Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 26;14(3):501-506.
doi: 10.1039/d2md00347c. eCollection 2023 Mar 22.

Structural rationalization of GSPT1 and IKZF1 degradation by thalidomide molecular glue derivatives

Radosław P Nowak  1   2 , Jianwei Che  1   2 , Silas Ferrao  1 , Nikki R Kong  1   2 , Hu Liu  1   2 , Breanna L Zerfas  1   2 , Lyn H Jones  1   2
Affiliations

Structural rationalization of GSPT1 and IKZF1 degradation by thalidomide molecular glue derivatives

Radosław P Nowak et al. RSC Med Chem. .

Abstract

Thalidomide and its derivatives are molecular glues that bind cereblon (CRBN), a component of an E3 ubiquitin ligase complex, and mediate protein interactions with neosubstrates resulting in their polyubiquitination and proteasomal degradation. The structural features of neosubstrate binding have been elucidated that highlight key interactions with a β-hairpin degron containing a glycine, which is present in a wide-range of proteins, including zinc-finger transcription factors such as IKZF1, and the translation termination factor GSPT1. Here, we profile 14 closely-related thalidomide derivatives in CRBN occupancy, and IKZF1 and GSPT1 degradation cell-based assays, and use crystal structures, computational docking and molecular dynamics to delineate subtle structure-activity relationships. Our findings will enable the rational design of CRBN modulators in the future, and help avoid the degradation of GSPT1 which is broadly cytotoxic.

PubMed Disclaimer

Conflict of interest statement

L. H. J. serves on the scientific advisory boards for, and holds equity in, Interline Therapeutics, Rapafusyn Pharmaceuticals, Ananke Therapeutics and Umbra Therapeutics, consults for Matchpoint Therapeutics, and holds equity in Jnana Therapeutics. The Center for Protein Degradation at DFCI receives research funding from Deerfield. J. C. is a consultant for Soltego, Allorion and Matchpoint Therapeutics, and holds equity in Soltego, Allorion, Matchpoint and M3 Bioinformatics & Technology Inc.

Figures

Fig. 1
Fig. 1. Cell-based cereblon binding potency of molecular glue degraders profiled in this work. The data are presented as IC50 ± Std. error of two replicates (N = 2).
Fig. 2
Fig. 2. Cell-based HiBiT IKZF1 and GSPT1 GFP/mCherry degradation data of phthalimides (A–C) and isoindolinones (D–F). Compounds were incubated for 24 h for IKZF1 and 5 h for GSPT1 assay and the data are presented as two replicates (N = 2). Dmax, presented as mean ± std. error, corresponds to the maximal depth of degradation. The DC50 reflects the concentration where 50% degradation was observed.
Fig. 3
Fig. 3. CRBN co-crystal structures of A) 4-NH2-Thal (pomalidomide) with IKZF1 ZnF2 (PDB: 6H0F), B) 5-OH-Thal with SALL4 ZnF2 (PDB: 7BQV), C) CC-885 with GSPT1 (PDB: 5HXB), and D) CC-90009 with GSPT1 (PDB: 6XK9). Dashed lines indicate hydrogen bonding. The residue numbers are based on the corresponding PDB structures – note residue index shift between the GSPT1 structures.
Fig. 4
Fig. 4. Docking models of A) 5-OH-EM12 in GSPT1/CRBN, B) 4-OH-Thal in IKZF1/CRBN, C) 5-NH2-EM12 in GSPT1/CRBN, and D) 5-NH2-EM12 in IKZF1/CRBN. The dotted lines indicate key potential hydrogen bonds that describe the data.
See this image and copyright information in PMC

References

    1. 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(5971):1345–1350. doi: 10.1126/science.1177319. doi: 10.1126/science.1177319. - DOI - PubMed
    1. Chamberlain P. P. Hamann L. G. Development of targeted protein degradation therapeutics. Nat. Chem. Biol. 2019;15(10):937–944. doi: 10.1038/s41589-019-0362-y. doi: 10.1038/s41589-019-0362-y. - DOI - PubMed
    1. Krönke J. Udeshi N. D. Narla A. Grauman P. Hurst S. N. McConkey M. Svinkina T. Heckl D. Comer E. Li X. et al., Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science. 2014;343(6168):301–305. doi: 10.1126/science.1244851. doi: 10.1126/science.1244851. - DOI - PMC - PubMed
    1. Fischer E. S. Böhm K. Lydeard J. R. Yang H. Stadler M. B. Cavadini S. Nagel J. Serluca F. Acker V. Lingaraju G. M. et al., Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature. 2014;512(7512):49–53. doi: 10.1038/nature13527. doi: 10.1038/nature13527. - DOI - PMC - PubMed
    1. 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. et al., Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs. Nat. Struct. Mol. Biol. 2014;21(9):803–809. doi: 10.1038/nsmb.2874. doi: 10.1038/nsmb.2874. - DOI - PubMed

LinkOut - more resources