Abstract

Immunomodulatory drugs bind to cereblon (CRBN) to confer differentiated substrate specificity on the CRL4CRBN E3 ubiquitin ligase. Here we report the identification of a new cereblon modulator, CC-885, with potent anti-tumour activity. The anti-tumour activity of CC-885 is mediated through the cereblon-dependent ubiquitination and degradation of the translation termination factor GSPT1. Patient-derived acute myeloid leukaemia tumour cells exhibit high sensitivity to CC-885, indicating the clinical potential of this mechanism. Crystallographic studies of the CRBN–DDB1–CC-885–GSPT1 complex reveal that GSPT1 binds to cereblon through a surface turn containing a glycine residue at a key position, interacting with both CC-885 and a ‘hotspot’ on the cereblon surface. Although GSPT1 possesses no obvious structural, sequence or functional homology to previously known cereblon substrates, mutational analysis and modelling indicate that the cereblon substrate Ikaros uses a similar structural feature to bind cereblon, suggesting a common motif for substrate recruitment. These findings define a structural degron underlying cereblon ‘neosubstrate’ selectivity, and identify an anti-tumour target rendered druggable by cereblon modulation.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Protein Data Bank

Data deposits

Coordinates for the structure of cereblon–DDB1–CC-885–GSPT1 have been deposited in the Protein Data Bank with the accession code 5HXB.

References

  1. 1.

    et al. Identification of a primary target of thalidomide teratogenicity. Science 327, 1345–1350 (2010)

  2. 2.

    , , & Current treatment landscape for relapsed and/or refractory multiple myeloma. Nat. Rev. Clin. Oncol. 12, 42–54 (2015)

  3. 3.

    et al. Cereblon is a direct protein target for immunomodulatory and antiproliferative activities of lenalidomide and pomalidomide. Leukemia 26, 2326–2335 (2012)

  4. 4.

    et al. Cereblon expression is required for the antimyeloma activity of lenalidomide and pomalidomide. Blood 118, 4771–4779 (2011)

  5. 5.

    et al. Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS. Nature 523, 183–188 (2015)

  6. 6.

    et al. Molecular architecture and assembly of the DDB1–CUL4A ubiquitin ligase machinery. Nature 443, 590–593 (2006)

  7. 7.

    et al. CUL4–DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat. Cell Biol. 8, 1277–1283 (2006)

  8. 8.

    , , , & A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1. Mol. Cell 23, 709–721 (2006)

  9. 9.

    , , , & DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4–ROC1 ubiquitin ligases. Genes Dev. 20, 2949–2954 (2006)

  10. 10.

    et al. Structure of the human Cereblon–DDB1–lenalidomide complex reveals basis for responsiveness to thalidomide analogs. Nat. Struct. Mol. Biol. 21, 803–809 (2014)

  11. 11.

    et al. Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512, 49–53 (2014). 10.1038/nature13527

  12. 12.

    & The Ikaros gene family: transcriptional regulators of hematopoiesis and immunity. Mol. Immunol. 48, 1272–1278 (2011)

  13. 13.

    et al. The role of Ikaros in human erythroid differentiation. Blood 111, 1138–1146 (2008)

  14. 14.

    et al. Immunomodulatory agents lenalidomide and pomalidomide co-stimulate T cells by inducing degradation of T cell repressors Ikaros and Aiolos via modulation of the E3 ubiquitin ligase complex CRL4(CRBN.). Br. J. Haematol. 164, 811–821 (2014)

  15. 15.

    et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014)

  16. 16.

    et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014)

  17. 17.

    et al. Structural insights into eRF3 and stop codon recognition by eRF1. Genes Dev. 23, 1106–1118 (2009)

  18. 18.

    et al. Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1. Cell Reports 8, 59–65 (2014)

  19. 19.

    et al. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO J. 14, 4065–4072 (1995)

  20. 20.

    et al. Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. Nature 417, 975–978 (2002)

  21. 21.

    et al. Structure of an HIF-1α-pVHL complex: hydroxyproline recognition in signaling. Science 296, 1886–1889 (2002)

  22. 22.

    , & Cyclin is degraded by the ubiquitin pathway. Nature 349, 132–138 (1991)

  23. 23.

    et al. Jasmonate perception by inositol-phosphate-potentiated COI1–JAZ co-receptor. Nature 468, 400–405 (2010)

  24. 24.

    et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640–645 (2007)

  25. 25.

    , & A yeast gene required for the G1-to-S transition encodes a protein containing an A-kinase target site and GTPase domain. EMBO J. 7, 1175–1182 (1988)

  26. 26.

    , & Human eukaryotic release factor 3a depletion causes cell cycle arrest at G1 phase through inhibition of the mTOR pathway. Mol. Cell. Biol. 27, 5619–5629 (2007)

  27. 27.

    Protein degradation: prime time for PROTACs. Nat. Chem. Biol. 11, 634–635 (2015)

  28. 28.

    et al. Drug development. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348, 1376–1381 (2015)

  29. 29.

    et al. Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. Chem. Biol. 22, 755–763 (2015)

  30. 30.

    , & Structural basis of lenalidomide-induced CK1α degradation by the CRL4(CRBN) ubiquitin ligase. Nature 532, 127–130 (2016)

  31. 31.

    et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

  32. 32.

    , , & Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

  33. 33.

    et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011)

  34. 34.

    et al. Pharmacological profiles of acute myeloid leukemia treatments in patient samples by automated flow cytometry: a bridge to individualized medicine. Clin. Lymphoma Myeloma Leuk. 14, 305–318 (2014)

Download references

Acknowledgements

Thanks to G. Reyes, C. Havens, P. Jackson and H. Hadjivassiliou for discussions relating to this manuscript, and P. Jackson, J. Hansen, M. Correa, B. Fahr, M. Abbasian, E. Ambing, E. Rychak, D. Mendy and K. Hughes for technical assistance. We thank K. Motamedchaboki (Proteomics Core, Sanford Burnham Prebys Medical Discovery Institute) for mass spectrometry-based proteomic analysis. Thanks to J. Ballesteros and P. Hernandez at Vivia for patient sample testing. Parts of this work were conducted at the Advanced Light Source. The Berkeley Center for Structural Biology is supported in part by the National Institutes of Health, National Institute of General Medical Sciences, and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under contract No. DE-AC02-05CH11231. This work was also supported by Grant-in-Aid for Scientific Research on Innovative Areas “Chemical Biology of Natural Products” from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (23102002 to H.H.), by JST, PRESTO (T.I.) and by Grant-in-Aid for Young Scientists (B) from MEXT (26750374 to T.I.).

Author information

Author notes

    • Mary E. Matyskiela
    • , Gang Lu
    •  & Takumi Ito

    These authors contributed equally to this work.

Affiliations

  1. Celgene Corporation, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, USA

    • Mary E. Matyskiela
    • , Gang Lu
    • , Barbra Pagarigan
    • , Chin-Chun Lu
    • , Karen Miller
    • , Wei Fang
    • , Nai-Yu Wang
    • , Derek Nguyen
    • , Jack Houston
    • , Gilles Carmel
    • , Tam Tran
    • , Mariko Riley
    • , Svetlana Gaidarova
    • , Shuichan Xu
    • , Alexander L. Ruchelman
    • , James Carmichael
    • , Thomas O. Daniel
    • , Brian E. Cathers
    • , Antonia Lopez-Girona
    •  & Philip P. Chamberlain
  2. Department of Nanoparticle Translational Research, Tokyo Medical University, Shinjuku-ku, Tokyo 160-8402, Japan

    • Takumi Ito
    •  & Hiroshi Handa
  3. The Scripps Research Institute, San Diego, California 92121, USA

    • Lyn’Al Nosaka
    •  & Gabriel C. Lander

Authors

  1. Search for Mary E. Matyskiela in:

  2. Search for Gang Lu in:

  3. Search for Takumi Ito in:

  4. Search for Barbra Pagarigan in:

  5. Search for Chin-Chun Lu in:

  6. Search for Karen Miller in:

  7. Search for Wei Fang in:

  8. Search for Nai-Yu Wang in:

  9. Search for Derek Nguyen in:

  10. Search for Jack Houston in:

  11. Search for Gilles Carmel in:

  12. Search for Tam Tran in:

  13. Search for Mariko Riley in:

  14. Search for Lyn’Al Nosaka in:

  15. Search for Gabriel C. Lander in:

  16. Search for Svetlana Gaidarova in:

  17. Search for Shuichan Xu in:

  18. Search for Alexander L. Ruchelman in:

  19. Search for Hiroshi Handa in:

  20. Search for James Carmichael in:

  21. Search for Thomas O. Daniel in:

  22. Search for Brian E. Cathers in:

  23. Search for Antonia Lopez-Girona in:

  24. Search for Philip P. Chamberlain in:

Contributions

M.E.M., P.P.C., B.P, W.F., J.H., T.I., G.C., and M.R. performed biochemical and crystallographic structural studies. G.L., C.-C.L., K.M., N.-Y.W., D.N., T.T., S.G., and S.X. performed molecular and cellular biology experiments. G.C.L, L.N., M.E.M, and P.P.C. performed electron microscopy studies. A.L.R. performed chemical synthesis. M.E.M., G.L., A.L.-G., J.C., T.I., H.H., T.O.D., B.C., and P.P.C. planned the work, and all authors contributed to the manuscript.

Competing interests

All authors are or have been employees or collaborators of Celgene.

Corresponding authors

Correspondence to Gang Lu or Philip P. Chamberlain.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Table 1, a Supplementary Discussion, Supplementary Methods and Supplementary Figure 1 (gel source data).

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature18611

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.