well plates  (OriGene)

Journal: Nature

Article Title: Metabolite glues as a means of purine sensing and chemotherapeutic response

doi: 10.1038/s41586-026-10790-3

Figure Lengend Snippet: a . Size exclusion chromatography (SEC) trace (left) and Coomassie-stained gel of PPAT–NUDT5–AMP complex (right) used for cryo-EM analysis. b . Motion-corrected and denoised micrograph of PPAT–NUDT5–AMP complex. c . Representative 2D class averages for PPAT–NUDT5–AMP complex. Micrographs and 2D class averages from the 6-meTIMP and 6-benzylTIMP datasets were highly similar to that of the AMP-bound dataset. d , e . SEC and Coomassie-stained gels of PPAT–NUDT5 complexes formed in the presence of d . 6-meTIMP and e . 6-benzylTIMP. f . Cryo-EM data processing particle flow for the three nucleotide-bound PPAT–NUDT5 structures. All processing steps were performed in cryoSPARC. g – i . Angular distribution of particles and FSC curves from refinements of PPAT–NUDT5–purine complexes with g . AMP, h . 6-meTIMP and i . 6-benzylTIMP.

Article Snippet: NUDT5 (75 μM) was incubated with PPAT (15 μM) directly after elution of PPAT from Strep-Tactin resin for 1 h in 2 ml Strep-Tactin elution buffer (50 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 1 mM DTT and 50 mM biotin) supplemented with 200 μM 6-meTIMP (Jena Biosciences, NU-1226) or 6-benzylTIMP (WuXi).

Techniques: Size-exclusion Chromatography, Staining, Cryo-EM Sample Prep

Journal: Nature

Article Title: Metabolite glues as a means of purine sensing and chemotherapeutic response

doi: 10.1038/s41586-026-10790-3

Figure Lengend Snippet: a , Metabolism of 6-MP and 6-TG. Orange asterisk indicates 6-TGMP conversion to 6-meTGMP, which is a PPAT–NUDT5 glue. b , AMP and 6-meTIMP structures. c , Left, alignment of the AMP and 6-meTIMP glue interface with cryo-EM density. Right, PPAT residue rearrangement in 6-meTIMP-bound (dark) versus AMP-bound (light) structures. d , PPAT hydrophobic pocket engaged by 6-meTIMP. e , 6-meTIMP glue interface. f , PPAT activity assay with wild-type NUDT5 and nucleotide (0.25 mM PRPP). Data are mean ± s.e.m. from n = 3 independent experiments ( n = 2 for 6-TIMP). g , PRPP-induced PPAT–NUDT5 dissociation (AlphaLisa) with AMP and 6-meTIMP. Data are mean ± s.e.m. from n = 3 independent experiments. Data are also shown in Fig. . h , NUDT5–3×Flag immunoprecipitation (left) and quantification (right) after treatment with MTX (2 µM) and/or 6-MP (50 µM). Data are mean ± s.e.m. with individual values from n = 3 independent biological replicate experiments. i , AMP (M+2) and GMP (M+3) fractional enrichment in [ 15 N-amide]-glutamine labelling of cells treated with 6-MP. Data are mean ± s.e.m. with individual values from n = 6 biological replicates from 2 independent experiments. j , FACS growth competition: ∆NUDT5 and NUDT5 L217A/L218A (LKAA) mutants versus wild-type HEK293T cells treated with 6-MP or 6-TG. Data are mean with individual values from n = 3 biological replicates. k , Viability of wild-type, ∆NUDT5 and NUDT5 L217A/L218A ALL cells treated with 6-meTIMP. Data are mean ± s.e.m. of n = 6 biological replicates from 3 independent experiments. FC (fold change) is the ratio of mutant to wild-type IC 50 . K i and IC 50 values in f , g , k were compared by global nonlinear regression using an extra sum-of-squares F-test. Significance was determined by two-tailed one-sample t -test relative to DMSO control in h and by one-way ANOVA followed by Dunnett’s multiple-comparisons test against wild type in i . NS, not significant. * P < 0.05 and *** P < 0.001. Exact P values are included as source data.

Article Snippet: NUDT5 (75 μM) was incubated with PPAT (15 μM) directly after elution of PPAT from Strep-Tactin resin for 1 h in 2 ml Strep-Tactin elution buffer (50 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 1 mM DTT and 50 mM biotin) supplemented with 200 μM 6-meTIMP (Jena Biosciences, NU-1226) or 6-benzylTIMP (WuXi).

Techniques: Cryo-EM Sample Prep, Residue, Activity Assay, Immunoprecipitation, Mutagenesis, Two Tailed Test, Control

Journal: Nature

Article Title: Metabolite glues as a means of purine sensing and chemotherapeutic response

doi: 10.1038/s41586-026-10790-3

Figure Lengend Snippet: a . FACS-based growth competition comparing Δ NUDT5 and rescue mutants with wild-type HEK293T cells treated with 6-TG. Data represent the mean with individual values from n = 3 biological replicates. b . Cryo-EM density of the PPAT–NUDT5 6-meTIMP molecular-glue interface with model fit. c , d . PPAT activity assay measuring inhibitory effects of 6-meTIMP in the absence and presence of wild-type NUDT5 and indicated mutants ( c ) and compared to AMP only ( d ) with 0.25 mM PRPP. Data represent the mean ± s.e.m. from n = 3 independent experiments. e . AlphaLisa binding assay quantifying the stabilization of PPAT–NUDT5 binding by AMP and 6-meTIMP in the presence of PRPP (1 mM). Data represent the mean ± s.e.m. from n = 3 independent experiments. Data for the AMP condition are also shown in Extended Data Fig. . f . Western blot of endogenous PPAT–3×Flag immunoprecipitations after 16-h treatment with MTX (2 µM), 6-MP (50 µM) and MTX + 6-MP. Blot is representative of two independent experiments g . Time-resolved microscopy (incucyte) growth assays of wild-type and mutant HEK293T cells treated with the indicated drugs. Data represent the mean ± s.e.m. of n = 6 biological replicates. h . Levels of intracellular 6-TIMP and 6-meTIMP metabolites after 16-h treatment with 6-MP (20 µM). Data represent the mean ± s.e.m. with individual values from n = 3 biological replicates. i . PPAT activity assay measuring inhibitory effects of 6-meTGMP in the absence and presence of wild-type NUDT5 and mutants. Data represent the mean ± s.e.m. from n = 3 independent experiments. K i values in c , d , i as well as EC 50 in e were compared by global nonlinear regression using an extra sum-of-squares F-test. Statistical significance in h was determined by one-way ANOVA followed by Dunnett’s multiple-comparisons test against wild type. Significance is indicated as ns (not significant), * P < 0.05, ** P < 0.01 and *** P < 0.001. Exact P values are included as source data.

Article Snippet: NUDT5 (75 μM) was incubated with PPAT (15 μM) directly after elution of PPAT from Strep-Tactin resin for 1 h in 2 ml Strep-Tactin elution buffer (50 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 1 mM DTT and 50 mM biotin) supplemented with 200 μM 6-meTIMP (Jena Biosciences, NU-1226) or 6-benzylTIMP (WuXi).

Techniques: Cryo-EM Sample Prep, Activity Assay, Binding Assay, Western Blot, Microscopy, Mutagenesis

Journal: Nature

Article Title: Metabolite glues as a means of purine sensing and chemotherapeutic response

doi: 10.1038/s41586-026-10790-3

Figure Lengend Snippet: a , Chemical structures of 6-meTIMP, 6-benzylthioinosine-5′-monophosphate (6-benzylTIMP) and 6-ethylthioinosine-5′-monophosphate (6-etTIMP). b , PPAT activity assay measuring nucleotide-dependent inhibition in the absence and presence of NUDT5. Data are mean ± s.e.m. from n = 3 independent experiments. The same data for 6-meTIMP are shown in both panels for clarity. c , Structural alignment of the region surrounding the molecular-glue interface for the 6-benzylTIMP- and 6-meTIMP-bound PPAT–NUDT5 structures. Cryo-EM density for the 6-benzylTIMP is shown as a transparent surface. d , Sharpened cryo-EM density of the I422–E436 loop in the 6-benzylTIMP and 6-meTIMP maps shown at the same contour. The dashed oval indicates a region of missing density in the 6-benzylTIMP map that is well-defined in the 6-meTIMP map. e , Viability of wild-type, ∆NUDT5 and endogenous NUDT5 L217/K218A mutant cells treated with 6-etTIMP for 72 h. Data are mean ± s.e.m. of n = 6 biological replicates from 3 independent experiments. FC (fold change) is the ratio of mutant to wild-type IC 50 , representing fold change in 6-etTIMP resistance. Selectivity index (SI) is the ratio of 6-etTIMP to 6-meTIMP fold change relative to wild type, quantifying relative on-target cytotoxicity. An SI greater than 1 is indicative of increased on-target cytotoxicity. f , Model of the NUDT5- and purine- or thiopurine-dependent metabolite-glue mechanism. The double asterisks represent the PPAT hydrophobic pocket. K i and IC 50 values in b , e were compared by global nonlinear regression using an extra sum-of-squares F-test. NS, not significant. *** P < 0.001. Exact P values are included as source data.

Article Snippet: NUDT5 (75 μM) was incubated with PPAT (15 μM) directly after elution of PPAT from Strep-Tactin resin for 1 h in 2 ml Strep-Tactin elution buffer (50 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 1 mM DTT and 50 mM biotin) supplemented with 200 μM 6-meTIMP (Jena Biosciences, NU-1226) or 6-benzylTIMP (WuXi).

Techniques: Activity Assay, Inhibition, Cryo-EM Sample Prep, Mutagenesis

Journal: Materials Today Bio

Article Title: Application of a novel myristoylproteomics approach identifies GLIPR2 as a key pro-ferroptotic substrate in non-small cell lung cancer

doi: 10.1016/j.mtbio.2026.102945

Figure Lengend Snippet: Augmented myristoylation is a feature and consequence of ferroptosis in sensitive cells. A. Workflow for metabolic labeling with YnMyr and detection of myristoylated proteins via CuAAC. B. Viability of Calu-1 cells pretreated with DMSO or 1 μM IMP-1088, then exposed to erastin or ML162 ± Fer-1. C. The impact of ferroptosis to N-myristoylation was detected by western blot. Calu-1 and H460 cells were first incubated with YnMyr for 18 h. For the final 8 h of YnMyr incubation, the cells were co-treated with 5 μM erastin in the presence or absence of 2 μM Fer-1. In a separate experiment, for the final 2 h of YnMyr incubation, the cells were co-treated with 1 μM RSL3 with or without 2 μM Fer-1. D. Samples were analyzed by TAMRA (top) or enriched by pull-down on streptavidin beads and analyzed by Western blot (bottom). The sample before pull-down (Input), pull-down sample (PD) and the supernatant from the pull-down (Spnt) were analyzed. C-SRC, PRKACA and CHCHD3 were enriched in the pull-down samples. GAPDH: loading control. E-F. The impact of ferroptosis to NMT1 or NMT2 was detected by western blot. Cells (Calu-1, E; H460, F) were treated with 5 μM erastin or 1 μM RSL3 for indicated time.Experiments in B were repeated in triplicate.

Article Snippet: IMP-1088 (#HY-112258), erastin (#HY-15763) were purchased from MedChemExpress (Monmouth, NJ, USA).

Techniques: Labeling, Western Blot, Incubation, Control

Journal: Materials Today Bio

Article Title: Application of a novel myristoylproteomics approach identifies GLIPR2 as a key pro-ferroptotic substrate in non-small cell lung cancer

doi: 10.1016/j.mtbio.2026.102945

Figure Lengend Snippet: Myristoylation-dependent ER localization is required for GLIPR2 to promote ferroptosis. A-B. Dose-response curves of GLIPR2 knockout Calu-1 cells with or without GLIPR2-WT or G2A overexpressed, following treated with erastin (A) or ML162 (B) for 24 h. Viability was assessed and normalized to control. C. Western blot analysis validating the expression of GLIPR2 (WT or G2A) in reconstituted GLIPR2-knockout Calu-1 cells. EV, empty vector. D. Western blot analysis of GLIPR2 myristoylation in GLIPR2-knockout Calu-1 cells reconstituted as indicated, and treated with or without 1 μM IMP-1088. E. Immunofluorescence analysis showing the subcellular localization of re-introduced wild-type GLIPR2 and the G2A mutant in GLIPR2-knockout Calu-1 cells. Scale bar, 20 μm. F-G. Dose-response curves of GLIPR2-knockout Calu-1 cells reconstituted with GLIPR2 (WT) or the indicated subcellular localization mutants, treated with erastin (F) or ML162 (G) for 24 h. H. Immunofluorescence analysis of the subcellular localization of the indicated GLIPR2 mutants in GLIPR2-knockout Calu-1 cells. Scale bar, 20 μm. I. Western blot analysis of the expression levels of GLIPR2 (WT) and the indicated mutants in GLIPR2-knockout Calu-1 cells. Data are mean ± SD; n = 3 (A–B and F-G).

Article Snippet: IMP-1088 (#HY-112258), erastin (#HY-15763) were purchased from MedChemExpress (Monmouth, NJ, USA).

Techniques: Knock-Out, Control, Western Blot, Expressing, Plasmid Preparation, Immunofluorescence, Mutagenesis

Journal: JCI Insight

Article Title: Purine metabolism enhances neovascularization of type H vessels in the induced membrane technique

doi: 10.1172/jci.insight.200820

Figure Lengend Snippet: ( A – D ) Representative immunohistochemical images showing expression of ADSS1 ( A ) and IMPDH2 ( B ) in the induced membrane. Quantification of ADSS1 ( C ) and IMPDH2 ( D ) staining using ImageJ. Each dot represents one animal (IM, n = 6; BD, n = 6). Data are presented as area fraction and normalized to DAPI areas. Box plots represent the median (line), interquartile range (box), and minimum to maximum values (whiskers). P < 0.05 was considered statistically significant. ( E ) Summary of showing alterations in serum and induced membrane at week 6 in IMT rats. Scale bars: 50 μm. ADSS1, adenylosuccinate synthase 1; IMPDH2, inosine monophosphate dehydrogenase 2; BD, bone defect; IM, induced membrane.

Article Snippet: The primary antibodies used included adenylosuccinate synthase 1 (ADSS1; A6516, rabbit polyclonal antibody, ABclonal), inosine monophosphate dehydrogenase 2 (IMPDH2; A15626, rabbit polyclonal antibody, ABclonal), CD31 conjugated with Alexa Flour 488 (#42777, clone 89C2, Cell Signaling), and endomucin (EMCN) conjugated with Alexa Flour 555 (BS-4808R-A555, rabbit polyclonal antibody, Bioss).

Techniques: Immunohistochemical staining, Expressing, Membrane, Staining