The complexity of cancer has led to recent interest in polypharmacological approaches for developing kinase-inhibitor drugs; however, optimal kinase-inhibition profiles remain difficult to predict. Using a Ret-kinase-driven Drosophila model of multiple endocrine neoplasia type 2 and kinome-wide drug profiling, here we identify that AD57 rescues oncogenic Ret-induced lethality, whereas related Ret inhibitors imparted reduced efficacy and enhanced toxicity. Drosophila genetics and compound profiling defined three pathways accounting for the mechanistic basis of efficacy and dose-limiting toxicity. Inhibition of Ret plus Raf, Src and S6K was required for optimal animal survival, whereas inhibition of the ‘anti-target’ Tor led to toxicity owing to release of negative feedback. Rational synthetic tailoring to eliminate Tor binding afforded AD80 and AD81, compounds featuring balanced pathway inhibition, improved efficacy and low toxicity in Drosophila and mammalian multiple endocrine neoplasia type 2 models. Combining kinase-focused chemistry, kinome-wide profiling and Drosophila genetics provides a powerful systems pharmacology approach towards developing compounds with a maximal therapeutic index.
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Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069–1075 (2008)
Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007)
Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007)
Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008)
Druker, B. J. Translation of the Philadelphia chromosome into therapy for CML. Blood 112, 4808–4817 (2008)
Flaherty, K. T. et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N. Engl. J. Med. 363, 809–819 (2010)
Geyer, C. E. et al. Lapatinib plus capecitabine for HER2-positive advanced breast cancer. N. Engl. J. Med. 355, 2733–2743 (2006)
Boss, D. S., Beijnen, J. H. & Schellens, J. H. Clinical experience with aurora kinase inhibitors: a review. Oncologist 14, 780–793 (2009)
Haura, E. B. et al. A Phase II study of PD-0325901, an oral MEK inhibitor, in previously treated patients with advanced non-small cell lung cancer. Clin. Cancer Res. 16, 2450–2457 (2010)
LoRusso, P. M. et al. Phase I pharmacokinetic and pharmacodynamic study of the oral MAPK/ERK kinase inhibitor PD-0325901 in patients with advanced cancers. Clin. Cancer Res. 16, 1924–1937 (2010)
Knight, Z. A., Lin, H. & Shokat, K. M. Targeting the cancer kinome through polypharmacology. Nature Rev. Cancer 10, 130–137 (2010)
Karaman, M. W. et al. A quantitative analysis of kinase inhibitor selectivity. Nature Biotechnol. 26, 127–132 (2008)
Mestres, J. et al. The topology of drug-target interaction networks: implicit dependence on drug properties and target families. Mol. Biosyst. 5, 1051–1057 (2009)
Wilhelm, S. et al. Discovery and development of sorafenib: a multikinase inhibitor for treating cancer. Nature Rev. Drug Discov. 5, 835–844 (2006)
Ahmad, T. & Eisen, T. Kinase inhibition with BAY 43-9006 in renal cell carcinoma. Clin. Cancer Res. 10, 6388S–6392S (2004)
Lairmore, T. C. et al. A 1.5-megabase yeast artificial chromosome contig from human chromosome 10q11.2 connecting three genetic loci (RET, D10S94, and D10S102) closely linked to the MEN2A locus. Proc. Natl Acad. Sci. USA 90, 492–496 (1993)
Almeida, M. Q. & Stratakis, C. A. Solid tumors associated with multiple endocrine neoplasias. Cancer Genet. Cytogenet. 203, 30–36 (2010)
Read, R. D. et al. A Drosophila model of multiple endocrine neoplasia type 2. Genetics 171, 1057–1081 (2005)
Vidal, M. et al. ZD6474 suppresses oncogenic RET isoforms in a Drosophila model for type 2 multiple endocrine neoplasia syndromes and papillary thyroid carcinoma. Cancer Res. 65, 3538–3541 (2005)
Wells, S. A., Jr et al. Vandetanib in patients with locally advanced or metastatic medullary thyroid cancer: a randomized, double-blind Phase III trial. J. Clin. Oncol. 30, 134–141 (2012)
Hinz, U., Giebel, B. & Campos-Ortega, J. A. The basic-helix-loop-helix domain of Drosophila lethal of scute protein is sufficient for proneural function and activates neurogenic genes. Cell 76, 77–87 (1994)
Wilhelm, S. M. et al. BAY 43-9006 exhibits broad spectrum oral antitumor activity and targets the RAF/MEK/ERK pathway and receptor tyrosine kinases involved in tumor progression and angiogenesis. Cancer Res. 64, 7099–7109 (2004)
Sun, L. et al. Discovery of 5-[5-fluoro-2-oxo-1,2- dihydroindol-(3Z)-ylidenemethyl]-2,4- dimethyl-1H-pyrrole-3-carboxylic acid (2-diethylaminoethyl)amide, a novel tyrosine kinase inhibitor targeting vascular endothelial and platelet-derived growth factor receptor tyrosine kinase. J. Med. Chem. 46, 1116–1119 (2003)
Dar, A. C., Lopez, M. S. & Shokat, K. M. Small molecule recognition of c-Src via the imatinib-binding conformation. Chem. Biol. 15, 1015–1022 (2008)
Vidal, M., Larson, D. E. & Cagan, R. L. Csk-deficient boundary cells are eliminated from normal Drosophila epithelia by exclusion, migration, and apoptosis. Dev. Cell 10, 33–44 (2006)
Read, R. D., Bach, E. A. & Cagan, R. L. Drosophila C-terminal Src kinase negatively regulates organ growth and cell proliferation through inhibition of the Src, Jun N-terminal kinase, and STAT pathways. Mol. Cell. Biol. 24, 6676–6689 (2004)
Vidal, M. et al. Differing Src signaling levels have distinct outcomes in Drosophila. Cancer Res. 67, 10278–10285 (2007)
Sawamoto, K. et al. The Drosophila secreted protein Argos regulates signal transduction in the Ras/MAPK pathway. Dev. Biol. 178, 13–22 (1996)
Guichard, A. et al. rhomboid and Star interact synergistically to promote EGFR/MAPK signaling during Drosophila wing vein development. Development 126, 2663–2676 (1999)
Gedaly, R. et al. PI-103 and sorafenib inhibit hepatocellular carcinoma cell proliferation by blocking Ras/Raf/MAPK and PI3K/AKT/mTOR pathways. Anticancer Res. 30, 4951–4958 (2010)
Carracedo, A. et al. Inhibition of mTORC1 leads to MAPK pathway activation through a PI3K-dependent feedback loop in human cancer. J. Clin. Invest. 118, 3065–3074 (2008)
Carlomagno, F. et al. ZD6474, an orally available inhibitor of KDR tyrosine kinase activity, efficiently blocks oncogenic RET kinases. Cancer Res. 62, 7284–7290 (2002)
Alon, U. Network motifs: theory and experimental approaches. Nature Rev. Genet. 8, 450–461 (2007)
Brachmann, C. B. et al. The Drosophila Bcl-2 family member dBorg-1 functions in the apoptotic response to UV-irradiation. Curr. Biol. 10, 547–550 (2000)
We thank the Bloomington Stock Center, Vienna Drosophila RNAi Center and C. Pfleger for reagents. T.K.D. and R.C. were supported by National Institutes of Health grants R01CA109730 and R01CA084309 and American Cancer Society Grant 120616-RSGM-11-018-01-CDD. T.K.D. was also supported by American Cancer Society Grant 120886-PFM-11-137-01-DDC. We thank members of the Shokat and Cagan laboratories for discussions. We thank members of the SelectScreen team at Invitrogen, in particular K. Vogel, for performing kinase-profiling services. K.M.S. thanks NIH R01EB001987, P01 CA081403-11 and The Waxman Foundation.
The authors are inventors on a joint University of California San Francisco and Mount Sinai patent application.
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Dar, A., Das, T., Shokat, K. et al. Chemical genetic discovery of targets and anti-targets for cancer polypharmacology. Nature 486, 80–84 (2012). https://doi.org/10.1038/nature11127
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