Abstract

Precision medicines exert selective pressure on tumour cells that leads to the preferential growth of resistant subpopulations, necessitating the development of next-generation therapies to treat the evolving cancer. The PIK3CA–AKT–mTOR pathway is one of the most commonly activated pathways in human cancers1, which has led to the development of small-molecule inhibitors that target various nodes in the pathway. Among these agents, first-generation mTOR inhibitors (rapalogs) have caused responses in ‘N-of-1’ cases, and second-generation mTOR kinase inhibitors (TORKi) are currently in clinical trials2,3,4. Here we sought to delineate the likely resistance mechanisms to existing mTOR inhibitors in human cell lines, as a guide for next-generation therapies. The mechanism of resistance to the TORKi was unusual in that intrinsic kinase activity of mTOR was increased, rather than a direct active-site mutation interfering with drug binding. Indeed, identical drug-resistant mutations have been also identified in drug-naive patients, suggesting that tumours with activating MTOR mutations will be intrinsically resistant to second-generation mTOR inhibitors. We report the development of a new class of mTOR inhibitors that overcomes resistance to existing first- and second-generation inhibitors. The third-generation mTOR inhibitor exploits the unique juxtaposition of two drug-binding pockets to create a bivalent interaction that allows inhibition of these resistant mutants.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    & The phosphatidylinositol 3-kinase AKT pathway in human cancer. Nature Rev. Cancer 2, 489–501 (2002)

  2. 2.

    et al. First-in-human pharmacokinetic and pharmacodynamic study of the dual m-TORC 1/2 inhibitor AZD2014. Clin. Cancer Res. 21, 3412–3419 (2015)

  3. 3.

    et al. Genome sequencing identifies a basis for everolimus sensitivity. Science 338, 221 (2012)

  4. 4.

    et al. Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib. Cancer Discov . 4, 546–553 (2014)

  5. 5.

    et al. Response and acquired resistance to everolimus in anaplastic thyroid cancer. N. Engl. J. Med. 371, 1426–1433 (2014)

  6. 6.

    et al. Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2. PLoS Biol. 7, e38 (2009)

  7. 7.

    et al. An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1. J. Biol. Chem. 284, 8023–8032 (2009)

  8. 8.

    et al. mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science 328, 1172–1176 (2010)

  9. 9.

    et al. Control of p70 s6 kinase by kinase activity of FRAP in vivo. Nature 377, 441–446 (1995)

  10. 10.

    , , & Identification of an 11-kDa FKBP12-rapamycin-binding domain within the 289-kDa FKBP12-rapamycin-associated protein and characterization of a critical serine residue. Proc. Natl Acad. Sci. USA 92, 4947–4951 (1995)

  11. 11.

    et al. Regulation of eIF-4E BP1 phosphorylation by mTOR. J. Biol. Chem. 272, 26457–26463 (1997)

  12. 12.

    & TOR mutations confer rapamycin resistance by preventing interaction with FKBP12-rapamycin. J. Biol. Chem. 270, 27531–27537 (1995)

  13. 13.

    et al. mTOR kinase structure, mechanism and regulation. Nature 497, 217–223 (2013)

  14. 14.

    et al. A diverse array of cancer-associated MTOR mutations are hyperactivating and can predict rapamycin sensitivity. Cancer Discov . 4, 554–563 (2014)

  15. 15.

    et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov . 2, 401–404 (2012)

  16. 16.

    , & Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors. Angew. Chem. Int. Ed. 37, 2754–2794 (1998)

  17. 17.

    et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485, 55–61 (2012)

  18. 18.

    Molecular Operating Environment (Chemical Computing Group Inc., Montreal, Canada, 2016)

  19. 19.

    et al. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. J. Am. Chem. Soc. 125, 4087–4096 (2003)

  20. 20.

    et al. FK506-binding protein (FKBP) partitions a modified HIV protease inhibitor into blood cells and prolongs its lifetime in vivo. Proc. Natl Acad. Sci. USA 106, 1336–1341 (2009)

  21. 21.

    et al. A phase I study evaluating continuous and intermittent AZD2014 in combination with fulvestrant in patients with ER+ advanced metastatic breast cancer (abstract). Proc. AACR 106th Ann. Meeting CT233.25 (AACR, 2015)

  22. 22.

    , , & The best of both worlds? Bitopic orthosteric/allosteric ligands of G protein-coupled receptors. Annu. Rev. Pharmacol. Toxicol. 52, 153–178 (2012)

  23. 23.

    , , , & Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A–Cdk2 complex. Nature 382, 325–331 (1996)

  24. 24.

    et al. Design and synthesis of benzoazepin-2-one analogs as allosteric binders targeting the PIF pocket of PDK1. Bioorg. Med. Chem. Lett. 20, 3897–3902 (2010)

  25. 25.

    et al. A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK. Nature 472, 366–369 (2011)

  26. 26.

    et al. Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor. Nature 518, 240–244 (2015)

  27. 27.

    et al. BRAF mutants evade ERK-dependent feedback by different mechanisms that determine their sensitivity to pharmacologic inhibition. Cancer Cell 28, 370–383 (2015)

  28. 28.

    , , & Analysis of kinase inhibitor selectivity using a thermodynamics-based partition index. J. Med. Chem. 53, 4502–4510 (2010)

  29. 29.

    et al. mTOR kinase inhibition causes feedback-dependent biphasic regulation of AKT signaling. Cancer Discov . 1, 248–259 (2011)

Download references

Acknowledgements

N.R. would like to thank the National Institutes of Health (NIH) (P01 CA094060) for funding, as well as the Breast Cancer Research Foundation grant and the National Cancer Institute Cancer Center Support grant P30 CA008748, W. H. Goodwin and A. Goodwin, the Commonwealth Foundation for Cancer Research, The Center for Experimental Therapeutics at Memorial Sloan Kettering Cancer Center, and the team up for a Cure Fund. K.M.S. would like to thank the NIH P50 AA017072, the Stand Up 2 Cancer Lung Cancer Dream Team, The Samuel Waxman Cancer Research Foundation and the Howard Hughes Medical Institute for funding. We would like to thank R. Mukherjee, S. Schwartz, J. Taunton and B. Roth for helpful comments.

Author information

Author notes

    • Vanessa S. Rodrik-Outmezguine
    • , Masanori Okaniwa
    •  & Zhan Yao

    These authors contributed equally to this work.

Affiliations

  1. Program in Molecular Pharmacology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Vanessa S. Rodrik-Outmezguine
    • , Zhan Yao
    • , Arpitha Banaji
    •  & Neal Rosen
  2. Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, USA

    • Masanori Okaniwa
    • , Chris J. Novotny
    •  & Kevan M. Shokat
  3. AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK

    • Claire McWhirter
    • , Derek G. Barratt
    • , Sabina Cosulich
    •  & Teresa Klinowska
  4. Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Helen Won
    •  & Mike Berger
  5. Anti-Tumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA

    • Wai Wong
    •  & Elisa de Stanchina
  6. Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA

    • Neal Rosen
  7. Department of Chemistry, University of California Berkeley, Berkeley, California 94720, USA

    • Kevan M. Shokat

Authors

  1. Search for Vanessa S. Rodrik-Outmezguine in:

  2. Search for Masanori Okaniwa in:

  3. Search for Zhan Yao in:

  4. Search for Chris J. Novotny in:

  5. Search for Claire McWhirter in:

  6. Search for Arpitha Banaji in:

  7. Search for Helen Won in:

  8. Search for Wai Wong in:

  9. Search for Mike Berger in:

  10. Search for Elisa de Stanchina in:

  11. Search for Derek G. Barratt in:

  12. Search for Sabina Cosulich in:

  13. Search for Teresa Klinowska in:

  14. Search for Neal Rosen in:

  15. Search for Kevan M. Shokat in:

Contributions

V.S.R.-O., M.O., Z.Y., C.J.N., N.R. and K.M.S. conceived the project, designed and analysed the experiments, and wrote the manuscript. V.S.R.-O., M.O., Z.Y., C.J.N., C.M., A.B., W.W., D.G.B., S.C. and T.K. performed and supervised the laboratory experiments. H.W. and M.B. performed and supervised the IMPACT sequencing and analysis. E.d.S. designed and supervised the in vivo experiments.

Competing interests

K.M.S. is an inventor on patents related to MLN0128 held by the University of California San Francisco (UCSF), and sublicensed to Takeda Pharmaceuticals. N.R. and K.M.S. are consultants and M.O. is an employee at Takeda Pharmaceuticals Company Limited, which is conducting MLN0128 clinical trials. C.M., D.G.B., S.C. and T.K. are employees at AstraZeneca, which is conducting AZD2014 (mTOR kinase inhibitor) trials. K.M.S. and M.O. are inventors on a patent application related to RapaLink held by UCSF and licensed to Kura Oncology. K.M.S. is a shareholder in Kura Oncology, K.M.S. and N.R. are consultants to Kura Oncology.

Corresponding authors

Correspondence to Neal Rosen or Kevan M. Shokat.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Figures 1-6 (the uncropped blots), Supplementary Table 1 and Supplementary Methods.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature17963

Further reading

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.