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.

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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.

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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.

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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.

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Correspondence to Kevan M. Shokat.

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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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