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.

A whole-animal platform to advance a clinical kinase inhibitor into new disease space

Abstract

Synthetic tailoring of approved drugs for new indications is often difficult, as the most appropriate targets may not be readily apparent, and therefore few roadmaps exist to guide chemistry. Here, we report a multidisciplinary approach for accessing novel target and chemical space starting from an FDA-approved kinase inhibitor. By combining chemical and genetic modifier screening with computational modeling, we identify distinct kinases that strongly enhance ('pro-targets') or limit ('anti-targets') whole-animal activity of the clinical kinase inhibitor sorafenib in a Drosophila medullary thyroid carcinoma (MTC) model. We demonstrate that RAF—the original intended sorafenib target—and MKNK kinases function as pharmacological liabilities because of inhibitor-induced transactivation and negative feedback, respectively. Through progressive synthetic refinement, we report a new class of 'tumor calibrated inhibitors' with unique polypharmacology and strongly improved therapeutic index in fly and human MTC xenograft models. This platform provides a rational approach to creating new high-efficacy and low-toxicity drugs.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Identifying sorafenib in a drug screening using a Drosophila cancer model.
Figure 2: Generation and efficacy of TCIs.
Figure 3: Pro-targets and anti-targets for LS1-15 identified through genetic screening.
Figure 4: Developing novel TCIs APS5-16-2 and APS6-45 by reducing activity toward BRAF and Lk6/MKNK.
Figure 5: Inhibition of RAS–MAPK signaling by APS6-45.
Figure 6: The novel TCI APS6-45 displays exceptional in vivo efficacy.

Accession codes

Primary accessions

Protein Data Bank

References

  1. 1

    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).

    CAS  PubMed  Article  Google Scholar 

  2. 2

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  3. 3

    Hollingsworth, S.J. Precision medicine in oncology drug development: a pharma perspective. Drug Discov. Today 20, 1455–1463 (2015).

    PubMed  Article  Google Scholar 

  4. 4

    Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333–339 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  5. 5

    Lawrence, M.S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  6. 6

    Hay, M., Thomas, D.W., Craighead, J.L., Economides, C. & Rosenthal, J. Clinical development success rates for investigational drugs. Nat. Biotechnol. 32, 40–51 (2014).

    CAS  PubMed  Article  Google Scholar 

  7. 7

    Meanwell, N.A. Improving drug candidates by design: a focus on physicochemical properties as a means of improving compound disposition and safety. Chem. Res. Toxicol. 24, 1420–1456 (2011).

    CAS  PubMed  Article  Google Scholar 

  8. 8

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  9. 9

    Fleuren, E.D.G., Zhang, L., Wu, J. & Daly, R.J. The kinome 'at large' in cancer. Nat. Rev. Cancer 16, 83–98 (2016).

    CAS  PubMed  Article  Google Scholar 

  10. 10

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

    CAS  PubMed  Article  Google Scholar 

  11. 11

    Anastassiadis, T., Deacon, S.W., Devarajan, K., Ma, H. & Peterson, J.R. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nat. Biotechnol. 29, 1039–1045 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. 12

    Vidal, M., Wells, S., Ryan, A. & Cagan, R. 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).

    CAS  PubMed  Article  Google Scholar 

  13. 13

    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).

    CAS  PubMed  Article  Google Scholar 

  14. 14

    Dar, A.C., Das, T.K., Shokat, K.M. & Cagan, R.L. Chemical genetic discovery of targets and anti-targets for cancer polypharmacology. Nature 486, 80–84 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15

    Sonoshita, M. & Cagan, R.L. Modeling human cancers in Drosophila. Curr. Top. Dev. Biol. 121, 287–309 (2017).

    CAS  PubMed  Article  Google Scholar 

  16. 16

    Mulligan, L.M. RET revisited: expanding the oncogenic portfolio. Nat. Rev. Cancer 14, 173–186 (2014).

    CAS  PubMed  Article  Google Scholar 

  17. 17

    Lam, E.T. et al. Phase II clinical trial of sorafenib in metastatic medullary thyroid cancer. J. Clin. Oncol. 28, 2323–2330 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. 18

    Ahmed, M. et al. Analysis of the efficacy and toxicity of sorafenib in thyroid cancer: a phase II study in a UK based population. Eur. J. Endocrinol. 165, 315–322 (2011).

    CAS  PubMed  Article  Google Scholar 

  19. 19

    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).

    CAS  PubMed  Article  Google Scholar 

  20. 20

    Wilhelm, S.M. et al. Regorafenib (BAY 73-4506): a new oral multikinase inhibitor of angiogenic, stromal and oncogenic receptor tyrosine kinases with potent preclinical antitumor activity. Int. J. Cancer 129, 245–255 (2011).

    CAS  PubMed  Article  Google Scholar 

  21. 21

    Gilmartin, A.G. et al. GSK1120212 (JTP-74057) is an inhibitor of MEK activity and activation with favorable pharmacokinetic properties for sustained in vivo pathway inhibition. Clin. Cancer Res. 17, 989–1000 (2011).

    CAS  PubMed  Article  Google Scholar 

  22. 22

    Carlomagno, F. et al. BAY 43-9006 inhibition of oncogenic RET mutants. J. Natl. Cancer Inst. 98, 326–334 (2006).

    CAS  PubMed  Article  Google Scholar 

  23. 23

    Koh, Y.W. et al. Sorafenib and Mek inhibition is synergistic in medullary thyroid carcinoma in vitro. Endocr. Relat. Cancer 19, 29–38 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. 24

    de Castroneves, L.A. et al. Sorafenib for the treatment of progressive metastatic medullary thyroid cancer: efficacy and safety analysis. Thyroid 26, 414–419 (2016).

    PubMed  Article  CAS  Google Scholar 

  25. 25

    Capdevila, J. et al. Sorafenib in metastatic thyroid cancer. Endocr. Relat. Cancer 19, 209–216 (2012).

    CAS  PubMed  Article  Google Scholar 

  26. 26

    Hescot, S., Vignaux, O. & Goldwasser, F. Pancreatic atrophy–a new late toxic effect of sorafenib. N. Engl. J. Med. 369, 1475–1476 (2013).

    CAS  PubMed  Article  Google Scholar 

  27. 27

    Brose, M.S. et al. Sorafenib in radioactive iodine-refractory, locally advanced or metastatic differentiated thyroid cancer: a randomised, double-blind, phase 3 trial. Lancet 384, 319–328 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. 28

    Fathi, A.T. et al. Extensive squamous cell carcinoma of the skin related to use of sorafenib for treatment of FLT3-mutant acute myeloid leukemia. J. Clin. Oncol. 34, e70–e72 (2016).

    PubMed  Article  CAS  Google Scholar 

  29. 29

    Teo, T. et al. An integrated approach for discovery of highly potent and selective Mnk inhibitors: screening, synthesis and SAR analysis. Eur. J. Med. Chem. 103, 539–550 (2015).

    CAS  PubMed  Article  Google Scholar 

  30. 30

    Basnet, S.K.C. et al. Identification of a highly conserved allosteric binding site on Mnk1 and Mnk2. Mol. Pharmacol. 88, 935–948 (2015).

    CAS  PubMed  Article  Google Scholar 

  31. 31

    Ung, P.M. & Schlessinger, A. DFGmodel: predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors. ACS Chem. Biol. 10, 269–278 (2015).

    CAS  PubMed  Article  Google Scholar 

  32. 32

    Huang, A.M. & Rubin, G.M. A misexpression screen identifies genes that can modulate RAS1 pathway signaling in Drosophila melanogaster. Genetics 156, 1219–1230 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Karim, F.D. & Rubin, G.M. Ectopic expression of activated Ras1 induces hyperplastic growth and increased cell death in Drosophila imaginal tissues. Development 125, 1–9 (1998).

    CAS  PubMed  Google Scholar 

  34. 34

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. 35

    Shyamala, B.V. & Bhat, K.M. A positive role for patched-smoothened signaling in promoting cell proliferation during normal head development in Drosophila. Development 129, 1839–1847 (2002).

    CAS  PubMed  Google Scholar 

  36. 36

    Slack, C. et al. The Ras-Erk-ETS-signaling pathway is a drug target for longevity. Cell 162, 72–83 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. 37

    Hatzivassiliou, G. et al. RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth. Nature 464, 431–435 (2010).

    CAS  PubMed  Article  Google Scholar 

  38. 38

    Poulikakos, P.I., Zhang, C., Bollag, G., Shokat, K.M. & Rosen, N. RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF. Nature 464, 427–430 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. 39

    Lyons, J.F., Wilhelm, S., Hibner, B. & Bollag, G. Discovery of a novel Raf kinase inhibitor. Endocr. Relat. Cancer 8, 219–225 (2001).

    CAS  PubMed  Article  Google Scholar 

  40. 40

    Zarrinkar, P.P. et al. AC220 is a uniquely potent and selective inhibitor of FLT3 for the treatment of acute myeloid leukemia (AML). Blood 114, 2984–2992 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. 41

    Lacy, S.A., Miles, D.R. & Nguyen, L.T. Clinical pharmacokinetics and pharmacodynamics of cabozantinib. Clin. Pharmacokinet. 56, 477–491 (2017).

    PubMed  Article  Google Scholar 

  42. 42

    Zhang, L., Zhou, Q., Ma, L., Wu, Z. & Wang, Y. Meta-analysis of dermatological toxicities associated with sorafenib. Clin. Exp. Dermatol. 36, 344–350 (2011).

    CAS  PubMed  Article  Google Scholar 

  43. 43

    Arquier, N., Bourouis, M., Colombani, J. & Léopold, P. Drosophila Lk6 kinase controls phosphorylation of eukaryotic translation initiation factor 4E and promotes normal growth and development. Curr. Biol. 15, 19–23 (2005).

    CAS  PubMed  Article  Google Scholar 

  44. 44

    Joshi, S. & Platanias, L.C. Mnk kinase pathway: cellular functions and biological outcomes. World J. Biol. Chem. 5, 321–333 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  45. 45

    Brown, M.C. & Gromeier, M. MNK Controls mTORC1:Substrate Association through Regulation of TELO2 Binding with mTORC1. Cell Rep. 18, 1444–1457 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. 46

    Müller, K., Faeh, C. & Diederich, F. Fluorine in pharmaceuticals: looking beyond intuition. Science 317, 1881–1886 (2007).

    PubMed  Article  CAS  Google Scholar 

  47. 47

    Curran, D.P. Chemistry. Fluorous tags unstick messy chemical biology problems. Science 321, 1645–1646 (2008).

    CAS  PubMed  Article  Google Scholar 

  48. 48

    Gillis, E.P., Eastman, K.J., Hill, M.D., Donnelly, D.J. & Meanwell, N.A. Applications of fluorine in medicinal chemistry. J. Med. Chem. 58, 8315–8359 (2015).

    CAS  PubMed  Article  Google Scholar 

  49. 49

    Eisenhauer, E.A. et al. New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur. J. Cancer 45, 228–247 (2009).

    CAS  PubMed  Article  Google Scholar 

  50. 50

    Pina, C. & Pignoni, F. Tubby-RFP balancers for developmental analysis: FM7c 2xTb-RFP, CyO 2xTb-RFP, and TM3 2xTb-RFP. Genesis 50, 119–123 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51

    Moore, M. et al. Phase I study to determine the safety and pharmacokinetics of the novel Raf kinase and VEGFR inhibitor BAY 43-9006, administered for 28 days on/7 days off in patients with advanced, refractory solid tumors. Ann. Oncol. 16, 1688–1694 (2005).

    CAS  PubMed  Article  Google Scholar 

  52. 52

    Kurzrock, R. et al. Activity of XL184 (Cabozantinib), an oral tyrosine kinase inhibitor, in patients with medullary thyroid cancer. J. Clin. Oncol. 29, 2660–2666 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  53. 53

    Clark, J.W., Eder, J.P., Ryan, D., Lathia, C. & Lenz, H.-J.Safetyand pharmacokinetics of the dual action Raf kinase and vascular endothelial growth factor receptor inhibitor, BAY 43-9006, in patients with advanced, refractory solid tumors. Clin. Cancer Res. 11, 5472–5480 (2005).

    CAS  PubMed  Article  Google Scholar 

  54. 54

    Sali, A. & Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993).

    CAS  PubMed  Article  Google Scholar 

  55. 55

    Durrant, J.D., Votapka, L., Sørensen, J. & Amaro, R.E. POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics. J. Chem. Theory Comput. 10, 5047–5056 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. 56

    McGann, M. FRED pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 51, 578–596 (2011).

    CAS  PubMed  Article  Google Scholar 

  57. 57

    Harder, E. et al. OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. J. Chem. Theory Comput. 12, 281–296 (2016).

    CAS  PubMed  Article  Google Scholar 

  58. 58

    Li, L., Li, C., Zhang, Z. & Alexov, E. On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi. J. Chem. Theory Comput. 9, 2126–2136 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

Download references

Acknowledgements

We thank K. Shokat, B. DeVita, and M. Birtwistle for critical comments on the manuscript. We thank members of the Cagan, Dar, and Schlessinger laboratories for important discussions. We thank P. Smibert (New York Genome Center) for ptc>dRetM955T flies, and K. Cook (Bloomington Drosophila Stock Center) for kinome mutant fly lines.M.S. was supported by The Kyoto University Young Scholars Overseas Visit Program. M.S. and R.L.C. were supported by NIH grants U54OD020353, R01-CA170495, and R01-CA109730 and DOD grant W81XWH-15-1-0111. P.M.U.U. and A.S. were supported by NIH grant R01-GM108911, and also by Department of Defense grant W81XWH-15-1-0539 (A.S.). The Dar laboratory is supported by Innovation awards from the NIH (DP2 CA186570-01) and Damon Runyon-Rachleff Foundation. A.C.D. is a Pew-Stewart Scholar in Cancer Research and Young Investigator of the Pershing-Square Sohn Cancer Research Alliance. We thank OpenEye Scientific Software, Inc. for granting us access to its high-performance molecular modeling applications through its academic license program. This work was also supported by Scientific Computing at the Icahn School of Medicine at Mount Sinai and NCI grant P30 CA196521 to the Tisch Cancer Institute. The data and reagents that support the findings of this study, including fly lines, homology models, and compounds, are available from the corresponding authors upon request.

Author information

Affiliations

Authors

Contributions

M.S., A.P.S., R.L.C., and A.C.D. designed the research; P.M.U.U. and A.S. designed the computational analysis. M.S. designed and conducted functional studies. A.P.S. designed and conducted chemical syntheses. L.S. assisted with chemical synthesis. M.A.M. assisted with Lk6 genetic analysis. A.Y.M. and A.R. assisted with RAF anti-target analysis in cell lines. All authors analyzed data, and M.S., A.P.S., P.M.U.U., A.S., R.L.C., and A.C.D. wrote the manuscript.

Corresponding authors

Correspondence to Ross L Cagan or Arvin C Dar.

Ethics declarations

Competing interests

M.S., A.P.S., R.L.C., and A.C.D. are inventors on a patent application submitted by the Icahn School of Medicine at Mount Sinai.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–5, Supplementary Figures 1–11 (PDF 5470 kb)

41589_2018_BFnchembio2556_MOESM2_ESM.pdf

Reporting Summary (PDF 129 kb)

Supplementary Data Set 1

In vitro inhibition of kinases by APS6-45 (10). (XLSX 53 kb)

Supplementary Data Set 2

Numbers of samples (XLSX 45 kb)

Supplementary Note 1

Synthetic procedures (PDF 9341 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Sonoshita, M., Scopton, A., Ung, P. et al. A whole-animal platform to advance a clinical kinase inhibitor into new disease space. Nat Chem Biol 14, 291–298 (2018). https://doi.org/10.1038/nchembio.2556

Download citation

Further reading

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