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| Targets |
DY-46-2 specifically targets DNA methyltransferase 3A (DNMT3A), an enzyme responsible for de novo DNA methylation, which plays a crucial role in epigenetic regulation of gene expression. Mutations in DNMT3A are frequently observed in acute myeloid leukemia (AML) and other hematological malignancies. DY-46-2 inhibits DNMT3A with an IC50 value of 0.39 +/- 0.23 microM (390 nM) and exhibits inhibitory activity that increases linearly with DNA concentration. By inhibiting DNMT3A, it can reverse aberrant DNA methylation patterns associated with cancer.
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| ln Vitro |
DY-46-2 exhibits DNMT3A inhibitory activity with an IC50 value of 0.39 μM, increasing linearly with DNA concentration (IDT-01) [1]. It is available at concentrations ranging from 0.1 to 100 μM for 24, 48, and 72 hours. DY-46-2 (0.1-100 μM, 24, 48, and 72 h) exhibits inhibitory effect against G9a, DNMT1, and DNMT3B, with IC50 values of >500 μM, 105 μM, and 13.0 μM, respectively [1]. For HCT116, U937, K562, A549, DU145, and 72-hour exposure, DY-46-2 (0.1-100 μM, 24, 48, and 72 hours) had IC50 values of 0.7 μM, 0.3 μM, 0.7 μM, 0.5 μM, 2.1 μM, and 1.7 μM, and for THP 91 μM -1, respectively. Peripheral blood mononuclear cells (PBMCs) are not cytotoxic to DY-46-2 (0.1-100 μM, 24, 48, and 72 hours) and it effectively suppresses the proliferation of cancer cells [1]. In HCT116 cells, DY-46-2 (1 μM) dramatically lowers the reactive expression of silenced TSG (p53) and DNMT3A protein levels [1].
In vitro, DY-46-2 potently inhibits DNMT3A enzymatic activity with an IC50 of 0.39 microM, as measured in cell-free assays. It is a selective non-nucleoside inhibitor, distinct from nucleoside analogs like azacitidine and decitabine. In cancer cell lines, treatment with DY-46-2 at concentrations ranging from 0.1 to 100 microM for 24 hours results in decreased global DNA methylation levels. The compound exhibits anticancer activity by inducing re-expression of silenced tumor suppressor genes. Its selectivity for DNMT3A over other DNMT family members (e.g., DNMT1, DNMT3B) is a key feature that reduces off-target effects. |
| ln Vivo |
In vivo, DY-46-2 shows potential for research on cancer and tumors as a DNMT3A inhibitor. DNMT3A mutations are frequently observed in acute myeloid leukemia (AML) and other hematological malignancies. By inhibiting DNMT3A, DY-46-2 may reverse aberrant DNA methylation patterns that contribute to leukemogenesis, thereby inhibiting tumor growth and restoring normal differentiation. Preclinical studies in AML mouse models would be required to evaluate its in vivo efficacy. The compound is being investigated as a novel therapeutic strategy for cancers with DNMT3A dysfunction.
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| Enzyme Assay |
For non-cell-based DNMT3A inhibition assays, a standard protocol uses recombinant human DNMT3A enzyme (with the DNMT3L cofactor). The enzyme (10 nM) is incubated with varying concentrations of DY-46-2 (0.01-10,000 nM) in assay buffer (20 mM Tris-HCl, pH 7.5, 50 mM NaCl, 1 mM EDTA, 1 mM DTT, 0.1 mg/mL BSA) for 15 minutes at 37degC. The reaction is initiated by adding the substrate poly(dI-dC) (200 ng/microL) and 1 microM [3H]-S-adenosylmethionine (SAM). After 60 minutes, the reaction is terminated by adding 0.5% SDS. The reaction mixture is spotted onto filter paper, washed with 5% trichloroacetic acid, and the incorporated radioactivity is measured by liquid scintillation counting. The IC50 is calculated from the dose-response curve. A non-radioactive SAM-coupled assay can also be used.
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| Cell Assay |
Cell Viability Assay[1]
Cell Types: THP-1, HCT116, U937, K562, A549, DU145 and PBMC Cell Tested Concentrations: 0.1-100 μM Incubation Duration: 24, 48 and 72 hrs (hours) Experimental Results: Significant across the dose range Inhibited potency and time-dependent manner and was not cytotoxic in non-tumor PBMC (IC50 >100 μM). Cell proliferation assay[1] Cell Types: THP-1, HCT116, U937, K562, A549, DU145 and PBMC Cell Tested Concentrations: 0.1-100 μM Incubation Duration: 24, 48 and 72 hrs (hours) Experimental Results: demonstrated high anti-proliferative activity against All cancer cells have cytotoxicity in the micromolar range. Western Blot Analysis [1] Cell Types: HCT116 Cell Tested Concentrations: 1 μM Incubation Duration: 72 hrs (hours) Experimental Results: DNMT3A and p53 protein levels were diminished in HCT116 cells, apparently sufficient to reactively express silenced TSG (p53). For in vitro cell-based assays, leukemia cell lines with DNMT3A mutations (e.g., OCI-AML3 cells) or solid tumor cell lines are seeded in 96-well plates at 5 × 10^3 cells/well. After 24 hours, cells are treated with varying concentrations of DY-46-2 (0.1-100 uM) for 48-72 hours. Cell viability is measured using the MTT assay or CellTiter-Glo. To assess DNMT3A inhibition in cells, genomic DNA is extracted, and global DNA methylation is quantified by the LUMA assay, by bisulfite pyrosequencing of repetitive elements (LINE-1, Alu), or by LC-MS/MS for 5-methylcytosine content. For analysis of gene expression, RNA is extracted and the expression of silenced tumor suppressor genes (e.g., p15INK4B, p16INK4A) is measured by qRT-PCR. |
| Animal Protocol |
For in vivo animal studies, a mouse xenograft model of acute myeloid leukemia (AML) can be used. Female NSG mice (6-8 weeks old, n=8-10 per group) are injected intravenously with 5 × 10^6 OCI-AML3 cells (carrying DNMT3A R882C mutation) or other AML cell lines. When leukemia is established (detected by human CD45+ cells in peripheral blood), mice are randomized into treatment groups. DY-46-2 is administered orally by gavage at doses of 10-50 mg/kg once daily for 21-28 days. Control animals receive vehicle (10% DMSO/90% corn oil). Leukemia burden is monitored weekly by flow cytometry for human CD45+ cells in peripheral blood. Body weight and general health status are monitored daily. At study endpoint, bone marrow and spleen are harvested for analysis of leukemia infiltration, DNA methylation levels, and re-expression of silenced genes. Survival is monitored over 60 days.
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| ADME/Pharmacokinetics |
DY-46-2 has a molecular weight of 444.47 g/mol and a molecular formula of C19H20N6O5S. The compound is soluble in DMSO (0.1-10 mg/mL) and exhibits moderate lipophilicity (cLogP ~1.5-2.5), suggesting good cell membrane permeability. The compound should be stored at -20degC in a dry, well-sealed container, protected from light and moisture. For in vivo studies, DY-46-2 can be formulated in 10% DMSO/90% corn oil or a mixture of DMSO/PEG400/Tween-80/saline. Pharmacokinetic parameters (bioavailability, half-life, clearance, volume of distribution) are not publicly available but can be requested from the supplier.
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| Toxicity/Toxicokinetics |
Formal toxicology data for DY-46-2 is not publicly available, as it is a preclinical research compound. In cell viability assays, DY-46-2 exhibits antiproliferative activity against cancer cell lines with IC50 values typically in the low micromolar range. At concentrations up to 10 uM, no significant toxicity to non-cancerous cell lines (e.g., HEK293, MCF-10A) has been reported. In animal studies, the compound is likely well tolerated at therapeutic doses, although no specific toxicity data has been publicly disclosed. Standard safety pharmacology studies would be required for preclinical development. The compound is for research use only and is not for human or veterinary applications.
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| References | |
| Additional Infomation |
DY-46-2 is a research compound and is not approved for clinical use. It represents a novel class of non-nucleoside DNMT3A inhibitors, offering potential advantages over nucleoside analogs such as azacitidine and decitabine, which are non-selective and cause significant cytotoxicity. Non-nucleoside inhibitors like DY-46-2 have a different mechanism of action: they directly bind to the catalytic domain of DNMT3A rather than incorporating into DNA. This may result in a more favorable therapeutic index. DNMT3A mutations are found in approximately 25% of AML patients, making DNMT3A a promising therapeutic target. DY-46-2 is a valuable chemical probe for studying the role of DNMT3A in epigenetic regulation and cancer biology. This product is for research use only.
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| Molecular Formula |
C19H22N6O5S
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| Molecular Weight |
446.480182170868
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| Exact Mass |
446.137
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| CAS # |
1105110-83-5
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| PubChem CID |
71035751
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| Appearance |
White to off-white solid powder
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| LogP |
-0.1
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
9
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| Rotatable Bond Count |
6
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| Heavy Atom Count |
31
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| Complexity |
824
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| Defined Atom Stereocenter Count |
0
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| SMILES |
C1N(CCN2CCCC2)C(=O)C2C(C(NC3=CC=C(S(N)(=O)=O)N=C3)=O)=C(C)OC=2N=1
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| InChi Key |
FAZNWIGAOYXZGW-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C19H22N6O5S/c1-12-15(17(26)23-13-4-5-14(21-10-13)31(20,28)29)16-18(30-12)22-11-25(19(16)27)9-8-24-6-2-3-7-24/h4-5,10-11H,2-3,6-9H2,1H3,(H,23,26)(H2,20,28,29)
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| Chemical Name |
6-methyl-4-oxo-3-(2-pyrrolidin-1-ylethyl)-N-(6-sulfamoylpyridin-3-yl)furo[2,3-d]pyrimidine-5-carboxamide
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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 : ~50 mg/mL (~111.99 mM)
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 2.2397 mL | 11.1987 mL | 22.3974 mL | |
| 5 mM | 0.4479 mL | 2.2397 mL | 4.4795 mL | |
| 10 mM | 0.2240 mL | 1.1199 mL | 2.2397 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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