Fig. 5: LC-1–40 is a specific and potent NUDT1 degrader.
From: Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability
a Co-crystal structure of Compound 32 (cyan) bound to NUDT1 (gray, PDB:7N13) revealing solvent-exposed amide (circled) as an exit vector for linker attachment. b Structure of LC-1-40. c Representative immunoblot of NUDT1 in SHEP MYCN-ER cells treated with the indicated concentration of LC-1-40 for 1 h. Relative NUDT1 levels were quantified and plotted based on averages of three independent experiments. d Time-dependent NUDT1 depletion by LC-1-40 (50 nM) in SHEP MYCN-ER cells. Relative NUDT1 levels were quantified and plotted based on averages of three independent experiments. e, f NUDT1 immunoblots using SF188 cells pretreated with TH287 (2 µM) (e) or pomalidomide (10 µM) (f) for 2 h, and then subjected to an additional 6 h treatment with DMSO or LC-1-40 (50 nM). g Quantitative proteomics showing relative abundance of proteins in SF188 cells treated with 100 nM LC-1-40 for 6 h. The analysis was performed by the DEP software (version 1.6.1), which was also used to calculate the p-values, based on SF188 samples from three independent experiments. h Assessment of NUDT1 (WT and the E77K mutant) enzymatic activity. Data shown as averages of technical triplicates. i Immunoblots of NUDT1 in 4-OHT induced SHEP MYCN-ER cells overexpressing NUDT1 WT or the E77K mutant, treated with LC-1-40 (50 nM) for 36 h. j Cell death analysis of 4-OHT induced SHEP MYCN-ER cells overexpressing NUDT1 WT or the E77K mutant, treated with LC-1-40 (50 nM). Data shown as averages of technical triplicates. Statistical significance was determined by one-way ANOVA (h) or two-way ANOVA (j). k Time course of plasma concentration of LC-1-40 in C57 mice (n = 3) after single IV (Intravenous), IP (Intraperitoneal), and PO (Oral) dose administration. Mean pharmacokinetics of LC-1-40 is shown on the right. Data are shown as mean ± SD. --, not calculated; T1/2, terminal elimination phase half-life; Tmax, time of the first occurrence of Cmax; Cmax, maximum observed concentration; AUCinf, area under the concentration-time curve from time 0 to infinity; CL plasma clearance, Vss steady-state volume of distribution, F bioavailability. c–f, h–j these experiments were independently repeated three times with similar results. Source data are provided as a Source Data file.
