Fig. 4: Structure-degradation relationship analysis of screened MGDs.

a t-SNE plot of MGDs clustered by core structure: lenalidomide (Lena), thalidomide (Thal), and phenyl-glutarimide (PG). Each dot represents a compound; black dots indicate the 100 analogs selected for proteomics. Representative core structures are shown. b Heat map of log₂ fold-changes (MGD vs. DMSO) for known and novel neosubstrates in Huh-7 cells. Compounds are grouped by IMiD-like or PG-based cores. The top bar chart shows the number of significantly downregulated neosubstrates per compound. Red boxes highlight G3BP2 degradation by SJ42229 and SJ41824. Proteins with predicted G-loop motifs are indicated. c Volcano plots depicting protein quantifications for the G3BP2 SJ42229 (IMiD-like), SJ41824 and SJ41813 (PG-based) in NB-4 cells (10 µM, 24 h). The x-axis shows log₂ fold-changes, and the standard errors are plotted on the y-axis (log₁₀ scale). Significant changes (LIMMA⁶⁹, FDR = 1%) are in red (down) and blue (up). IMiD-derived neosubstrates are highlighted for SJ42229. The compound structures are shown. n.s. not significant. d MS quantified SALL4 levels in SUSA cells after treatment with IMiD-like (blue) and PG-based (red) compounds (10 µM, 24 h). Box plots represent log₂-transformed intensity values for four biological replicates per compound, with 15 DMSO-treated samples included as controls. Horizontal lines indicate the median (bold) and interquartile range (thin). e Western blot analysis of the indicated proteins in SK-N-BE(2)-C wild-type and CRBN knockout (CRBN^KO) cells treated with SJ41813 (10 µM, 24 h). Shown are the results of one experiment. f Volcano plot of biotinylated proteins from TurboID-CRBN HEK293 cells treated with SJ41813, showing log₂ fold-changes (x-axis) and log₁₀ standard error (y-axis). Significantly enriched proteins (LIMMA⁶⁹, FDR = 1%, n = 3) are labeled in blue. n.s. not significant. g Immunoblots for G3BP2 and USP10 in SK-N-BE(2)-C cells treated with increasing doses (in µM) of SJ41813 (24 h). Blots are representative of three independent experiments. h Quantification of G3BP2 and USP10 blots from (g). DC₅₀ values were calculated from band intensities (mean ± S.D., n = 3) and normalized to DMSO controls. i Volcano plot of ubiquitinated peptides in NB-4 cells treated with SJ41813 (30 min). Significantly upregulated peptides (LIMMA⁶⁹, FDR = 5%; n = 4) are in blue; G3BP2 sites are highlighted. n.s. not significant. Source Data are provided as a Source Data file.