Abstract

In the 1950s, the drug thalidomide, administered as a sedative to pregnant women, led to the birth of thousands of children with multiple defects. Despite the teratogenicity of thalidomide and its derivatives lenalidomide and pomalidomide, these immunomodulatory drugs (IMiDs) recently emerged as effective treatments for multiple myeloma and 5q-deletion-associated dysplasia. IMiDs target the E3 ubiquitin ligase CUL4–RBX1–DDB1–CRBN (known as CRL4CRBN) and promote the ubiquitination of the IKAROS family transcription factors IKZF1 and IKZF3 by CRL4CRBN. Here we present crystal structures of the DDB1–CRBN complex bound to thalidomide, lenalidomide and pomalidomide. The structure establishes that CRBN is a substrate receptor within CRL4CRBN and enantioselectively binds IMiDs. Using an unbiased screen, we identified the homeobox transcription factor MEIS2 as an endogenous substrate of CRL4CRBN. Our studies suggest that IMiDs block endogenous substrates (MEIS2) from binding to CRL4CRBN while the ligase complex is recruiting IKZF1 or IKZF3 for degradation. This dual activity implies that small molecules can modulate an E3 ubiquitin ligase and thereby upregulate or downregulate the ubiquitination of proteins.

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

Gene Expression Omnibus

Data deposits

Structural coordinates for human DDB1–G. gallus CRBN–thalidomide, human DDB1–G. gallus CRBN–lenalidomide and human DDB1–G. gallus CRBN–pomalidomide have been deposited in the Protein Data Bank under accession numbers 4CI1, 4CI2 and 4CI3. Human protein microarray data sets for this study have been deposited in the Gene Expression Omnibus database under accession number GSE57554.

References

  1. 1.

    , & The evolution of thalidomide and its IMiD derivatives as anticancer agents. Nature Rev. Cancer 4, 314–322 (2004)

  2. 2.

    , & Thalidomide-analogue biology: immunological, molecular and epigenetic targets in cancer therapy. Oncogene 32, 4191–4202 (2013)

  3. 3.

    & The thalidomide saga. Int. J. Biochem. Cell Biol. 39, 1489–1499 (2007)

  4. 4.

    Thalidomide and congenital abnormalities. Lancet 278, 1358 (1961)

  5. 5.

    , , & Thalidomide and congenital abnormalities. Lancet 279, 45–46 (1962)

  6. 6.

    Thalidomide in the treatment of lepra reactions. Clin. Pharmacol. Ther. 6, 303–306 (1965)

  7. 7.

    , , & Thalidomide is an inhibitor of angiogenesis. Proc. Natl Acad. Sci. USA 91, 4082–4085 (1994)

  8. 8.

    & The application and biology of immunomodulatory drugs (IMiDs) in cancer. Pharmacol. Ther. 136, 56–68 (2012)

  9. 9.

    et al. Antitumor activity of thalidomide in refractory multiple myeloma. N. Engl. J. Med. 341, 1565–1571 (1999)

  10. 10.

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

  11. 11.

    , , & A mutation in a novel ATP-dependent Lon protease gene in a kindred with mild mental retardation. Neurology 63, 1927–1931 (2004)

  12. 12.

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

  13. 13.

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

  14. 14.

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

  17. 17.

    , , , & Structure of DDB1 in complex with a Paramyxovirus V protein: viral hijack of a propeller cluster in ubiquitin ligase. Cell 124, 105–117 (2006)

  18. 18.

    et al. Structural basis of UV DNA-damage recognition by the DDB1–DDB2 complex. Cell 135, 1213–1223 (2008)

  19. 19.

    , , , & A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4–DDB1 ubiquitin ligase machinery. Nature Struct. Mol. Biol. 17, 105–111 (2010)

  20. 20.

    et al. Detecting UV-lesions in the genome: The modular CRL4 ubiquitin ligase does it best!. FEBS Lett. 585, 2818–2825 (2011)

  21. 21.

    , & Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective. J. Biol. Chem. 281, 38969–38973 (2006)

  22. 22.

    et al. Isosteric analogs of lenalidomide and pomalidomide: Synthesis and biological activity. Bioorg. Med. Chem. Lett. 23, 360–365 (2013)

  23. 23.

    , , , & 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)

  24. 24.

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

  25. 25.

    et al. The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture, targeting, and activation. Cell 147, 1024–1039 (2011)

  26. 26.

    et al. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261–D270 (2012)

  27. 27.

    et al. Phase I trial of lenalidomide and CCI-779 in patients with relapsed multiple myeloma: evidence for lenalidomide-CCI-779 interaction via P-glycoprotein. J. Clin. Oncol. 29, 3427–3434 (2011)

  28. 28.

    et al. Transport of thalidomide by the human intestinal caco-2 monolayers. Eur. J. Drug Metab. Pharmacokinet. 30, 49–61 (2005)

  29. 29.

    et al. Development, validation and application of a sensitive LC-MS/MS method for the quantification of thalidomide in human serum, cells and cell culture medium. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 902, 16–26 (2012)

  30. 30.

    et al. Further evidence for the possible role of MEIS2 in the development of cleft palate and cardiac septum. Am. J. Med. Genet. A. 152A, 1326–1327 (2010)

  31. 31.

    , , , & Control of vertebrate limb outgrowth by the proximal factor Meis2 and distal antagonism of BMPs by Gremlin. Mol. Cell 4, 839–849 (1999)

  32. 32.

    et al. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell 151, 221–232 (2012)

  33. 33.

    , & Mechanisms and function of substrate recruitment by F-box proteins. Nature Rev. Mol. Cell Biol. 14, 369–381 (2013)

  34. 34.

    , , & Dynamics of Cullin-RING Ubiquitin Ligase Network Revealed by Systematic Quantitative Proteomics. Cell 143, 951–965 (2010)

  35. 35.

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

  36. 36.

    et al. Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes. Proc. Natl Acad. Sci. USA 99, 12037–12042 (2002)

  37. 37.

    et al. Crystal structures of human calcineurin and the human FKBP12–FK506-calcineurin complex. Nature 378, 641–644 (1995)

  38. 38.

    et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33, W299–W302 (2005)

  39. 39.

    , , , & A promiscuous α-helical motif anchors viral hijackers and substrate receptors to the CUL4–DDB1 ubiquitin ligase machinery. Nature Struct. Mol. Biol. 17, 105–111 (2010)

  40. 40.

    , & A mental retardation-linked nonsense mutation in cereblon is rescued by proteasome inhibition. J. Biol. Chem. 288, 29573–29585 (2013)

  41. 41.

    , , , & The deubiquitinating protein USP24 interacts with DDB2 and regulates DDB2 stability. Cell Cycle 11, 4378–4384 (2012)

  42. 42.

    et al. Mutations in UVSSA cause UV-sensitive syndrome and destabilize ERCC6 in transcription-coupled DNA repair. Nature Genet. 44, 593–597 (2012)

  43. 43.

    et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39, D945–D950 (2011)

Download references

Acknowledgements

This work was supported by the Novartis Research Foundation and grants to N.H.T. from the European Research Council (ERC-2010-StG 260481-MoBa-CS) and to J.W.H. from the National Institutes of Health (AG011085). J.R.L. was supported by a Damon Runyon Postdoctoral Fellowship (DRG 2061-10). We acknowledge J. Reilly for performing immobilized artificial membrane (IAM) experiments. We thank J. Tallarico, J. Porter, W. Sellers, S. Cottens and M. Renatus for help and comments. D. Hess, R. Sack and J. Seebacher for the mass spectrometry analysis and J. Keusch and H. Gut for support. We thank W. Kaelin for kindly providing the IKZF1 reporter plasmid (pCMV–IRES–Renilla luciferase–IRES–Gateway–firefly luciferase). Part of this work was performed at the Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland.

Author information

Affiliations

  1. Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland

    • Eric S. Fischer
    • , Kerstin Böhm
    • , Michael B. Stadler
    • , Simone Cavadini
    • , Gondichatnahalli M. Lingaraju
    •  & Nicolas H. Thomä
  2. University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland

    • Eric S. Fischer
    • , Kerstin Böhm
    • , Michael B. Stadler
    • , Simone Cavadini
    • , Gondichatnahalli M. Lingaraju
    •  & Nicolas H. Thomä
  3. Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA

    • John R. Lydeard
    •  & J. Wade Harper
  4. Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA

    • Haidi Yang
    • , Jane Nagel
    • , Fabrizio Serluca
    • , Ritesh B. Tichkule
    • , Michael Schebesta
    • , William C. Forrester
    • , Markus Schirle
    • , Marc Hild
    • , Rohan E. J. Beckwith
    •  & Jeremy L. Jenkins
  5. Swiss Institute of Bioinformatics, Maulbeerstrasse 66, CH-4058 Basel, Switzerland

    • Michael B. Stadler
  6. Novartis Pharma AG, Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland

    • Vincent Acker
    • , Ulrich Hassiepen
    •  & Johannes Ottl

Authors

  1. Search for Eric S. Fischer in:

  2. Search for Kerstin Böhm in:

  3. Search for John R. Lydeard in:

  4. Search for Haidi Yang in:

  5. Search for Michael B. Stadler in:

  6. Search for Simone Cavadini in:

  7. Search for Jane Nagel in:

  8. Search for Fabrizio Serluca in:

  9. Search for Vincent Acker in:

  10. Search for Gondichatnahalli M. Lingaraju in:

  11. Search for Ritesh B. Tichkule in:

  12. Search for Michael Schebesta in:

  13. Search for William C. Forrester in:

  14. Search for Markus Schirle in:

  15. Search for Ulrich Hassiepen in:

  16. Search for Johannes Ottl in:

  17. Search for Marc Hild in:

  18. Search for Rohan E. J. Beckwith in:

  19. Search for J. Wade Harper in:

  20. Search for Jeremy L. Jenkins in:

  21. Search for Nicolas H. Thomä in:

Contributions

E.S.F., N.H.T., J.L.J. and W.C.F. initiated the project. E.S.F. and K.B. conducted the protein purification and crystallization. G.M.L. provided recombinant CSN, and S.C. pre-screened protein complexes by electron microscopy. E.S.F. collected data and processed and refined X-ray data. E.S.F. and N.H.T. analysed the structures. E.S.F. performed in vitro experiments and, with the help of U.H., developed and performed TR-FRET and fluorescence polarization assays. E.S.F. performed protein array experiments. M.B.S. and E.S.F. analysed the data. E.S.F., K.B., J.R.L., H.Y., M.H., J.W.H. and N.H.T. conceived and performed the cell-biological characterization. R.B.T. and R.E.J.B. conceived and conducted the chemical syntheses. J.N. and M. Schirle performed proteomics. V.A. and J.O. carried out the differential scanning fluorimetry experiments. F.S. and M. Schebesta carried out the zebrafish experiments. E.S.F. and N.H.T. wrote the manuscript. All authors assisted in editing the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nicolas H. Thomä.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Methods, a Supplementary Discussion and Supplementary References.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature13527

Further reading 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.