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Structure of the human Cereblon–DDB1–lenalidomide complex reveals basis for responsiveness to thalidomide analogs

Abstract

The Cul4–Rbx1–DDB1–Cereblon E3 ubiquitin ligase complex is the target of thalidomide, lenalidomide and pomalidomide, therapeutically important drugs for multiple myeloma and other B-cell malignancies. These drugs directly bind Cereblon (CRBN) and promote the recruitment of substrates Ikaros (IKZF1) and Aiolos (IKZF3) to the E3 complex, thus leading to substrate ubiquitination and degradation. Here we present the crystal structure of human CRBN bound to DDB1 and the drug lenalidomide. A hydrophobic pocket in the thalidomide-binding domain (TBD) of CRBN accommodates the glutarimide moiety of lenalidomide, whereas the isoindolinone ring is exposed to solvent. We also solved the structures of the mouse TBD in the apo state and with thalidomide or pomalidomide. Site-directed mutagenesis in lentiviral-expression myeloma models showed that key drug-binding residues are critical for antiproliferative effects.

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Figure 1: The structures of thalidomide analogs and human CRBN in complex with human DDB1 and lenalidomide.
Figure 2: Structural comparisons of CRBN–DDB1.
Figure 3: Structure of the TBD of human and mouse CRBN.
Figure 4: Sequence-alignment differences mapped onto the surface of the TBD of CRBN.
Figure 5: Conserved tryptophan residues (Trp386 and Trp400) confer binding of CRBN to IMiD compounds and are required for drug function in cells.
Figure 6: Mouse CRBN does not rescue pomalidomide effects in DF15R cells.

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Acknowledgements

Thanks to G. Reyes, R. Chopra, P. Schafer, P. Jackson, A. Mahmoudi, G. Lu and W. Fang for discussions regarding this manuscript. Thanks to G. Ranieri and R. Walter for data-collection services. Thanks to M. Abbasian, J. Evans and W. Kehayias for technical assistance. We would like to thank BL41XU and BL44XU beamlines at the SPring-8 synchrotron facility for the provision of synchrotron data-collection facilities (proposal nos. 2012A6738, 2012B1205 and 2012B6738). Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract no. W-31-109-Eng-38. Portions of this research were conducted at the Advanced Light Source, a national user facility operated by the Lawrence Berkeley National Laboratory, on behalf of the US Department of Energy, Office of Basic Energy Sciences. The Berkeley Center for Structural Biology is supported in part by the Department of Energy, Office of Biological and Environmental Research, and by the US National Institutes of Health, National Institute of General Medical Sciences. Research described in this paper was performed at beamline 08ID-1 at the Canadian Light Source, which is supported by the Natural Sciences and Engineering Research Council of Canada, the National Research Council Canada, the Canadian Institutes of Health Research, the Province of Saskatchewan, Western Economic Diversification Canada and the University of Saskatchewan. Research was funded by a Grant-in-Aid for Scientific Research on Innovative Areas from the Japanese Ministry of Education, Culture, Sports, Science and Technology, Grant-in-Aid for Scientific Research (A) from the Japan Society for the Promotion of Science (H.H. and T.H.).

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P.P.C., G.C., B.P., B.C.-L., S.L.D., M.R., T.M., Y.H. and T.H. performed protein chemistry and structural studies. A.L.-G., K.M., E.R., L.G.C., Y.J.R., M.W., T.I. and H.A. performed biochemical and cellular experiments. P.P.C., A.L.-G., H.H., T.H., T.O.D. and B.E.C. planned the work, and all authors contributed to the manuscript.

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Correspondence to Philip P Chamberlain.

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P.P.C., A.L.-G., K.M., G.C., B.P., B.C.-L., E.R., L.G.C., Y.J.R., M.W., M.R., S.L.D., T.O.D. and B.E.C. are employees of Celgene. H.H. receives research support from Celgene.

Integrated supplementary information

Supplementary Figure 1 CRBN binding assay with thalidomide enantiomers.

(a) Competitive elution assay using thalidomide-immobilized beads coupled with racemic thalidomide. Beads were washed three times with 0.5% NP-40 lysis buffer and bound proteins were eluted with wash buffer containing 1 mM S-, R-thalidomide (S-Thal or R-Thal) or 0.1% DMSO for the indicated time. The eluate was then analysed by SDS-PAGE and immunoblotting (IB). (b) As in a but eluted with a buffer solution containing the indicated concentrations of S or R-thalidomide (S- or R-Thal). (c) Inhibitory effects of thalidomide enantiomers on auto-ubiquitylation of FH-CRBN were detected in the presence of MG132. Cells were treated with DMSO or the indicated concentrations of S- or R-thalidomide for 4 hours prior to harvesting.

Supplementary Figure 2 The thalidomide-binding domain (TBD) of mouse Cereblon showing the crystal contacts formed between protein monomers, bridged by thalidomide molecules.

Chain B is shown in orange and chain D is shown in yellow.

Supplementary Figure 3 Structural comparison between the TBD tri-Trp pockets.

(a) Comparison between thalidomide bound and apo CRBN showing that the binding pocket is formed in the absence of IMiD. The thalidomide bound form is shown with carbons in cyan/yellow and the apo form is shown with carbons in grey. Comparison of the Tri-Trp hole with related modified amine-binding sites. (b), The trimethyl lysine-binding pocket of HP1 chromodomain (grey). The pocket is composed of one Trp and two Tyr residues for binding to histone H3 trimethylated Lys. HP1 is a member of the royal family group of proteins which possess an aromatic methylated lysine and/or arginine-binding pocket. The binding pocket is usually composed of two to four aromatic residues, providing electrostatic and hydrophobic contacts to accommodate the insertion of methylated ligand of the binding partner proteins. The pocket of BPTF PHD finger is composed of one Trp and three Tyr residues for binding to histone H3 trimethylated Lys42(not shown). (c) The dimethyl lysine-binding pocket of 53BP1 Tudor domain (grey) of the royal family. The pocket is formed by one Trp, two Tyr, one Phe and one Asp residue (green), forming an aromatic environment with a salt bridge (dotted line) between the Lys dimethyl amino group and the Asp side-chain carboxyl group. (d) The acetyl lysine-binding pocket of GCN5 bromodomain (grey). The pocket is formed by a mixture of aromatic (three Tyr and one Phe), aliphatic (Val and Pro) and Asn residues (green). The acetyl group is recognized by formation of a direct hydrogen bond to Asn and water-mediated hydrogen bonds (broken lines). (e) Overlay of the tryptophan box forming the betaine-binding pocket of E. coli ProX (green) on the Tri-Trp hole ofpocket of the CRBN TBDMBS domain (cyan). Three Trp residues are labeled. S-thalidomide (SThal, yellow) bound to the Tri-Trp hole pocket is also shown. (f) The betaine-binding site of E. coli ProX (grey). The tryptophan box formed by three conserved Trp and one Tyr residue (green) creates an aromatic environment for binding to betaine (N,N,Ntrimethyl glycine) by cation-pi interactions and van der Waals contacts. In contrast to the CRBN Tri-Trp pocket, the ProX betaine-binding site is located at the cleft between two domains, and the Trp residues of the tryptophan box and the bound betaine are completely occluded inside the protein. (g) As in f, but for the betaine-binding pocket of E. coli BetP (grey). The Trp residues and the bound betaine are completely occluded inside the protein as in ProX.

Supplementary Figure 4 Structural superposition of Cereblon TBD with homologs.

Cereblon TBD is shown in blue, methionine sulfoxide reductase is shown in green and RIG-I in magenta.

Supplementary Figure 5 Immunoblot and immunohistochemical quantiification of CRBN.

(a) Immunoblot analysis of CRBN protein in lysates from DF15, DF15R, DF15R RFP (RFP Ctrl), DF15R CRBNWT (CRBN wt), DF15R CRBN W386A and CRBN W400A cells. (b) CRBN analysis in DF15 and DF15R and DF15R derived cell lines by immunohistochemistry. Images were obtained using a Olympus BX45 microscope at a 40x objective. CRBN signal is shown as brown color and hematoxylin counterstain identifies the nucleus of cells. (c) Immunoblot of anti-Flag immunoprecipitation from cell extracts expressing Flag-tagged CRBN proteins. (d) Immunoblot of thalidomide analog affinity bead binding to CRBN in DF15, DF15R and DF15R CRBNWT cell extracts. Lane description in order left to right: In = DF15 input prior to bead purification; V = DF15 extract control (1% DMSO preincubation); L = DF15 extract preincubated with lenalidomide (30 μM); P = DF15 extract preincubated with Pomalidomide (30 μM); In = DF15R input prior to bead purification; V = DF15R control (1% DMSO preincubation); L = DF15R extract preincubated with lenalidomide (30 μM). P = DF15R extract preincubated with Pomalidomide (30 μM); In = DF15R CRBNWT input prior to bead purification; V = DF15R CRBNWT control (1% DMSO preincubation); L = DF15R CRBNWT extract preincubated with lenalidomide (30 μM). P = DF15R CRBNWT extract preincubated with Pomalidomide (30 μM); Representative immunoblot from two independent experiments with similar results.

Supplementary Figure 6 IL-2 co-stimulation by pomalidomide in human PBMCs but not in mouse splenocytes.

(a) Co-stimulation of IL-2 release by pomalidomide in human PBMC cells treated with anti-CD3. Data shown as means ±s.d.. (b) Co-stimulation of IL-2 release by anti-CD28 (red) or pomalidomide (blue) in mouse PBMC cellssplenocytes treated with anti-CD3. Data shown as means ±s.d.

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Supplementary Figures 1–6 (PDF 2185 kb)

Supplementary Data Set 1

Original images of gels and western blots used in this manuscript (PDF 178 kb)

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Chamberlain, P., Lopez-Girona, A., Miller, K. 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). https://doi.org/10.1038/nsmb.2874

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