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| Targets |
CDK9-IN-2 targets cyclin-dependent kinase 9 (CDK9), a key regulator of transcription elongation. CDK9 forms a complex with cyclin T1 (P-TEFb) and phosphorylates the C-terminal domain (CTD) of RNA polymerase II, which is essential for productive transcription elongation. By inhibiting CDK9, the compound disrupts this process, leading to decreased transcription of genes, including those critical for cancer cell survival.
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| ln Vitro |
MEPCE expression is decreased by CDK9-IN-2 (200 nM), suggesting that MEPCE is a pharmacodynamic (PD) marker for all CDK9 inhibitors. Following treatment, MCL1 protein expression declined for two hours, and this reduction continued for sixteen hours following exposure to 500 nM CDK9-IN-2 [1].
CDK9-IN-2 is a specific CDK9 inhibitor with potent activity in cancer cell lines. It has an IC50 of 5 nM in H929 multiple myeloma cells and 7 nM in A2058 melanoma cells (72 hours). The compound inhibits CDK9-mediated phosphorylation of RNA polymerase II, leading to reduced transcription and cell death. |
| ln Vivo |
Specific in vivo activity data for CDK9-IN-2 is not extensively detailed in the available literature. As a potent CDK9 inhibitor with activity in multiple myeloma and melanoma cell lines, it has potential for the treatment of these cancers. Further studies are needed to evaluate its in vivo efficacy and pharmacokinetic properties.
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| Enzyme Assay |
CDK9-IN-2's activity as a CDK9 inhibitor is assessed using in vitro kinase assays. These assays measure the compound's ability to inhibit the phosphorylation activity of CDK9/cyclin T1. IC50 values are determined from dose-response curves. Selectivity profiling against other kinases is performed to evaluate its specificity.
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| Cell Assay |
Cellular assays for CDK9-IN-2 involve treating cancer cell lines (e.g., H929, A2058) with the compound and measuring cell proliferation and viability. The compound's ability to inhibit CDK9-mediated phosphorylation of RNA polymerase II is assessed by Western blot analysis.
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| Animal Protocol |
In vivo animal model protocols for CDK9-IN-2 would involve its administration to tumor-bearing mice, particularly models of multiple myeloma and melanoma. The compound's antitumor efficacy, effects on transcription, and pharmacokinetic properties would be assessed.
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| ADME/Pharmacokinetics |
CDK9-IN-2 has a molecular weight of 425.9 and a molecular formula of C23H25ClFN5. It is supplied as a light yellow solid. Specific pharmacokinetic data is not extensively detailed in the available literature. As a small molecule inhibitor, its pharmacokinetic properties would need to be evaluated in preclinical studies.
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| Toxicity/Toxicokinetics |
The toxicological profile of CDK9-IN-2 has not been extensively characterized. As a research compound, it is intended for research use only and not for human consumption. Standard safety assessments would be required for clinical development.
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| References | |
| Additional Infomation |
CDK9-IN-2 (CAS# 1263369-28-3) is a research compound used to study the role of CDK9 in transcription and cancer. It is a specific CDK9 inhibitor with potent activity in multiple myeloma and melanoma cell lines. It is not approved for clinical use and is supplied as a research chemical.
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| Molecular Formula |
C23H25CLFN5
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|---|---|
| Molecular Weight |
425.9364
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| Exact Mass |
425.178
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| CAS # |
1263369-28-3
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| PubChem CID |
49855228
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| Appearance |
Light yellow to yellow solid powder
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| LogP |
6.076
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| Hydrogen Bond Donor Count |
3
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| Hydrogen Bond Acceptor Count |
6
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| Rotatable Bond Count |
6
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| Heavy Atom Count |
30
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| Complexity |
518
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| Defined Atom Stereocenter Count |
0
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| InChi Key |
XKHXPTSUVPZYDW-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C23H25ClFN5/c24-20-14-28-23(29-18-9-7-17(26)8-10-18)12-19(20)21-5-2-6-22(30-21)27-13-15-3-1-4-16(25)11-15/h1-6,11-12,14,17-18H,7-10,13,26H2,(H,27,30)(H,28,29)
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| Chemical Name |
4-N-[5-chloro-4-[6-[(3-fluorophenyl)methylamino]pyridin-2-yl]pyridin-2-yl]cyclohexane-1,4-diamine
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| Synonyms |
CDK9-In-2; CDK9 Inhibitor 2; CDK9 Inhibitor II
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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 (~117.39 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (5.87 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (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 25.0 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: ≥ 2.5 mg/mL (5.87 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (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 25.0 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. 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. View More
Solubility in Formulation 3: ≥ 2.5 mg/mL (5.87 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 2.3477 mL | 11.7387 mL | 23.4775 mL | |
| 5 mM | 0.4695 mL | 2.3477 mL | 4.6955 mL | |
| 10 mM | 0.2348 mL | 1.1739 mL | 2.3477 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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