Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Chemical genetic discovery of targets and anti-targets for cancer polypharmacology

Abstract

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Screening for an optimal therapeutic index in a Drosophila MEN2B model yields a polypharmacological kinase inhibitor.
Figure 2: Multiple-pathway inhibition by AD57 mitigates dRet-directed phenotypes.
Figure 3: Feedback downregulation of the Ras pathway through the anti-target Tor.
Figure 4: Balanced kinase polypharmacology provides optimal efficacy and toxicity.
Figure 5: Differential polypharmacology and outcomes from the AD compounds.

Similar content being viewed by others

References

  1. Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069–1075 (2008)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  2. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  3. Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008)

    Article  Google Scholar 

  5. Druker, B. J. Translation of the Philadelphia chromosome into therapy for CML. Blood 112, 4808–4817 (2008)

    Article  CAS  PubMed  Google Scholar 

  6. Flaherty, K. T. et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N. Engl. J. Med. 363, 809–819 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Geyer, C. E. et al. Lapatinib plus capecitabine for HER2-positive advanced breast cancer. N. Engl. J. Med. 355, 2733–2743 (2006)

    Article  CAS  PubMed  Google Scholar 

  8. Boss, D. S., Beijnen, J. H. & Schellens, J. H. Clinical experience with aurora kinase inhibitors: a review. Oncologist 14, 780–793 (2009)

    Article  CAS  PubMed  Google Scholar 

  9. 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)

    Article  CAS  PubMed  Google Scholar 

  10. 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)

    Article  CAS  PubMed  Google Scholar 

  11. Knight, Z. A., Lin, H. & Shokat, K. M. Targeting the cancer kinome through polypharmacology. Nature Rev. Cancer 10, 130–137 (2010)

    Article  CAS  Google Scholar 

  12. Karaman, M. W. et al. A quantitative analysis of kinase inhibitor selectivity. Nature Biotechnol. 26, 127–132 (2008)

    Article  CAS  Google Scholar 

  13. 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)

    Article  CAS  PubMed  Google Scholar 

  14. Wilhelm, S. et al. Discovery and development of sorafenib: a multikinase inhibitor for treating cancer. Nature Rev. Drug Discov. 5, 835–844 (2006)

    Article  CAS  Google Scholar 

  15. Ahmad, T. & Eisen, T. Kinase inhibition with BAY 43-9006 in renal cell carcinoma. Clin. Cancer Res. 10, 6388S–6392S (2004)

    Article  CAS  PubMed  Google Scholar 

  16. 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)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  17. Almeida, M. Q. & Stratakis, C. A. Solid tumors associated with multiple endocrine neoplasias. Cancer Genet. Cytogenet. 203, 30–36 (2010)

    Article  PubMed  PubMed Central  Google Scholar 

  18. Read, R. D. et al. A Drosophila model of multiple endocrine neoplasia type 2. Genetics 171, 1057–1081 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. 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)

    Article  CAS  PubMed  Google Scholar 

  20. 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)

    Article  CAS  PubMed  Google Scholar 

  21. 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)

    Article  CAS  PubMed  Google Scholar 

  22. 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)

    Article  CAS  PubMed  Google Scholar 

  23. 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)

    Article  CAS  PubMed  Google Scholar 

  24. 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)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 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)

    Article  CAS  PubMed  Google Scholar 

  26. 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)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Vidal, M. et al. Differing Src signaling levels have distinct outcomes in Drosophila. Cancer Res. 67, 10278–10285 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sawamoto, K. et al. The Drosophila secreted protein Argos regulates signal transduction in the Ras/MAPK pathway. Dev. Biol. 178, 13–22 (1996)

    Article  CAS  PubMed  Google Scholar 

  29. Guichard, A. et al. rhomboid and Star interact synergistically to promote EGFR/MAPK signaling during Drosophila wing vein development. Development 126, 2663–2676 (1999)

    CAS  PubMed  Google Scholar 

  30. 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 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)

    CAS  PubMed  Google Scholar 

  33. Alon, U. Network motifs: theory and experimental approaches. Nature Rev. Genet. 8, 450–461 (2007)

    Article  CAS  PubMed  Google Scholar 

  34. 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)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

Authors

Contributions

A.C.D. and T.K.D. contributed equally and are listed alphabetically. A.C.D. and T.K.D. conceived and designed experiments with K.M.S. and R.C. A.C.D. performed chemical synthesis, modelling, IC50 measurements, informatics and western blots on cancer cell lines. T.K.D. performed, imaged and analysed all Drosophila assays and cancer cell line viability assays. All authors discussed experimental data and wrote the manuscript.

Corresponding author

Correspondence to Kevan M. Shokat.

Ethics declarations

Competing interests

The authors are inventors on a joint University of California San Francisco and Mount Sinai patent application.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-4, Supplementary Figures 1-9 and Supplementary Methods. (PDF 8942 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11127

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing