Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide

Nat Commun. 2020 Sep 14;11(1):4578. doi: 10.1038/s41467-020-18488-4.


Thalidomide and its derivatives exert not only therapeutic effects as immunomodulatory drugs (IMiDs) but also adverse effects such as teratogenicity, which are due in part to different C2H2 zinc-finger (ZF) transcription factors, IKZF1 (or IKZF3) and SALL4, respectively. Here, we report the structural bases for the SALL4-specific proteasomal degradation induced by 5-hydroxythalidomide, a primary thalidomide metabolite generated by the enzymatic activity of cytochrome P450 isozymes, through the interaction with cereblon (CRBN). The crystal structure of the metabolite-mediated human SALL4-CRBN complex and mutagenesis studies elucidate the complex formation enhanced by the interaction between CRBN and an additional hydroxy group of (S)-5-hydroxythalidomide and the variation in the second residue of β-hairpin structure that underlies the C2H2 ZF-type neo-morphic substrate (neosubstrate) selectivity of 5-hydroxythalidomide. These findings deepen our understanding of the pharmaceutical action of IMiDs and provide structural evidence that the glue-type E3 ligase modulators cause altered neosubstrate specificities through their metabolism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry
  • Adaptor Proteins, Signal Transducing / metabolism
  • Amino Acid Sequence
  • HEK293 Cells
  • Humans
  • Immunologic Factors / chemistry*
  • Immunologic Factors / pharmacology*
  • Protein Binding / drug effects
  • Protein Domains
  • Stereoisomerism
  • Structural Homology, Protein
  • Substrate Specificity
  • Thalidomide / analogs & derivatives*
  • Thalidomide / chemistry
  • Thalidomide / pharmacology
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism
  • Ubiquitin-Protein Ligases


  • Adaptor Proteins, Signal Transducing
  • CRBN protein, human
  • Immunologic Factors
  • SALL4 protein, human
  • Transcription Factors
  • 5-hydroxythalidomide
  • Thalidomide
  • Ubiquitin-Protein Ligases