| Size | Price | Stock | Qty |
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| 10mg |
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| 25mg |
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| 50mg |
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| 100mg |
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| 250mg |
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| 500mg | |||
| Other Sizes |
Purity: ≥98%
| Targets |
BRD9539 targets G9a (EHMT2) and PRC2 (polycomb repressive complex 2), which catalyze histone H3K9 and H3K27 methylation, respectively. It is selective for these enzymes over SUV39H1, NSD2, and DNMT1 up to a concentration of 40 µM.
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| ln Vitro |
In HeLa cells, BRD9539 lowers ATP levels in a dose-dependent manner [1]. Compared to its methyl ester counterpart BRD4770, BRD9539 is a more powerful biochemical inhibitor, having a residual G9a activity of 20% at screening doses as opposed to 45% for BRD4770. In contrast to BRD4770, BRD9539 did not do well in cell-based experiments, perhaps because of decreased cell permeability. Furthermore, in the presence of 5 or 10 μM BRD9539, the activity of 100 kinases and 16 additional chromatin-modifying enzymes implicated in cancer cell biology and cell cycle regulation was examined; no activity was detected in these assays [1].
BRD9539 inhibits G9a and PRC2 enzymatic activity in cell-free assays. It is more potent than the related compound BRD4770 in enzyme-based assays. However, it shows no activity in cell-based assays when used at concentrations of 5 and 10 µM. The compound is inactive against SUV39H1, NSD2, and DNMT1. |
| ln Vivo |
In vivo activity data for BRD9539 are limited. The compound's lack of cellular activity at concentrations up to 10 µM suggests that its utility for in vivo applications may be limited due to poor cell permeability or rapid metabolism. Further optimization would be required to develop cell-active analogs for in vivo studies.
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| Enzyme Assay |
Cell-free histone methyltransferase assays for BRD9539 utilize purified recombinant G9a or PRC2 enzymes and histone peptide or nucleosome substrates. The methylation reaction is performed in the presence of SAM and increasing concentrations of the compound. Methylation of H3K9 (for G9a) or H3K27 (for PRC2) is quantified using radiometric or fluorescence-based detection. IC50 values are determined from concentration-response curves.
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| Cell Assay |
Cells (e.g., cancer cell lines) are treated with BRD9539 at concentrations up to 10 µM. Global H3K9me2 and H3K27me3 levels are assessed by Western blot or immunofluorescence. Gene expression changes are analyzed by qRT-PCR. Cell proliferation and viability assays are performed to evaluate functional consequences. However, BRD9539 shows no activity in cell-based assays at tested concentrations, likely due to poor cellular uptake.
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| Animal Protocol |
In vivo animal studies for BRD9539 have not been reported. The compound's lack of cellular activity makes it unsuitable for in vivo applications without further chemical optimization to improve cell permeability and cellular target engagement.
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| ADME/Pharmacokinetics |
Pharmacokinetic properties of BRD9539 have not been characterized. As a small molecule (MW 399.44, formula C24H21N3O3) with moderate molecular weight, its poor cellular activity suggests that it may have limited cell permeability. The compound is likely soluble in DMSO. Detailed PK parameters remain to be determined.
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| Toxicity/Toxicokinetics |
Toxicity data for BRD9539 are limited. As a research compound targeting histone methyltransferases, standard toxicological assessments would be required for development. The compound's selectivity for G9a and PRC2 over other histone methyltransferases suggests a relatively favorable off-target profile. However, its lack of cellular activity limits its utility.
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| References | |
| Additional Infomation |
BRD9539 (molecular formula C24H21N3O3, MW 399.44) is also known as 2-(benzoylamino)-1-(3-phenylpropyl)-1H-benzimidazole-5-carboxylic acid. It is selective for G9a and PRC2 over SUV39H1, NSD2, and DNMT1. While more potent than BRD4770 in enzyme assays, it lacks cellular activity. The compound is intended for research use only.
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| Molecular Formula |
C24H21N3O3
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|---|---|
| Molecular Weight |
399.4418
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| Exact Mass |
399.158
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| CAS # |
1374601-41-8
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| PubChem CID |
73755260
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| Appearance |
White to off-white solid powder
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| Density |
1.3±0.1 g/cm3
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| Boiling Point |
676.4±57.0 °C at 760 mmHg
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| Flash Point |
362.9±32.1 °C
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| Vapour Pressure |
0.0±2.2 mmHg at 25°C
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| Index of Refraction |
1.650
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| LogP |
5.82
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
4
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| Rotatable Bond Count |
7
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| Heavy Atom Count |
30
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| Complexity |
586
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| Defined Atom Stereocenter Count |
0
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| InChi Key |
WPXMEOBILYVKBC-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C24H21N3O3/c28-22(18-11-5-2-6-12-18)26-24-25-20-16-19(23(29)30)13-14-21(20)27(24)15-7-10-17-8-3-1-4-9-17/h1-6,8-9,11-14,16H,7,10,15H2,(H,29,30)(H,25,26,28)
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| Chemical Name |
2-benzamido-1-(3-phenylpropyl)benzimidazole-5-carboxylic acid
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
DMSO : ~16.67 mg/mL (~41.73 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: 1.67 mg/mL (4.18 mM) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), suspension solution; with sonication.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 16.7 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 1.67 mg/mL (4.18 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 16.7 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 2.5035 mL | 12.5175 mL | 25.0350 mL | |
| 5 mM | 0.5007 mL | 2.5035 mL | 5.0070 mL | |
| 10 mM | 0.2504 mL | 1.2518 mL | 2.5035 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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