yingweiwo

CDK9/HDAC1/HDAC3-IN-1

Cat No.:V131306 Purity: ≥98%
CDK9/HDAC1/HDAC3-IN-1 is a bifunctional inhibitor of CDK9 and HDAC.
CDK9/HDAC1/HDAC3-IN-1
CDK9/HDAC1/HDAC3-IN-1 Chemical Structure CAS No.: 2197029-81-3
Product category: HDAC
This product is for research use only, not for human use. We do not sell to patients.
Size Price
500mg
1g
Other Sizes
Official Supplier of:
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text
Alternate Text

 

  • Business Relationship with 5000+ Clients Globally
  • Major Universities, Research Institutions, Biotech & Pharma
  • Citations by Top Journals: Nature, Cell, Science, etc.
Top Publications Citing lnvivochem Products
Product Description
CDK9/HDAC1/HDAC3-IN-1 is a bifunctional inhibitor of CDK9 and HDAC. The IC50 values for inhibiting the protein activity of CDK9, HDAC1, and HDAC3 by CDK9/HDAC1/HDAC3-IN-1 are 0.17 μM, 1.73 μM, and 1.11 μM, respectively. CDK9/HDAC1/HDAC3-IN-1 inhibits cancer cells by inducing apoptosis and G2/M phase cell cycle arrest, and inhibits tumor growth in a mouse triple-negative breast cancer (TNBC) MDA-MB-231 xenograft model. CDK9/HDAC1/HDAC3-IN-1 possesses broad-spectrum anticancer activity and can be used to treat various cancers, including breast cancer, cervical cancer, and liver cancer.
Biological Activity I Assay Protocols (From Reference)
ln Vitro
CDK9/HDAC1/HDAC3-IN-1 (compound 13EA) (24 hours) showed potent antiproliferative activity in various cancer cell lines (e.g., IC50 values of 1.51 μM, 2.47 μM and 4.52 μM for HeLa, MDA-MB-231 and HepG2, respectively)[1]. CDK9/HDAC1/HDAC3-IN-1 (MDA-MB-231 cells: 0.625-5 μM, HeLa: 0.625-1.25 μM, 24 hours) inhibited the expression of p-Ser2 mRNA in MDA-MB-231 cells in a time- and dose-dependent manner[1]. CDK9/HDAC1/HDAC3-IN-1 (MDA-MB-231 cells: 0.625-5 μM, 24 h) significantly reduced the protein expression of p-Ser2 (a substrate of CDK9) in MDA-MB-231 cells and HeLa cells, while increasing the protein expression of Ac-H3 (a substrate of HDAC) [1]. CDK9/HDAC1/HDAC3-IN-1 (0.625-5 μM, 24 h) induced mitochondrial-related apoptosis in MDA-MB-231 cells and HeLa cells in a concentration-dependent manner, upregulated the expression of cleaved PARP, and arrested the cell cycle in the G2/M phase [1].
ln Vivo
CDK9/HDAC1/HDAC3-IN-1 (30 mg/kg, intraperitoneal injection, once daily for 10 days) significantly inhibited tumor growth in the MDA-MB-231 mouse xenograft model [1].
Cell Assay
Western Blot Analysis [1]
Cell Types: MDA-MB-231 cells, HeLa cells
Tested Concentrations: MDA-MB-231 cells (0.625, 1.25, 2.5, 5 μM), HeLa cells (0.625, 1.25 μM)
Incubation Duration: 24 hours
Experimental Results: Dose-dependently inhibited p-Ser2 (a substrate of CDK9) levels and upregulated Ac-H3 (a substrate of HDAC) levels.
Real-time quantitative PCR[1]
Cell Types: MDA-MB-231 cells
Tested Concentrations: 0.625, 1.25, 2.5, 5 μM
Incubation Duration: 3, 6, 12, 24 hours Experimental
Experimental Results: CDK9 mRNA expression was downregulated in a time- and dose-dependent manner, reaching maximum inhibition at 24 hours.
Immunofluorescence [1]
Cell Types: MDA-MB-231 cells, HeLa cells
Tested Concentrations: 3 μM
Incubation Duration: 24 hours
Experimental Results: p-Ser2 levels were decreased and Ac-H3 levels were upregulated in HeLa and MDA-MB-231 cells.
.summary { text-align: center; } .summary font:hover { cursor: pointer; } .icon-angle{ font-family: FontAwesome; margin-left: 11px; font-weight: bold; display: inline; } .icon-angle-up{ display: none; } .icon-angle-down:before { content: "\f107"; } .icon-angle-up:before { content: "\f106"; }

View More


Apoptosis analysis [1]
Cell Types: MDA-MB-231 cells, HeLa cells
Tested Concentrations: 2.5 μM/3 μM
Incubation Duration: 24 hours
Experimental Results: In MDA-MB-231 cells, the expression of Bcl-2 and Mcl-1 proteins decreased in a dose-dependent manner, while the expression of cleaved PARP protein increased in both MDA-MB-231 and HeLa cells in a dose-dependent manner. Annexin V-FITC/PI double staining showed that the induced apoptosis rate increased in a dose-dependent manner, ranging from 11.30% (0.31 μM) to 77.38% (2.5 μM). The concentration-dependent reduction of mitochondrial membrane potential (MMP, Δψ) in MDA-MB-231 cells was observed. At concentrations of 0.31, 0.63, 1.35, and 2.5 μM, Δψ was reduced by 17.06%, 26.83%, 41.97%, and 52.73%, respectively.
Cell cycle analysis [1]
Cell Types: MDA-MB-231 cells
Tested Concentrations: 0.31, 0.63, 1.35 and 2.5 μM
Incubation Duration: 24 hours
Experimental Results: Significantly increased the number of cells in the G2/M phase [(27.43% (0.31 μM), 79.47% (0.63 μM), 47.58% (1.25 μM) and 42.20% (2.5 μM)], and gradually promoted the number of cells in the sub-G1 phase [(3.00% (0.31 μM), 7.64% (0.63 μM), 23.89% (1.25 μM) and 42.20% (2.5 μM)]. 27.94% (2.5 μM)].

Animal Protocol
Animal/Disease Models:MDA-MB-231 cells in logarithmic growth phase (3 × 10⁷ cells/mouse) were subcutaneously injected into 6-week-old female BALB/c nude mice [1].
Doses: 30 mg/kg
Route of Administration: Intraperitoneal injection, once daily for 10 consecutive days until the tumor volume reached approximately 100 mm³.
Experimental Results: The drug inhibited the growth of MDA-MB-231 xenograft tumors over time and significantly reduced tumor volume. Immunohistochemical staining showed a significant increase in cleaved caspase-3 and a significant decrease in PCNA levels in the tumor tissue.
References

[1]. Design, synthesis, and biological evaluation of N-(2-amino-phenyl)-5-(4-aryl-pyrimidin-2-yl) amino)-1H-indole-2-carboxamide derivatives as novel inhibitors of CDK9 and class I HDACs for cancer treatment[J]. Bioorganic Chemistry, 2025: 108577.

These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C24H22N8OS
Molecular Weight
470.55
CAS #
2197029-81-3
Appearance
Typically exists as solids at room temperature
SMILES
CNC1=NC(C)=C(S1)C2=NC(NC3=CC=C4C(C=C(C(NC5=CC=CC=C5N)=O)N4)=C3)=NC=C2
HS Tariff Code
2934.99.9001
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)
Solubility Data
Solubility (In Vitro)
May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples
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
(e.g. IP/IV/IM/SC)
Injection Formulation 1: DMSO : Tween 80: Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution 50 μL Tween 80 850 μL Saline)
*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 : PEG300Tween 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)]
*Preparation of 20% SBE-β-CD in Saline (4°C,1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution.
Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin 500 μL Saline)
Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO 100 μLPEG300 200 μL castor oil 650 μL Saline)
Injection Formulation 7: Ethanol : Cremophor : Saline = 10: 10 : 80 (i.e. 100 μL Ethanol 100 μL Cremophor 800 μL Saline)
Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline
Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH 900 μL Corn oil)
Injection Formulation 10: EtOH : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH 400 μLPEG300 50 μL Tween 80 450 μL 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
Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose
Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose
Oral Formulation 6: Mixing with food powders


Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.

 (Please use freshly prepared in vivo formulations for optimal results.)
Preparing Stock Solutions 1 mg 5 mg 10 mg
1 mM 2.1252 mL 10.6259 mL 21.2517 mL
5 mM 0.4250 mL 2.1252 mL 4.2503 mL
10 mM 0.2125 mL 1.0626 mL 2.1252 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.

Calculator

Molarity Calculator allows you to calculate the mass, volume, and/or concentration required for a solution, as detailed below:

  • Calculate the Mass of a compound required to prepare a solution of known volume and concentration
  • Calculate the Volume of solution required to dissolve a compound of known mass to a desired concentration
  • Calculate the Concentration of a solution resulting from a known mass of compound in a specific volume
An example of molarity calculation using the molarity calculator is shown below:
What is the mass of compound required to make a 10 mM stock solution in 5 ml of DMSO given that the molecular weight of the compound is 350.26 g/mol?
  • Enter 350.26 in the Molecular Weight (MW) box
  • Enter 10 in the Concentration box and choose the correct unit (mM)
  • Enter 5 in the Volume box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 17.513 mg appears in the Mass box. In a similar way, you may calculate the volume and concentration.

Dilution Calculator allows you to calculate how to dilute a stock solution of known concentrations. For example, you may Enter C1, C2 & V2 to calculate V1, as detailed below:

What volume of a given 10 mM stock solution is required to make 25 ml of a 25 μM solution?
Using the equation C1V1 = C2V2, where C1=10 mM, C2=25 μM, V2=25 ml and V1 is the unknown:
  • Enter 10 into the Concentration (Start) box and choose the correct unit (mM)
  • Enter 25 into the Concentration (End) box and select the correct unit (mM)
  • Enter 25 into the Volume (End) box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 62.5 μL (0.1 ml) appears in the Volume (Start) box
g/mol

Molecular Weight Calculator allows you to calculate the molar mass and elemental composition of a compound, as detailed below:

Note: Chemical formula is case sensitive: C12H18N3O4  c12h18n3o4
Instructions to calculate molar mass (molecular weight) of a chemical compound:
  • To calculate molar mass of a chemical compound, please enter the chemical/molecular formula and click the “Calculate’ button.
Definitions of molecular mass, molecular weight, molar mass and molar weight:
  • Molecular mass (or molecular weight) is the mass of one molecule of a substance and is expressed in the unified atomic mass units (u). (1 u is equal to 1/12 the mass of one atom of carbon-12)
  • Molar mass (molar weight) is the mass of one mole of a substance and is expressed in g/mol.
/

Reconstitution Calculator allows you to calculate the volume of solvent required to reconstitute your vial.

  • Enter the mass of the reagent and the desired reconstitution concentration as well as the correct units
  • Click the “Calculate” button
  • The answer appears in the Volume (to add to vial) box
In vivo Formulation Calculator (Clear solution)
Step 1: Enter information below (Recommended: An additional animal to make allowance for loss during the experiment)
Step 2: Enter in vivo formulation (This is only a calculator, not the exact formulation for a specific product. Please contact us first if there is no in vivo formulation in the solubility section.)
+
+
+

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.

Contact Us