Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
15 Oct 2024
15 Oct 2024
Historique:
received:
14
03
2024
accepted:
19
09
2024
medline:
16
10
2024
pubmed:
16
10
2024
entrez:
15
10
2024
Statut:
epublish
Résumé
The ubiquitin E3 ligase cereblon (CRBN) is the target of therapeutic drugs thalidomide and lenalidomide and is recruited by most targeted protein degraders (PROTACs and molecular glues) in clinical development. Biophysical and structural investigation of CRBN has been limited by current constructs that either require co-expression with the adaptor DDB1 or inadequately represent full-length protein, with high-resolution structures of degrader ternary complexes remaining rare. We present the design of CRBN
Identifiants
pubmed: 39406745
doi: 10.1038/s41467-024-52871-9
pii: 10.1038/s41467-024-52871-9
doi:
Substances chimiques
Ubiquitin-Protein Ligases
EC 2.3.2.27
CRBN protein, human
0
Adaptor Proteins, Signal Transducing
0
Thalidomide
4Z8R6ORS6L
Lenalidomide
F0P408N6V4
DNA-Binding Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
8885Informations de copyright
© 2024. The Author(s).
Références
Békés, M., Langley, D. R. & Crews, C. M. PROTAC targeted protein degraders: the past is prologue. Nat. Rev. Drug Discov. 21, 181–200 (2022).
pubmed: 35042991
pmcid: 8765495
doi: 10.1038/s41573-021-00371-6
Yoon, H., Rutter, J. C., Li, Y. D. & Ebert, B. L. Induced protein degradation for therapeutics: past, present, and future. J. Clin. Invest. 134, e175265 (2024).
Kozicka, Z. & Thomä, N. H. Haven’t got a glue: Protein surface variation for the design of molecular glue degraders. Cell Chem. Biol. 28, 1032–1047 (2021).
pubmed: 33930325
doi: 10.1016/j.chembiol.2021.04.009
Cowan, A. D. & Ciulli, A. Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory. Annu. Rev. Biochem. 91, 295–319 (2022).
pubmed: 35320687
doi: 10.1146/annurev-biochem-032620-104421
Kong, N. R. & Jones, L. H. Clinical Translation of Targeted Protein Degraders. Clin. Pharmacol. Ther. 114, 558–568 (2023).
pubmed: 37399310
doi: 10.1002/cpt.2985
Ciulli, A. et al. The 17th EFMC Short Course on Medicinal Chemistry on Small Molecule Protein Degraders. ChemMedChem 18, e202300464 (2023).
pubmed: 37817354
doi: 10.1002/cmdc.202300464
Yamamoto, J., Ito, T., Yamaguchi, Y. & Handa, H. Discovery of CRBN as a target of thalidomide: a breakthrough for progress in the development of protein degraders. Chem. Soc. Rev. 51, 6234–6250 (2022).
pubmed: 35796627
doi: 10.1039/D2CS00116K
Oleinikovas, V., Gainza, P., Ryckmans, T., Fasching, B. & Thomä, N. H. From Thalidomide to Rational Molecular Glue Design for Targeted Protein Degradation. Annu. Rev. Pharmacol. Toxicol. 64, 291–312 (2024).
Fischer, E. S. et al. Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512, 49–53 (2014).
pubmed: 25043012
pmcid: 4423819
doi: 10.1038/nature13527
Chamberlain, P. P. 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).
pubmed: 25108355
doi: 10.1038/nsmb.2874
Ichikawa, S. et al. The E3 ligase adapter cereblon targets the C-terminal cyclic imide degron. Nature 610, 775–782 (2022).
pubmed: 36261529
pmcid: 10316063
doi: 10.1038/s41586-022-05333-5
Gandhi, A. K. 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).
pubmed: 24328678
doi: 10.1111/bjh.12708
Krönke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014).
pubmed: 24292625
doi: 10.1126/science.1244851
Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014).
pubmed: 24292623
doi: 10.1126/science.1244917
Chamberlain, P. P. et al. Evolution of Cereblon-Mediated Protein Degradation as a Therapeutic Modality. ACS Med. Chem. Lett. 10, 1592–1602 (2019).
pubmed: 31857833
pmcid: 6912861
doi: 10.1021/acsmedchemlett.9b00425
Min, J. et al. Phenyl-Glutarimides: Alternative Cereblon Binders for the Design of PROTACs. Angew. Chem. Int. Ed. 60, 26663–26670 (2021).
doi: 10.1002/anie.202108848
Jarusiewicz, J. A. et al. Phenyl Dihydrouracil: An Alternative Cereblon Binder for PROTAC Design. ACS Med. Chem. Lett. 14, 141–145 (2023).
pubmed: 36793425
pmcid: 9923830
doi: 10.1021/acsmedchemlett.2c00436
Matyskiela, M. E. et al. A novel cereblon modulator recruits GSPT1 to the CRL4(CRBN) ubiquitin ligase. Nature 535, 252–257 (2016).
pubmed: 27338790
doi: 10.1038/nature18611
Petzold, G., Fischer, E. S. & Thomä, N. H. Structural basis of lenalidomide-induced CK1α degradation by the CRL4CRBN ubiquitin ligase. Nature 532, 127–130 (2016).
pubmed: 26909574
doi: 10.1038/nature16979
Nowak, R. P. et al. Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat. Chem. Biol. 14, 706–714 (2018).
pubmed: 29892083
pmcid: 6202246
doi: 10.1038/s41589-018-0055-y
Sievers, Q. L. et al. Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science 362, eaat0572 (2018).
Matyskiela, M. E. et al. Crystal structure of the SALL4–pomalidomide–cereblon–DDB1 complex. Nat. Struct. Mol. Biol. 27, 319–322 (2020).
pubmed: 32251415
doi: 10.1038/s41594-020-0405-9
Surka, C. et al. CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Blood 137, 661–677 (2021).
pubmed: 33197925
pmcid: 8215192
doi: 10.1182/blood.2020008676
Wang, E. S. et al. Acute pharmacological degradation of Helios destabilizes regulatory T cells. Nat. Chem. Biol. 17, 711–717 (2021).
pubmed: 34035522
pmcid: 8162940
doi: 10.1038/s41589-021-00802-w
Watson, E. R. et al. Molecular glue CELMoD compounds are regulators of cereblon conformation. Science 378, 549–553 (2022).
pubmed: 36378961
pmcid: 9714526
doi: 10.1126/science.add7574
Bonazzi, S. et al. Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy. Cell Chem. Biol. 30, 235–247.e212 (2023).
pubmed: 36863346
doi: 10.1016/j.chembiol.2023.02.005
Eron, S. J. et al. Structural Characterization of Degrader-Induced Ternary Complexes Using Hydrogen–Deuterium Exchange Mass Spectrometry and Computational Modeling: Implications for Structure-Based Design. ACS Chem. Biol. 16, 2228–2243 (2021).
pubmed: 34582690
doi: 10.1021/acschembio.1c00376
Ichikawa, S. et al. The Cyclimids: Degron-inspired cereblon binders for targeted protein degradation. Cell. Chem. Biol. 31, 1162–1175.e1110 (2024).
Ma, X. et al. Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon. Sci. Rep. 13, 22088 (2023).
pubmed: 38086859
pmcid: 10716131
doi: 10.1038/s41598-023-48606-3
Gadd, M. S. et al. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat. Chem. Biol. 13, 514–521 (2017).
pubmed: 28288108
pmcid: 5392356
doi: 10.1038/nchembio.2329
Farnaby, W. et al. BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat. Chem. Biol. 15, 672–680 (2019).
pubmed: 31178587
pmcid: 6600871
doi: 10.1038/s41589-019-0294-6
Testa, A., Hughes, S. J., Lucas, X., Wright, J. E. & Ciulli, A. Structure-Based Design of a Macrocyclic PROTAC. Angew. Chem. Int. Ed. Engl. 59, 1727–1734 (2020).
pubmed: 31746102
doi: 10.1002/anie.201914396
Yu, X. et al. A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models. Sci. Transl. Med. 13, eabj1578 (2021).
pubmed: 34586829
pmcid: 8500670
doi: 10.1126/scitranslmed.abj1578
Kofink, C. et al. A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. Nat. Commun. 13, 5969 (2022).
Wijaya, A. J., Farnaby, W. & Ciulli, A. Crystallization of VHL-based PROTAC-induced ternary complexes. Methods Enzymol. 681, 241–263 (2023).
pubmed: 36764760
doi: 10.1016/bs.mie.2022.10.005
Krieger, J. et al. Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design. ChemMedChem 18, e202200615 (2023).
pubmed: 36749883
doi: 10.1002/cmdc.202200615
Roy, M. J. et al. SPR-Measured Dissociation Kinetics of PROTAC Ternary Complexes Influence Target Degradation Rate. ACS Chem. Biol. 14, 361–368 (2019).
pubmed: 30721025
pmcid: 6423499
doi: 10.1021/acschembio.9b00092
Wurz, R. P. et al. Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Nat. Commun. 14, 4177 (2023).
pubmed: 37443112
pmcid: 10344917
doi: 10.1038/s41467-023-39904-5
Słabicki, M. et al. The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature 585, 293–297 (2020).
pubmed: 32494016
pmcid: 7486275
doi: 10.1038/s41586-020-2374-x
Mayor-Ruiz, C. et al. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat. Chem. Biol. 16, 1199–1207 (2020).
pubmed: 32747809
pmcid: 7116640
doi: 10.1038/s41589-020-0594-x
Lv, L. et al. Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation. Elife 9, 59994 (2020).
Kozicka, Z. et al. Design principles for cyclin K molecular glue degraders. Nat. Chem. Biol. 20, 93–102 (2024).
pubmed: 37679459
doi: 10.1038/s41589-023-01409-z
Bouguenina, H. et al. A degron blocking strategy towards improved CRL4CRBN recruiting PROTAC selectivity. ChemBioChem 24, e202300351 (2023).
pubmed: 37418539
doi: 10.1002/cbic.202300351
Furihata, H. et al. Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide. Nat. Commun. 11, 4578 (2020).
pubmed: 32929090
pmcid: 7490372
doi: 10.1038/s41467-020-18488-4
Heim, C., Spring, A.-K., Kirchgäßner, S., Schwarzer, D. & Hartmann, M. D. Identification and structural basis of C-terminal cyclic imides as natural degrons for cereblon. Biochem. Biophys. Res. Commun. 637, 66–72 (2022).
pubmed: 36375252
doi: 10.1016/j.bbrc.2022.11.001
Heim, C., Spring, A.-K., Kirchgäßner, S., Schwarzer, D. & Hartmann, M. D. Cereblon neo-substrate binding mimics the recognition of the cyclic imide degron. Biochem. Biophys. Res. Commun. 646, 30–35 (2023).
pubmed: 36701892
doi: 10.1016/j.bbrc.2023.01.051
Goldenzweig, A. et al. Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability. Mol. Cell 63, 337–346 (2016).
pubmed: 27425410
pmcid: 4961223
doi: 10.1016/j.molcel.2016.06.012
Chen, X., Zaro, J. L. & Shen, W. C. Fusion protein linkers: property, design and functionality. Adv. Drug. Deliv. Rev. 65, 1357–1369 (2013).
pubmed: 23026637
doi: 10.1016/j.addr.2012.09.039
Durand, D. et al. NADPH oxidase activator p67phox behaves in solution as a multidomain protein with semi-flexible linkers. J. Struct. Biol. 169, 45–53 (2010).
pubmed: 19723583
doi: 10.1016/j.jsb.2009.08.009
Akuffo, A. A. et al. Ligand-mediated protein degradation reveals functional conservation among sequence variants of the CUL4-type E3 ligase substrate receptor cereblon. J. Biol. Chem. 293, 6187–6200 (2018).
pubmed: 29449372
pmcid: 5912449
doi: 10.1074/jbc.M117.816868
Yamaguchi, J.-I. et al. Synthesis of new hydantoins bearing glutarimide or succinimide moiety and their evaluation for cell differentiation-inducing and anti-angiogenic activities. Heterocycles 91, 764–781, (2015).
doi: 10.3987/COM-15-13184
Vonrhein, C. et al. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr. D. Biol. 67, 293–302 (2011).
doi: 10.1107/S0907444911007773
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
pubmed: 19461840
pmcid: 2483472
doi: 10.1107/S0021889807021206
Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D. Biol. 68, 352–367 (2012).
doi: 10.1107/S0907444912001308
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Vonrhein, C. et al. Advances in automated data analysis and processing within autoPROC, combined with improved characterisation, mitigation and visualisation of the anisotropy of diffraction limits using STARANISO. Acta Crystallogr. A 74, a360 (2018).
doi: 10.1107/S010876731809640X
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
pubmed: 35637307
pmcid: 9184281
doi: 10.1038/s41592-022-01488-1
Winter, G. et al. DIALS: implementation and evaluation of a new integration package. Acta Crystallogr. D. Biol. 74, 85–97 (2018).
doi: 10.1107/S2059798317017235
Schüttelkopf, A. W. & van Aalten, D. M. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D. Biol. 60, 1355–1363 (2004).
doi: 10.1107/S0907444904011679
Cowieson, N. P. et al. Beamline B21: high-throughput small-angle X-ray scattering at Diamond Light Source. J. Synchrotron Radiat. 27, 1438–1446 (2020).
pubmed: 32876621
pmcid: 7467336
doi: 10.1107/S1600577520009960
Panjkovich, A. & Svergun, D. I. CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data. Bioinformatics 34, 1944–1946 (2017).
pmcid: 5972624
doi: 10.1093/bioinformatics/btx846
Manalastas-Cantos, K. et al. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J. Appl. Crystallogr. 54, 343–355 (2021).
pubmed: 33833657
pmcid: 7941305
doi: 10.1107/S1600576720013412
Svergun, D. I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25, 495–503 (1992).
doi: 10.1107/S0021889892001663
Svergun, D., Barberato, C. & Koch, M. H. J. CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates. J. Appl. Crystallogr. 28, 768–773 (1995).
doi: 10.1107/S0021889895007047
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).
pubmed: 29788355
pmcid: 6030848
doi: 10.1093/nar/gky427
Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R. & Sherman, W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aided Mol. Des. 27, 221–234 (2013).
pubmed: 23579614
doi: 10.1007/s10822-013-9644-8
Jacobson, M. P. et al. A hierarchical approach to all-atom protein loop prediction. Proteins: Struct. Funct. Bioinf. 55, 351–367 (2004).
doi: 10.1002/prot.10613
Lu, C. et al. OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. J. Chem. Theory Comput. 17, 4291–4300 (2021).
pubmed: 34096718
doi: 10.1021/acs.jctc.1c00302
Bowers, K. J. et al. in Proceedings of the 2006 ACM/IEEE conference on Supercomputing 84–es (Association for Computing Machinery, Tampa, Florida, 2006).
De Vita, S., Chini, M. G., Bifulco, G. & Lauro, G. Insights into the Ligand Binding to Bromodomain-Containing Protein 9 (BRD9): A Guide to the Selection of Potential Binders by Computational Methods. Molecules 26, 7192 (2021).
pubmed: 34885774
pmcid: 8659208
doi: 10.3390/molecules26237192
Predescu, C. et al. The u-series: A separable decomposition for electrostatics computation with improved accuracy. J. Chem. Phys. 152, 084113 (2020).
pubmed: 32113352
doi: 10.1063/1.5129393