idh1 protein  (Proteintech)

Journal: bioRxiv

Article Title: Sampling Function-Related Metastable States of Proteins With DASH

doi: 10.64898/2025.12.24.696448

Figure Lengend Snippet: a. Problem description and physical function for seed selection. b-c. Two examples of sampling the opening of cryptic allosteric site. b. Change of pocket exposure along iterations. Error bars represent standard deviations. c. Dimension reduction by CTMAE and metastable states for open/closed conformations. d. Comparison of pocket exposure by different MD methods. DASH is calculated using all rounds of trajectories. e. DASH simulation of apo IDH1, free energy surface (CTMAE CV reweighted by MSM), and novel pockets detected. f. Calculation of AlloReverse score and pocket exposure of the 6 pockets. g. Pocket 5 in different conformations. h. Validation workflow of pocket 5. i. SPR experiment of fragment Fr13454. j. Comparison of crystal and docking pose of Fr13454. Error bars represent standard deviations. N=400 for b , N=8 for d , N=10000 for f and N=3 for i .

Article Snippet: The library for virtual screening is L7800 ( https://www.targetmol.com/compound-library/High_Solubility_Fragment_Library ) for SIRT6 and a manual library (Data S3) for IDH1.

Techniques: Selection, Sampling, Comparison, Biomarker Discovery

Journal: bioRxiv

Article Title: Sampling Function-Related Metastable States of Proteins With DASH

doi: 10.64898/2025.12.24.696448

Figure Lengend Snippet: a. Top 10 selected compounds by virtual screening on the selected allosteric pocket of IDH1. b. Comparison of the solved crystal structures of apo and Fr13454-bound IDH1. c. Distribution of helix degree calculated from 1000 samples generated by IDPSAM. Range of helix degree is set between 0 and the largest value (length of IDR minus 5).

Article Snippet: The library for virtual screening is L7800 ( https://www.targetmol.com/compound-library/High_Solubility_Fragment_Library ) for SIRT6 and a manual library (Data S3) for IDH1.

Techniques: Comparison, Generated

Journal: Cell Death & Disease

Article Title: Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

doi: 10.1038/s41419-024-06625-6

Figure Lengend Snippet: A Chemical structure of Scu-B. B Schematic of the procedure for detecting binding events by HuProt TM proteome microarray and IDH1 was identified as a direct cellular target of Scu. C IDH1 recombinant protein chip analysis identified IDH1 as a direct cellular target of Scu. D The expression profile of IDH1 in various tissues from the TCGA database. E Kaplan‒Meier plots of the disease-free survival (DFS) rates of groups with differential IDH1 expression in the liver cancer RNA-seq dataset. F IDH1 expression levels were decreased in tumor tissues ( n = 64) compared with their matched adjacent nontumoral tissues ( n = 32), as shown in representative immunohistochemical images and mean staining scores. G and H Growth curves of cells that were cultured in 24-well plates (1 × 10 4 per well) for the indicated times under different oxygen concentrations. n = 3. I Colony formation assays of cells cultured in six-well plates (0.5 × 10 4 per well) under different oxygen concentrations for two weeks. n = 3. J The growth of OE_IDH1 and OE_CON H22 cells in BALB/c mice was photographed 4 weeks after transplantation. n = 5. The dynamic change in K tumor volume, and the changes in L tumor weight in the subcutaneous model mice at four weeks after injection are shown. Scale bars, 200 μm. The data are mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001 compared to the control group.

Article Snippet: To detect the direct effect of Scu on the IDH1 protein in vitro, antibody plates were generated by coating the IDH1 antibody (Proteintech) onto 96-well plates (100 ng/well) overnight at 4 °C.

Techniques: Binding Assay, Microarray, Recombinant, Expressing, RNA Sequencing, Immunohistochemical staining, Staining, Cell Culture, Transplantation Assay, Injection, Control

Journal: Cell Death & Disease

Article Title: Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

doi: 10.1038/s41419-024-06625-6

Figure Lengend Snippet: A Schematic representation of the IDH1-α-KG-HIF1a signaling axis regulating tumor growth. B Correlation analysis of IDH1 and HIF1a protein expression levels in the CRISPR liver cancer dataset. The correlation coefficient R and P values are shown on the graphs. C The level of α-KG in OE_IDH1 and OE_CON HepG2 cells under hypoxia. n = 3. D Relative mRNA levels of the indicated genes in OE_IDH1 and OE_CON HepG2 cells under hypoxia. n = 3. E Western blot of the indicated proteins in OE_IDH1 and OE_CON HepG2 cells under hypoxia. n = 3. F Immunofluorescence staining of HIF1a and OH-HIF1a proteins in OE_IDH1 and OE_CON HepG2 cells under hypoxia. Arrows indicate that fluorescent signals are located in the nucleus or cytoplasm. G Detection of the phenotypic transformation of energy metabolism in OE_IDH1 and OE_CON HepG2 cells under hypoxia by a Seahorse energy metabolic instrument. n = 6. H , I Seahorse glycolysis rate curves of OE_IDH1 and OE_CON HepG2 cells under hypoxia. n = 6. J The 2-NBDG probe revealed glucose uptake levels in OE_IDH1 and OE_CON HepG2 cells under hypoxia. K Measurement of lactate secretion in OE_IDH1 and OE_CON HepG2 cells under hypoxia. n = 3. L Representative histological analysis of tumor specimens stained with H&E, Ki67, HIF1a, GLUT1, and VEGFA and quantification of OE_IDH1 and OE_CON H22 transplanted tumors from BALB/c mice. n = 5. M Representative images of IHC staining for CD4, CD8, F4/80, CD56, and PD-L1 in OE_IDH1 and OE_CON H22 cell transplanted tumor tissue and quantification in BALB/c mice. The black arrows indicate positively stained cells. n = 5. Scale bars, 25 μm. The data are mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001 compared to the control group.

Article Snippet: To detect the direct effect of Scu on the IDH1 protein in vitro, antibody plates were generated by coating the IDH1 antibody (Proteintech) onto 96-well plates (100 ng/well) overnight at 4 °C.

Techniques: Expressing, CRISPR, Western Blot, Immunofluorescence, Staining, Transformation Assay, Immunohistochemistry, Control

Journal: Cell Death & Disease

Article Title: Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

doi: 10.1038/s41419-024-06625-6

Figure Lengend Snippet: A The 48-h proliferation curve of different tumor cell lines treated with Scu at different oxygen concentrations. n = 5. B Comparison of the 48-hour IC 50 values of Scu in different tumor cell lines treated with different oxygen concentrations. C Detection of the energy metabolism phenotype of tumor cells under different oxygen concentrations by a Seahorse energy metabolism instrument. n = 6. D Inhibitory effect of Scu on glycolysis in HepG2 cells subjected to hypoxia for 12 h. n = 6. E Cell viability assays of Sh_IDH1 and Sh_CON HepG2 cells treated with Scu for 48 h under hypoxia. n = 3. F Growth curves of Sh_IDH1 and Sh_CON HepG2 cells treated with Scu for 6 days under hypoxia. n = 3. G The growth of Sh_IDH1 and Sh_CON H22 cells in BALB/c mice was photographed after four weeks of 40 mg/kg/day Scu administration. n = 5. H Changes in tumor weight in H22 xenograft tumor models after four weeks of Scu administration are shown. I Relative expression of IDH1 and HIF1a proteins in different cells under hypoxia. n = 3. J Correlation analysis of IDH1 and HIF1a protein expression in different cells under hypoxia. n = 3. K Correlation analysis between IDH1 protein expression and sensitivity to Scu in different cells under hypoxia. n = 3. The data are mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001 compared to the control group.

Article Snippet: To detect the direct effect of Scu on the IDH1 protein in vitro, antibody plates were generated by coating the IDH1 antibody (Proteintech) onto 96-well plates (100 ng/well) overnight at 4 °C.

Techniques: Comparison, Expressing, Control

Journal: Cell Death & Disease

Article Title: Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

doi: 10.1038/s41419-024-06625-6

Figure Lengend Snippet: A Proteome reactivity profile of HepG2 cells treated with Scu-B (100 μM). A protein affinity pull-down assay was subsequently performed. Then, the whole-cell lysates were pulled down with streptavidin beads, and the precipitated proteins were separated by SDS‒PAGE and processed by silver staining and LC‒MS/MS. B Labeling of recombinant IDH1 with Scu-B (100 μM). Immunofluorescence analysis of IDH1-Scu-B by Cy3-streptavidin. C , D CETSA confirmed the binding of Scu to IDH1. n = 3. E BLI assay showing the interaction of Scu with IDH1. F Schematic representation of the Scu activation of IDH1-mediated NADPH and α-KG production. G Scu increased α-KG production in HepG2 cells after treatment with Scu for 12 h. n = 3. H Quantitative analysis of the effect of Scu on the enzymatic activity of the IDH1 protein in HepG2 cells after treatment with Scu for 12 h. n = 3. I Scu dose-dependently activated the IDH1 protein in HepG2 cells. n = 3. J Scu had no influence on the level of D-2-hydroxyglutarate (D2HG) in HT1080 (IDH1-R132C) cells. n = 4. The data are mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001 compared to the control group.

Article Snippet: To detect the direct effect of Scu on the IDH1 protein in vitro, antibody plates were generated by coating the IDH1 antibody (Proteintech) onto 96-well plates (100 ng/well) overnight at 4 °C.

Techniques: Pull Down Assay, Silver Staining, Labeling, Recombinant, Immunofluorescence, Binding Assay, Activation Assay, Activity Assay, Control

Journal: Cell Death & Disease

Article Title: Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

doi: 10.1038/s41419-024-06625-6

Figure Lengend Snippet: A The absorption spectra of Scu (200 μM) in the presence or absence of GSH or recombinant IDH1 protein. B Scu competed with IAA-yne for binding to the recombinant IDH1 protein in the in-gel fluorescence assay. C LC‒MS/MS analysis showing the modification of IDH1 by Scu at the Cys297 residue. The recombinant IDH1 protein was incubated with IDH1 for 2 h at 37 °C. D Protein chip analysis showed that the Cys297 mutation blocked the interaction of biotin-labeled Scu with IDH1. n = 3. E An enzyme-linked affinity assay showed that the Cys297 mutation blocked the interaction of biotin-labeled Scu with IDH1. n = 4. F Scu had no effect on the enzyme activity of the IDH1-C297S mutant. n = 3. G BLI experiments to assess the binding kinetics between Scu and IDH1-WT or the IDH1-C297S mutant. H Proposed reaction of IDH1 adducts with Scu. I Molecular docking analysis of the predicted binding mode of Scu to IDH1. J Proposed scutellarin-cysteine reaction pathway in aqueous solution. K Scu (20 μM) promoted IDH1 active dimer formation in HepG2 cells under hypoxia. n = 3. The data are mean ± SD; * P < 0.05; ** P < 0.01; *** P < 0.001 compared to the control group.

Article Snippet: To detect the direct effect of Scu on the IDH1 protein in vitro, antibody plates were generated by coating the IDH1 antibody (Proteintech) onto 96-well plates (100 ng/well) overnight at 4 °C.

Techniques: Recombinant, Binding Assay, Fluorescence, Modification, Residue, Incubation, Mutagenesis, Labeling, Activity Assay, Control

Journal: Cell Death & Disease

Article Title: Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

doi: 10.1038/s41419-024-06625-6

Figure Lengend Snippet: A Schematic plan for the administration of Scu (60 and 100 mg/kg/day). C The tumor weight and D tumor volume were monitored every week for four weeks. After the mice were sacrificed, the resected tumors were B photographed and processed for pathological and immunohistochemical assays for E , F necrosis area and Ki67, L , M HIF1α, GLUT1, VEGFA, and N , O CD4, CD8, F4/80, CD56 and PD-L1 expression. G The relative mRNA levels of the indicated genes, H , I the expression levels of the indicated proteins, J the level of α-KG, and K IDH1 activity in tumor tissue were detected after treatment with Scu in vivo. The black arrows indicate positively stained cells. Scale bars, 50 μm. n ≥ 5. The data are mean ± SD; *P < 0.05; **P < 0.01; ***P < 0.001 compared to the control group.

Article Snippet: To detect the direct effect of Scu on the IDH1 protein in vitro, antibody plates were generated by coating the IDH1 antibody (Proteintech) onto 96-well plates (100 ng/well) overnight at 4 °C.

Techniques: Immunohistochemical staining, Expressing, Activity Assay, In Vivo, Staining, Control

Journal: Experimental and Therapeutic Medicine

Article Title: Clinical characteristics and prognostic analysis of patients with HIV and glioma: A case series and literature review

doi: 10.3892/etm.2024.12380

Figure Lengend Snippet: Characteristics of HIV-positive patients with brain glial tumors treated at Beijing Ditan Hospital.

Article Snippet: The primary antibodies CD31 (cat. no. ZA-0568), CD68 (cat. no. ZM-0060), CD163 (cat. no. ZM-0428), IDH1 R132H mutation-specific (cat. no. ZM-0447) and Ki-67 (cat. no. ZM-0166) were purchased from ZSGB-BIO (OriGene Technologies, Inc.) and used at a dilution of 1:100.

Techniques: