accounts for its selective cancer cell killing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Walton, K. M. et al. Selective inhibition of casein kinase 1ɛ minimally alters circadian clock period. J. Pharmacol. Exp. Ther. 330, 430–439 (2009).

    Article  CAS  PubMed  Google Scholar 

  23. Gurgis, F. et al. Cytotoxic activity of the MK2 inhibitor CMPD1 in glioblastoma cells is independent of MK2. Cell Death Discov. 1, 15028 (2015). This study showed that an allosteric inhibitor of MK2 activation potently inhibits tubulin polymerization and leads to paradoxical MK2 pathway activation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Mourey, R. J. et al. A benzothiophene inhibitor of mitogen-activated protein kinase-activated protein kinase 2 inhibits tumor necrosis factor α production and has oral anti-inflammatory efficacy in acute and chronic models of inflammation. J. Pharmacol. Exp. Ther. 333, 797–807 (2010).

    Article  CAS  PubMed  Google Scholar 

  25. Anderson, D. R. et al. Pyrrolopyridine inhibitors of mitogen-activated protein kinase-activated protein kinase 2 (MK-2). J. Med. Chem. 50, 2647–2654 (2007).

    Article  CAS  PubMed  Google Scholar 

  26. Ross-Macdonald, P. et al. Identification of a nonkinase target mediating cytotoxicity of novel kinase inhibitors. Mol. Cancer Ther. 7, 3490–3498 (2008).

    Article  CAS  PubMed  Google Scholar 

  27. Li, L. et al. Comparison of cancer cell survival triggered by microtubule damage after turning Dyrk1B kinase on and off. ACS Chem. Biol. 9, 731–742 (2014).

    Article  CAS  PubMed  Google Scholar 

  28. Mahale, S. et al. Antitumour potential of BPT: a dual inhibitor of cdk4 and tubulin polymerization. Cell Death Dis. 6, e1743 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Tanabe, K. Image-based compound profiling reveals a dual inhibitor of tyrosine kinase and microtubule polymerization. Sci. Rep. 6, 25095 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Marzaro, G. et al. Discovery of biarylaminoquinazolines as novel tubulin polymerization inhibitors. J. Med. Chem. 57, 4598–4605 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Carta, D. et al. Novel 3-substituted 7-phenylpyrrolo[3,2-f]quinolin-9(6H)-ones as single entities with multitarget antiproliferative activity. J. Med. Chem. 58, 7991–8010 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Wang, C.-Y. & Filippakopoulos, P. Beating the odds: BETs in disease. Trends Biochem. Sci. 40, 468–479 (2015).

    Article  CAS  PubMed  Google Scholar 

  33. Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Nicodeme, E. et al. Suppression of inflammation by a synthetic histone mimic. Nature 468, 1119–1123 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Devaiah, B. N. et al. BRD4 is an atypical kinase that phosphorylates serine2 of the RNA polymerase II carboxy-terminal domain. Proc. Natl Acad. Sci. USA 109, 6927–6932 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Manning, G., Whyte, D. B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912–1934 (2002).

    Article  CAS  PubMed  Google Scholar 

  37. Parry, D. et al. Dinaciclib (SCH 727965), a novel and potent cyclin-dependent kinase inhibitor. Mol. Cancer Ther. 9, 2344–2353 (2010).

    Article  CAS  PubMed  Google Scholar 

  38. Martin, M. P., Olesen, S. H., Georg, G. I. & Schönbrunn, E. Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains. ACS Chem. Biol. 8, 2360–2365 (2013).

    Article  CAS  PubMed  Google Scholar 

  39. Ember, S. W. J. et al. Acetyl-lysine binding site of bromodomain-containing protein 4 (BRD4) interacts with diverse kinase inhibitors. ACS Chem. Biol. 9, 1160–1171 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Steegmaier, M. et al. BI 2536, a potent and selective inhibitor of Polo-like kinase 1, inhibits tumor growth in vivo. Curr. Biol. 17, 316–322 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Pardanani, A. et al. TG101209, a small molecule JAK2-selective kinase inhibitor potently inhibits myeloproliferative disorder-associated JAK2V617F and MPLW515L//K mutations. Leukemia 21, 1658–1668 (2007).

    Article  CAS  PubMed  Google Scholar 

  42. Wernig, G. et al. Efficacy of TG101348, a selective JAK2 inhibitor, in treatment of a murine model of JAK2V617F-induced polycythemia vera. Cancer Cell 13, 311–320 (2008).

    Article  CAS  PubMed  Google Scholar 

  43. Ciceri, P. et al. Dual kinase-bromodomain inhibitors for rationally designed polypharmacology. Nat. Chem. Biol. 10, 305–312 (2014). A panel of 628 kinase inhibitors was screened for binding to bromodomains, and numerous inhibitors were identified as dual kinase and BET inhibitors. Inhibition of BET proteins has been shown to contribute to the anticancer activity of fedratinib and BI2536.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ramakrishnan, V. et al. TG101209, a novel JAK2 inhibitor, has significant in vitro activity in multiple myeloma and displays preferential cytotoxicity for CD45+ myeloma cells. Am. J. Hematol. 85, 675–686 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wyspianska, B. S. et al. BET protein inhibition shows efficacy against JAK2V617F-driven neoplasms. Leukemia 28, 88–97 (2014).

    Article  CAS  PubMed  Google Scholar 

  46. Dittmann, A. et al. The commonly used PI3-kinase probe LY294002 is an inhibitor of BET bromodomains. ACS Chem. Biol. 9, 495–502 (2014).

    Article  CAS  PubMed  Google Scholar 

  47. Poh, T. W. & Pervaiz, S. LY294002 and LY303511 sensitize tumor cells to drug-induced apoptosis via intracellular hydrogen peroxide production independent of the phosphoinositide 3-kinase-Akt pathway. Cancer Res. 65, 6264–6274 (2005).

    Article  CAS  PubMed  Google Scholar 

  48. Shenoy, K., Wu, Y. & Pervaiz, S. LY303511 enhances TRAIL sensitivity of SHEP-1 neuroblastoma cells via hydrogen peroxide–mediated mitogen-activated protein kinase activation and up-regulation of death receptors. Cancer Res. 69, 1941–1950 (2009).

    Article  CAS  PubMed  Google Scholar 

  49. Mellier, G., Liu, D., Bellot, G., Holme, A. L. & Pervaiz, S. Small molecule sensitization to TRAIL is mediated via nuclear localization, phosphorylation and inhibition of chaperone activity of Hsp27. Cell Death Dis. 4, e890 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Stratikopoulos, E. E. et al. Kinase and BET inhibitors together clamp inhibition of PI3K signaling and overcome resistance to therapy. Cancer Cell 27, 837–851 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Stuhlmiller, T. J. et al. Inhibition of lapatinib-induced kinome reprogramming in ERBB2-positive breast cancer by targeting BET family bromodomains. Cell Rep. 11, 390–404 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Bantscheff, M. et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25, 1035–1044 (2007).

    Article  CAS  PubMed  Google Scholar 

  53. Rix, U. et al. Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets. Blood 110, 4055–4063 (2007). References 52 and 53 were the first studies to identify a non-kinase target (NQO2) for protein kinase inhibitors.

    Article  CAS  PubMed  Google Scholar 

  54. Winger, J. A., Hantschel, O., Superti-Furga, G. & Kuriyan, J. The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2). BMC Struct. Biol. 9, 7 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Druker, B. J. et al. Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N. Engl. J. Med. 344, 1031–1037 (2001).

    Article  CAS  PubMed  Google Scholar 

  56. Long, D. J. et al. Disruption of dihydronicotinamide riboside:quinone oxidoreductase 2 (NQO2) leads to myeloid hyperplasia of bone marrow and decreased sensitivity to menadione toxicity. J. Biol. Chem. 277, 46131–46139 (2002).

    Article  CAS  PubMed  Google Scholar 

  57. Iskander, K., Paquet, M., Brayton, C. & Jaiswal, A. K. Deficiency of NRH:quinone oxidoreductase 2 increases susceptibility to 7,12-dimethylbenz(a)anthracene and benzo(a)pyrene-induced skin carcinogenesis. Cancer Res. 64, 5925–5928 (2004).

    Article  CAS  PubMed  Google Scholar 

  58. Xu, J., Patrick, B. A. & Jaiswal, A. K. NRH:quinone oxidoreductase 2 (NQO2) protein competes with the 20 S proteasome to stabilize transcription factor CCAAT enhancer-binding protein α (C/EBPα), leading to protection against γ radiation-induced myeloproliferative disease. J. Biol. Chem. 288, 34799–34808 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Janda, E. et al. Parkinsonian toxin-induced oxidative stress inhibits basal autophagy in astrocytes via NQO2/quinone oxidoreductase 2: implications for neuroprotection. Autophagy 11, 1063–1080 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Barf, T. & Kaptein, A. Irreversible protein kinase inhibitors: balancing the benefits and risks. J. Med. Chem. 55, 6243–6262 (2012).

    Article  CAS  PubMed  Google Scholar 

  61. Cheng, H. et al. Discovery of 1-{(3R,4R)-3-[({5-chloro-2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)methyl]-4-methoxypyrrolidin-1-yl}prop-2-en-1-one (PF-06459988), a potent, WT sparing, irreversible inhibitor of T790M-containing EGFR mutants. J. Med. Chem. 59, 2005–2024 (2016).

    Article  CAS  PubMed  Google Scholar 

  62. Lanning, B. R. et al. A road map to evaluate the proteome-wide selectivity of covalent kinase inhibitors. Nat. Chem. Biol. 10, 760–767 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Schwartz, P. A. et al. Covalent EGFR inhibitor analysis reveals importance of reversible interactions to potency and mechanisms of drug resistance. Proc. Natl Acad. Sci. USA 111, 173–178 (2014).

    Article  CAS  PubMed  Google Scholar 

  64. Honigberg, L. A. et al. The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy. Proc. Natl Acad. Sci. USA 107, 13075–13080 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Webber, J. L. & Tooze, S. A. Coordinated regulation of autophagy by p38α MAPK through mAtg9 and p38IP. EMBO J. 29, 27–40 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Wei, Y. et al. The stress-responsive kinases MAPKAPK2/MAPKAPK3 activate starvation-induced autophagy through Beclin 1 phosphorylation. eLife 4, e05289 (2015).

    Article  PubMed Central  Google Scholar 

  67. Desideri, E. et al. MAPK14/p38α-dependent modulation of glucose metabolism affects ROS levels and autophagy during starvation. Autophagy 10, 1652–1665 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Paillas, S. et al. MAPK14/p38α confers irinotecan resistance to TP53-defective cells by inducing survival autophagy. Autophagy 8, 1098–1112 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. de la Cruz-Morcillo, M. A. et al. P38MAPK is a major determinant of the balance between apoptosis and autophagy triggered by 5-fluorouracil: implication in resistance. Oncogene 31, 1073–1085 (2012).

    Article  CAS  PubMed  Google Scholar 

  70. Menon, M. B., Dhamija, S., Kotlyarov, A. & Gaestel, M. The problem of pyridinyl imidazole class inhibitors of MAPK14/p38α and MAPK11/p38β in autophagy research. Autophagy 11, 1425–1427 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Menon, M. B., Kotlyarov, A. & Gaestel, M. SB202190-induced cell type-specific vacuole formation and defective autophagy do not depend on p38 MAP kinase inhibition. PLoS ONE 6, e23054 (2011). References 70 and 71 provide evidence for SB203580 and SB202190 interference with autophagic flux in a p38-independent manner.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Zhang, H. et al. Induction of autophagy in hepatocellular carcinoma cells by SB203580 requires activation of AMPK and DAPK but not p38 MAPK. Apoptosis 17, 325–334 (2011).

    Article  CAS  Google Scholar 

  73. Silke, J., Rickard, J. A. & Gerlic, M. The diverse role of RIP kinases in necroptosis and inflammation. Nat. Immunol. 16, 689–697 (2015).

    Article  CAS  PubMed  Google Scholar 

  74. Brumatti, G. et al. The caspase-8 inhibitor emricasan combines with the SMAC mimetic birinapant to induce necroptosis and treat acute myeloid leukemia. Sci. Transl Med. 8, 339ra69 (2016).

    Article  PubMed  CAS  Google Scholar 

  75. Degterev, A. et al. Chemical inhibitor of nonapoptotic cell death with therapeutic potential for ischemic brain injury. Nat. Chem. Biol. 1, 112–119 (2005).

    Article  CAS  PubMed  Google Scholar 

  76. Degterev, A. et al. Identification of RIP1 kinase as a specific cellular target of necrostatins. Nat. Chem. Biol. 4, 313–321 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Takahashi, N. et al. Necrostatin-1 analogues: critical issues on the specificity, activity and in vivo use in experimental disease models. Cell Death Dis. 3, e437 (2012). This study identifies IDO as a target of necrostatin-1 and described the development of Nec-1s, which is an analogue that is more specific for RIPK1 and lacks the IDO-targeting effect.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Fallarino, F., Grohmann, U. & Puccetti, P. Indoleamine 2,3-dioxygenase: from catalyst to signaling function. Eur. J. Immunol. 42, 1932–1937 (2012).

    Article  CAS  PubMed  Google Scholar 

  79. Tattevin, P. et al. Enhanced indoleamine 2,3-dioxygenase activity in patients with severe sepsis and septic shock. J. Infect. Dis. 201, 956–966 (2010).

    Article  CAS  PubMed  Google Scholar 

  80. Jung, I. D. et al. Blockade of indoleamine 2,3-dioxygenase protects mice against lipopolysaccharide-induced endotoxin shock. J. Immunol. 182, 3146–3154 (2009).

    Article  CAS  PubMed  Google Scholar 

  81. Adams, S. et al. The kynurenine pathway in brain tumor pathogenesis. Cancer Res. 72, 5649–5657 (2012).

    Article  CAS  PubMed  Google Scholar 

  82. Dixon, S. J. et al. Pharmacological inhibition of cystine–glutamate exchange induces endoplasmic reticulum stress and ferroptosis. eLife 3, e02523 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Elkins, J. M. et al. Comprehensive characterization of the published kinase inhibitor set. Nat. Biotechnol. 34, 95–103 (2016).

    Article  CAS  PubMed  Google Scholar 

  84. Munoz, L., Selig, R., Yeung, Y., Peifer, C. & Laufer, S. A. Fluorescence polarisation binding assay to develop inhibitors of inactive p38a mitogen-activated protein kinase. Anal. Biochem. 401, 125–133 (2010).

    Article  CAS  PubMed  Google Scholar 

  85. Abbassi, R., Johns, T. G., Kassiou, M. & Munoz, L. DYRK1A in neurodegeneration and cancer: molecular basis and clinical implications. Pharmacol. Ther. 115, 87–98 (2015).

    Article  CAS  Google Scholar 

  86. Thorarensen, A. et al. ATP-mediated kinome selectivity: the missing link in understanding the contribution of individual JAK kinase isoforms to cellular signaling. ACS Chem. Biol. 9, 1552–1558 (2014).

    Article  CAS  PubMed  Google Scholar 

  87. Knight, Z. A. & Shokat, K. M. Features of selective kinase inhibitors. Chem. Biol. 12, 621–637 (2005).

    Article  CAS  PubMed  Google Scholar 

  88. Nomura, D. K., Dix, M. M. & Cravatt, B. F. Activity-based protein profiling for biochemical pathway discovery in cancer. Nat. Rev. Cancer 10, 630–638 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Wang, K. et al. Chemistry-based functional proteomics for drug target deconvolution. Exp. Rev. Proteomics 9, 293–310 (2012).

    Article  CAS  Google Scholar 

  90. Yang, P. & Liu, K. Activity-based protein profiling: recent advances in probe development and applications. ChemBioChem 16, 712–724 (2015).

    Article  CAS  PubMed  Google Scholar 

  91. Bunnage, M. E., Chekler, E. L. P. & Jones, L. H. Target validation using chemical probes. Nat. Chem. Biol. 9, 195–199 (2013).

    Article  CAS  PubMed  Google Scholar 

  92. Schenone, M., Dancik, V., Wagner, B. K. & Clemons, P. A. Target identification and mechanism of action in chemical biology and drug discovery. Nat. Chem. Biol. 9, 232–240 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Molina, D. M. et al. Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay. Science 341, 84–87 (2013). This study describes the development of CETSA, which is a straightforward method to demonstrate target engagement.

    Article  CAS  Google Scholar 

  94. Gad, H. et al. MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool. Nature 508, 215–221 (2014).

    Article  CAS  PubMed  Google Scholar 

  95. Kettle, J. G. et al. Potent and selective inhibitors of MTH1 probe its role in cancer cell survival. J. Med. Chem. 59, 2346–2361 (2016). This study demonstrates the important discovery that MTH1 is dispensable for cancer cell survival and that MTH1 inhibition does not induce cell death.

    Article  CAS  PubMed  Google Scholar 

  96. Huber, K. V. M. et al. Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy. Nature 508, 222–227 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Tan, B. X. et al. Assessing the efficacy of Mdm2/Mdm4-inhibiting stapled peptides using cellular thermal shift assays. Sci. Rep. 5, 12116 (2015).

    Article  PubMed  Google Scholar 

  98. Jafari, R. et al. The cellular thermal shift assay for evaluating drug target interactions in cells. Nat. Protoc. 9, 2100–2122 (2014).

    Article  CAS  PubMed  Google Scholar 

  99. Kawamura, T. et al. Proteomic profiling of small-molecule inhibitors reveals dispensability of MTH1 for cancer cell survival. Sci. Rep. 6, 26521 (2016). This study identifies tubulin as a target of the MTH1 inhibitors TH287 and TH588.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Savitski, M. M. et al. Tracking cancer drugs in living cells by thermal profiling of the proteome. Science 346, 1255784 (2014). This study shows the extension of CETSA to TPP and target identification.

    Article  PubMed  CAS  Google Scholar 

  101. Lecha, M., Puy, H. & Deybach, J.-C. Erythropoietic protoporphyria. Orphanet J. Rare Dis. 4, 19 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  102. Klaeger, S. et al. Chemical proteomics reveals ferrochelatase as a common off-target of kinase inhibitors. ACS Chem. Biol. 11, 1245–1254 (2016).

    Article  CAS  PubMed  Google Scholar 

  103. Reinhard, F. B. M. et al. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. Nat. Methods 12, 1129–1131 (2015).

    Article  CAS  PubMed  Google Scholar 

  104. Huber, K. V. M. et al. Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling. Nat. Methods 12, 1055–1057 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Jinek, M. et al. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Lisnock, J. et al. Molecular basis for p38 protein kinase inhibitor specificity. Biochemistry 37, 16573–16581 (1998).

    Article  CAS  PubMed  Google Scholar 

  109. Wacker, S., Houghtaling, B., Elemento, O. & Kapoor, T. Using transcriptome sequencing to identify mechanisms of drug action and resistance. Nat. Chem. Biol. 8, 235–237 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Smurnyy, Y. et al. DNA sequencing and CRISPR–Cas9 gene editing for target validation in mammalian cells. Nat. Chem. Biol. 10, 623–625 (2014).

    Article  CAS  PubMed  Google Scholar 

  111. Kasap, C., Elemento, O. & Kapoor, T. M. DrugTargetSeqR: a genomics- and CRISPR–Cas9-based method to analyze drug targets. Nat. Chem. Biol. 10, 626–628 (2014). References 110 and 111 established a platform using CRISPR–Cas9 methodology to validate targets of drugs in intact cells.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Neggers, J. E. et al. Identifying drug-target selectivity of small-molecule CRM1/XPO1 inhibitors by CRISPR/Cas9 genome editing. Chem. Biol. 22, 107–116 (2015).

    Article  CAS  PubMed  Google Scholar 

  113. Chu, J. et al. CRISPR-mediated drug-target validation reveals selective pharmacological inhibition of the RNA helicase, eIF4A. Cell Rep. 15, 2340–2347 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Wanzel, M. et al. CRISPR–Cas9-based target validation for p53-reactivating model compounds. Nat. Chem. Biol. 12, 22–28 (2016).

    Article  CAS  PubMed  Google Scholar 

  115. Bailey, F. P., Byrne, D. P., McSkimming, D., Kannan, N. & Eyers, P. A. Going for broke: targeting the human cancer pseudokinome. Biochem. J. 465, 195–211 (2015).

    Article  CAS  PubMed  Google Scholar 

  116. Eyers, Patrick, A. & Murphy, J. M. Dawn of the dead: protein pseudokinases signal new adventures in cell biology. Biochem. Soc. Trans. 41, 969–974 (2013).

    Article  CAS  Google Scholar 

  117. Weihua, Z. et al. Survival of cancer cells is maintained by EGFR independent of its kinase activity. Cancer Cell 13, 385–393 (2008). In this study, a new cancer cell survival mechanism that requires EGFR independently of its kinase activity is described.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  118. Tan, X., Thapa, N., Sun, Y., Anderson, R. A. A kinase-independent role for EGF receptor in autophagy initiation. Cell 160, 145–160 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Zhu, H., Cao, X., Ali-Osman, F., Keir, S. & Lo, H.-W. EGFR and EGFRvIII interact with PUMA to inhibit mitochondrial translocalization of PUMA and PUMA-mediated apoptosis independent of EGFR kinase activity. Cancer Lett. 294, 101–110 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Dannappel, M. et al. RIPK1 maintains epithelial homeostasis by inhibiting apoptosis and necroptosis. Nature 513, 90–94 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Polykratis, A. et al. Cutting edge: RIPK1 kinase inactive mice are viable and protected from TNF-induced necroptosis in vivo. J. Immunol. 193, 1539–1543 (2014).

    Article  CAS  PubMed  Google Scholar 

  122. Mandal, P. et al. RIP3 induces apoptosis independent of pronecrotic kinase activity. Mol. Cell 56, 481–495 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Newton, K. et al. Activity of protein kinase RIPK3 determines whether cells die by necroptosis or apoptosis. Science 343, 1357–1360 (2014).

    Article  CAS  PubMed  Google Scholar 

  124. Newton, K. RIPK1 and RIPK3: critical regulators of inflammation and cell death. Trends Cell Biol. 25, 347–353 (2015).

    Article  CAS  PubMed  Google Scholar 

  125. Medina, J. R. Selective 3-phosphoinositide-dependent kinase 1 (PDK1) inhibitors: dissecting the function and pharmacology of PDK1. J. Med. Chem. 56, 2726–2737 (2013).

    Article  CAS  PubMed  Google Scholar 

  126. Najafov, A., Shpiro, N. & Alessi, D. R. Akt is efficiently activated by PIF-pocket- and PtdIns(3,4,5)P3-dependent mechanisms leading to resistance to PDK1 inhibitor. Biochem. J. 448, 285–295 (2012).

    Article  CAS  PubMed  Google Scholar 

  127. Ellwood-Yen, K. et al. PDK1 attenuation fails to prevent tumor formation in PTEN-deficient transgenic mouse models. Cancer Res. 71, 3052–3065 (2011).

    Article  CAS  PubMed  Google Scholar 

  128. Busschots, K. et al. Substrate-selective inhibition of protein kinase PDK1 by small compounds that bind to the PIF-pocket allosteric docking site. Chem. Biol. 19, 1152–1163 (2012).

    Article  CAS  PubMed  Google Scholar 

  129. Rettenmaier, T. J. et al. A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proc. Natl Acad. Sci. USA 111, 18590–18595 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Alavi, A. S., Acevedo, L., Min, W. & Cheresh, D. A. Chemoresistance of endothelial cells induced by basic fibroblast growth factor depends on Raf-1-mediated inhibition of the proapoptotic kinase, ASK1. Cancer Res. 67, 2766–2772 (2007).

    Article  CAS  PubMed  Google Scholar 

  131. Advani, S. J. et al. Kinase-independent role for CRAF-driving tumour radioresistance via CHK2. Nat. Commun. 6, 8154 (2015).

    Article  PubMed  Google Scholar 

  132. Haling, J. R. et al. Structure of the BRAF-MEK complex reveals a kinase activity independent role for BRAF in MAPK signaling. Cancer Cell 26, 402–413 (2014).

    Article  CAS  PubMed  Google Scholar 

  133. Mielgo, A. et al. A MEK-independent role for CRAF in mitosis and tumor progression. Nat. Med. 17, 1641–1645 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Speroni, J., Federico, M. B., Mansilla, S. F., Soria, G. & Gottifredi, V. Kinase-independent function of checkpoint kinase 1 (Chk1) in the replication of damaged DNA. Proc. Natl Acad. Sci. USA 109, 7344–7349 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Au-Yeung, B. B. et al. A genetically selective inhibitor demonstrates a function for the kinase Zap70 in regulatory T cells independent of its catalytic activity. Nat. Immunol. 11, 1085–1092 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Middendorp, S., Dingjan, G. M., Maas, A., Dahlenborg, K. & Hendriks, R. W. Function of Bruton's tyrosine kinase during B cell development is partially independent of its catalytic activity. J. Immunol. 171, 5988–5996 (2003).

    Article  CAS  PubMed  Google Scholar 

  137. Vivanco, I. et al. A kinase-independent function of AKT promotes cancer cell survival. eLife 3, e03751 (2014).

    Article  PubMed Central  Google Scholar 

  138. Zheng, F. et al. Nuclear AURKA acquires kinase-independent transactivating function to enhance breast cancer stem cell phenotype. Nat. Commun. 7, 10180 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Hett, E. C. et al. Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis. Nat. Chem. Biol. 9, 398–405 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Rauch, J., Volinsky, N., Romano, D. & Kolch, W. The secret life of kinases: functions beyond catalysis. Cell Commun. Signal. 9, 23 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Mellinghoff, I. et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N. Engl. J. Med. 353, 2012–2024 (2005).

    Article  CAS  PubMed  Google Scholar 

  142. Hildebrand, J. M. et al. Activation of the pseudokinase MLKL unleashes the four-helix bundle domain to induce membrane localization and necroptotic cell death. Proc. Natl Acad. Sci. USA 111, 15072–15077 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Athuluri-Divakar, S. K. et al. A small molecule RAS-mimetic disrupts RAS association with effector proteins to block signaling. Cell 165, 643–655 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Janecek, M. et al. Allosteric modulation of AURKA kinase activity by a small-molecule inhibitor of its protein–protein interaction with TPX2. Sci. Rep. 6, 28528 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Frye, S. V. et al. Tackling reproducibility in academic preclinical drug discovery. Nat. Rev. Drug Discov. 14, 733–734 (2015).

    Article  CAS  PubMed  Google Scholar 

  146. Arrowsmith, C. H. et al. The promise and peril of chemical probes. Nat. Chem. Biol. 11, 536–541 (2015). This study established the Chemical Probes Portal through which scientists have access to highly selective inhibitors.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Blagg, J. & Workman, P. Chemical biology approaches to target validation in cancer. Curr. Opin. Pharmacol. 17, 87–100 (2014).

    Article  CAS  PubMed  Google Scholar 

  148. Baell, J. & Walters, M. A. Chemistry: chemical con artists foil drug discovery. Nature 513, 481–483 (2014).

    Article  CAS  PubMed  Google Scholar 

  149. Baell, J. B. Feeling nature's PAINS: natural products, natural product drugs, and Pan Assay INterference compounds (PAINS). J. Nat. Prod. 79, 616–628 (2016).

    Article  CAS  PubMed  Google Scholar 

  150. Bunnage, M. E., Gilbert, A. M., Jones, L. H. & Hett, E. C. Know your target, know your molecule. Nat. Chem. Biol. 11, 368–372 (2015). This is an excellent overview of questions to be asked and answered in drug discovery.

    Article  CAS  PubMed  Google Scholar 

  151. Baell, J. B. & Holloway, G. A. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J. Med. Chem. 53, 2719–2740 (2010).

    Article  CAS  PubMed  Google Scholar 

  152. Carter, M. et al. Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2. Nat. Commun. 6, 8871 (2015).

    Article  CAS  Google Scholar 

  153. Petrocchi, A. et al. Identification of potent and selective MTH1 inhibitors. Bioorg. Med. Chem. Lett. 26, 1503–1507 (2016).

    Article  CAS  PubMed  Google Scholar 

  154. Warpman Berglund, U. et al. Validation and development of MTH1 inhibitors for treatment of cancer. Ann. Oncol. 27, 2275–2283 (2016).

    Article  CAS  PubMed  Google Scholar 

  155. Muroi, M. et al. Application of proteomic profiling based on 2D-DIGE for classification of compounds according to the mechanism of action. Chem. Biol. 17, 460–470 (2010).

    Article  CAS  PubMed  Google Scholar 

  156. Minegishi, H. et al. Methyl 3-((6-methoxy-1,4-dihydroindeno[1,2-c]pyrazol-3-yl)amino)benzoate (GN39482) as a tubulin polymerization inhibitor identified by MorphoBase and ChemProteoBase profiling methods. J. Med. Chem. 58, 4230–4241 (2015).

    Article  CAS  PubMed  Google Scholar 

  157. Cappuzzo, F. et al. Management of crizotinib therapy for ALK-rearranged non-small cell lung carcinoma: an expert consensus. Lung Cancer 87, 89–95 (2015).

    Article  PubMed  Google Scholar 

  158. Schreiber, S. L. et al. Advancing biological understanding and therapeutics discovery with small-molecule probes. Cell 161, 1252–1265 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Lamb, J. et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313, 1929–1935 (2006).

    Article  CAS  PubMed  Google Scholar 

  160. Lamb, J. The Connectivity Map: a new tool for biomedical research. Nat. Rev. Cancer 7, 54–60 (2007).

    Article  CAS  PubMed  Google Scholar 

  161. Basu, A. et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 154, 1151–1161 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Seashore-Ludlow, B. et al. Harnessing connectivity in a large-scale small-molecule sensitivity dataset. Cancer Discov. 5, 1210–1223 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Rees, M. G. et al. Correlating chemical sensitivity and basal gene expression reveals mechanism of action. Nat. Chem. Biol. 12, 109–116 (2016).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

L.M. is a Cancer Institute New South Wales (NSW) Career Development Fellow supported by the National Health and Medical Research Council (NHMRC Project grant APP1106145), the Cancer Institute NSW (Grant reference: 15/CDF/1-07), the National Foundation for Medical Research and Innovation (NFMRI), The University of Sydney, the Brain Foundation Australia and the Sydney Medical School Foundation. The author thanks J. Silke for critical revision of the Review.

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Km (ATP)

The concentration of ATP that permits the kinase to achieve half the maximum rate of reaction (Vmax). Higher Km (ATP) values indicate a lower affinity of the kinase for ATP.

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Munoz, L. Non-kinase targets of protein kinase inhibitors. Nat Rev Drug Discov 16, 424–440 (2017). https://doi.org/10.1038/nrd.2016.266

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