Thalidomide mimics uridine binding to an aromatic cage in cereblon

Journal of Structural Biology

Volumn 188, Issue 3, 2014, Pages 225-232

  Hartmann, Marcus D ^a   Boichenko, Iuliia ^a   Coles, Murray ^a   Zanini, Fabio ^a   Lupas, Andrei N ^a   Hernandez Alvarez, Birte ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

IMiD; Immunomodulatory drug; Pomalyst; Revlimid

Indexed keywords

CEREBLON PROTEIN; CHOLINE; DNA BINDING PROTEIN; MEMBRANE PROTEIN; THALIDOMIDE; TRYPTOPHAN; UNCLASSIFIED DRUG; URIDINE; ANTINEOPLASTIC AGENT; PEPTIDE HYDROLASE;

ARTICLE; CRYSTAL STRUCTURE; DRUG BINDING; DRUG STRUCTURE; IN VIVO STUDY; MOLECULAR RECOGNITION; NONHUMAN; VALIDATION PROCESS; BINDING SITE; ESCHERICHIA COLI; METABOLISM;

BACTERIA (MICROORGANISMS); EUKARYOTA;

ANTINEOPLASTIC AGENTS; BINDING SITES; ESCHERICHIA COLI; PEPTIDE HYDROLASES; THALIDOMIDE; URIDINE;

EID: 84918578594     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2014.10.010     Document Type: Article

References (31)

1. Bartlett J.B., Dredge K., Dalgleish A.G. The evolution of thalidomide and its IMiD derivatives as anticancer agents. Nat. Rev. Cancer 2004, 4:314-322.
2. Chang X.B., Stewart A.K. What is the functional role of the thalidomide binding protein cereblon?. Int. J. Biochem. Mol. Biol. 2011, 2:287-294.
3. Dalvit C., Pevarello P., Tato M., Veronesi M., Vulpetti A., Sundstrom M. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J. Biomol. NMR 2000, 18:65-68.
4. Chamberlain P.P., Lopez-Girona A., Miller K., Carmel G., Pagarigan B., Chie-Leon B., Rychak E., Corral L.G., Ren Y.J., Wang M., Riley M., Delker S.L., Ito T., Ando H., Mori T., Hirano Y., Handa H., Hakoshima T., Daniel T.O., Cathers B.E. Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs. Nat. Struct. Mol. Biol. 2014, 21:803-809.
5. Dougherty D.A. Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science 1996, 271:163-168.
6. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2126-2132.
7. Fischer E.S., Böhm K., Lydeard J.R., Yang H., Stadler M.B., Cavadini S., Nagel J., Serluca F., Acker V., Lingaraju G.M., Tichkule R.B., Schebesta M., Forrester W.C., Schirle M., Hassiepen U., Ottl J., Hild M., Beckwith R.E., Harper J.W., Jenkins J.L., Thomä N.H. Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 2014, 512:49-53.
8. Franks M.E., Macpherson G.R., Figg W.D. Thalidomide. Lancet 2004, 363:1802-1811.
9. Gandhi A.K., Kang J., Havens C.G., Conklin T., Ning Y., Wu L., Ito T., Ando H., Waldman M.F., Thakurta A., Klippel A., Handa H., Daniel T.O., Schafer P.H., Chopra R. 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. 2014, 164:811-821.
10. Gayatri S., Bedford M.T. Readers of histone methylarginine marks. Biochim. Biophys. Acta 2014, 1839:702-710.
11. Higa L.A., Wu M., Ye T., Kobayashi R., Sun H., Zhang H. CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat. Cell Biol. 2006, 8:1277-1283.
12. Iovine B., Iannella M.L., Bevilacqua M.A. Damage-specific DNA binding protein 1 (DDB1): a protein with a wide range of functions. Int. J. Biochem. Cell Biol. 2011, 43:1664-1667.
13. Ito T., Ando H., Suzuki T., Ogura T., Hotta K., Imamura Y., Yamaguchi Y., Handa H. Identification of a primary target of thalidomide teratogenicity. Science 2010, 327:1345-1350.
14. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 1993, 26:795-800.
15. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 1991, 24:946-950.
16. Kronke J., Udeshi N.D., Narla A., Grauman P., Hurst S.N., McConkey M., Svinkina T., Heckl D., Comer E., Li X., Ciarlo C., Hartman E., Munshi N., Schenone M., Schreiber S.L., Carr S.A., Ebert B.L. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 2014, 343:301-305.
17. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
18. Lee J.M., Lee J.S., Kim H., Kim K., Park H., Kim J.Y., Lee S.H., Kim I.S., Kim J., Lee M., Chung C.H., Seo S.B., Yoon J.B., Ko E., Noh D.Y., Kim K.I., Kim K.K., Baek S.H. EZH2 generates a methyl degron that is recognized by the DCAF1/DDB1/CUL4 E3 ubiquitin ligase complex. Mol. Cell 2012, 48:572-586.
19. Lee K.M., Jo S., Kim H., Lee J., Park C.S. Functional modulation of AMP-activated protein kinase by cereblon. Biochim. Biophys. Acta 2011, 1813:448-455.
20. Li H., Ilin S., Wang W., Duncan E.M., Wysocka J., Allis C.D., Patel D.J. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 2006, 442:91-95.
21. Liu J., Ye J., Zou X., Xu Z., Feng Y., Zou X., Chen Z., Li Y., Cang Y. CRL4A(CRBN) E3 ubiquitin ligase restricts BK channel activity and prevents epileptogenesis. Nat. Commun. 2014, 5:3924.
22. Lopez-Girona A., Mendy D., Ito T., Miller K., Gandhi A.K., Kang J., Karasawa S., Carmel G., Jackson P., Abbasian M., Mahmoudi A., Cathers B., Rychak E., Gaidarova S., Chen R., Schafer P.H., Handa H., Daniel T.O., Evans J.F., Chopra R. Cereblon is a direct protein target for immunomodulatory and antiproliferative activities of lenalidomide and pomalidomide. Leukemia 2012, 26:2326-2335.
23. Lupas A.N., Zhu H., Korycinski M. The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the β-tent fold. PLOS Comp. Biol. 2014, in press.
24. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 1997, 277:505-524.
25. Meyer B., Peters T. NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. Engl. 2003, 42:864-890.
26. Murshudov G.N., Vagin A.A., Lebedev A., Wilson K.S., Dodson E.J. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D Biol. Crystallogr. 1999, 55:247-255.
27. Perrakis A., Morris R., Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 1999, 6:458-463.
28. Sheldrick G.M. A short history of SHELX. Acta Crystallogr. A 2008, 64:112-122.
29. Su X., Zhu G., Ding X., Lee S.Y., Dou Y., Zhu B., Wu W., Li H. Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev. 2014, 28:622-636.
30. Visnes T., Doseth B., Pettersen H.S., Hagen L., Sousa M.M., Akbari M., Otterlei M., Kavli B., Slupphaug G., Krokan H.E. Uracil in DNA and its processing by different DNA glycosylases. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2009, 364:563-568.
31. Yun M., Wu J., Workman J.L., Li B. Readers of histone modifications. Cell Res. 2011, 21:564-578.