HDAC3-IN-2
Based on 1 Customer Validation
HDAC3-IN-2 (compound 4i) is a pyrazinyl hydrazide-based HDAC3 inhibitor (IC50: 14 nM) that efficiently targets triple-negative breast cancer cells. HDAC3-IN-2 is cytotoxic with an IC50 of 0.55 μM against 4T1 and an IC50 of 0.74 μM against MDA-MB-231. HDAC3-IN-2 has anti-tumor efficacy in vivo in tumor-bearing mouse models, selectively increasing the acetylation levels of H3K9, H3K27 and H4K12, increasing the contents of apoptosis-related caspase-3, caspase-7 and cytochrome c, and reducing Proliferation-related Bcl-2, CD44, EGFR, and Ki-67 levels.
For research use only. We do not sell to patients.
- CAS No.: 3033039-28-7
- Formula: C16H21N5O2
- Molecular Weight:315.37
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Storage:Powder -20°C, 3 years , 4°C, 2 years ; In solvent -80°C, 6 months , -20°C, 1 month
To place orders, for customer services and technical support, please contact: MedChemExpress USA
Tel: 609-228-6898 E-mail: [email protected] [email protected]
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Biological Activity
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Chemical Information
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Solvent & Solubility
- Protocols
- Purity & Documentation
- References
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Help & FAQs
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Biological Activity
Description
IC50 & Target
IC50: 14 nM (HDAC3)[1]
Cellular Effect
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Cell Line
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Type | Value | Description | References |
|---|---|---|---|---|
| 4T1 | IC50 |
0.55 μM
Compound: 4i
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Cytotoxicity against mouse 4T1 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
Cytotoxicity against mouse 4T1 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
| HEK293 | IC50 |
238.7 μM
Compound: 4i
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Cytotoxicity against human HEK293 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
Cytotoxicity against human HEK293 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
| MCF-10A | IC50 |
211.9 μM
Compound: 4i
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Cytotoxicity against human MCF-10A cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
Cytotoxicity against human MCF-10A cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
| MCF7 | IC50 |
0.95 μM
Compound: 4i
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Cytotoxicity against human MCF7 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
Cytotoxicity against human MCF7 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
| MDA-MB-231 | IC50 |
0.403 μM
Compound: 4i
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Cytotoxicity against wild type human MDA-MB-231 cells assessed as reduction in cell viability incubated for 72 hrs in presence of oxaliplatin by MTT assay
Cytotoxicity against wild type human MDA-MB-231 cells assessed as reduction in cell viability incubated for 72 hrs in presence of oxaliplatin by MTT assay
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[PMID: 37660352] |
| MDA-MB-231 | IC50 |
0.74 μM
Compound: 4i
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Cytotoxicity against human MDA-MB-231 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
Cytotoxicity against human MDA-MB-231 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
| MDA-MB-231 | IC50 |
0.743 μM
Compound: 4i
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Cytotoxicity against wild type human MDA-MB-231 cells assessed as reduction in cell viability incubated for 72 hrs by MTT assay
Cytotoxicity against wild type human MDA-MB-231 cells assessed as reduction in cell viability incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
| MDA-MB-453 | IC50 |
1.72 μM
Compound: 4i
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Cytotoxicity against human MDA-MB-453 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
Cytotoxicity against human MDA-MB-453 cells assessed as inhibition of cell growth incubated for 72 hrs by MTT assay
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[PMID: 37660352] |
Chemical Information
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CAS No. 3033039-28-7
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Appearance Solid
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Molecular Weight 315.37
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Formula C16H21N5O2
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Color Off-white to light yellow
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SMILES
COC1=CC=C(CNC2=CN=C(C(NNCCC)=O)C=N2)C=C1
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month
Solvent & Solubility
In Vitro:
DMSO : 100 mg/mL (317.09 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
In Vivo:
Select the appropriate dissolution method based on your experimental animal and administration route.
- For the following dissolution methods, please ensure to first prepare a clear stock solution using an In Vitro approach and then sequentially add co-solvents:
- To ensure reliable experimental results, the clarified stock solution can be appropriately stored based on storage conditions. As for the working solution for In Vivo experiments, it is recommended to prepare freshly and use it on the same day.
- The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.
Add each solvent one by one: 10% DMSO 40% PEG300 5% Tween-80 45% Saline
Solubility: ≥ 2.5 mg/mL (7.93 mM); Clear solution
This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).
Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 400 μL PEG300, and mix evenly; then add 50 μL Tween-80 and mix evenly; then add 450 μL Saline to adjust the volume to 1 mL.
Preparation of Saline: Dissolve 0.9 g sodium chloride in ddH₂O and dilute to 100 mL to obtain a clear Saline solution.
Add each solvent one by one: 10% DMSO 90% (20% SBE-β-CD in Saline)
Solubility: ≥ 2.5 mg/mL (7.93 mM); Clear solution
This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).
Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 900 μL 20% SBE-β-CD in Saline, and mix evenly.
Preparation of 20% SBE-β-CD in Saline (4°C, storage for one week): 2 g SBE-β-CD powder is dissolved in 10 mL Saline, completely dissolve until clear.
In Vivo Dissolution Calculator
Please enter the basic information of animal experiments:
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Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
Please enter your animal formula composition:
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%DMSO +
Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
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%+
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+%Tween-80 + +
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%Saline +
The co-solvents required include: DMSO, . All of co-solvents are available by MedChemExpress (MCE). , Tween 80. All of co-solvents are available by MedChemExpress (MCE).
Working solution concentration: 0.22 mg/mL
Method for preparing stock solution: mg drug dissolved in μL DMSO. Stock solution concentration: mg/mL.
1. Take μL DMSO stock solution;
2. Add μL .
μL , mix evenly;
3. Then add μL Tween 80, mix evenly;
4. Then add μL
Please ensure that the stock solution in the first step is dissolved to a clear state, and add co-solvents in sequence. You can use ultrasonic heating (ultrasonic cleaner, recommended frequency 20-40 kHz), vortexing, etc. to assist dissolution.
Protocols
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Apoptosis
Apoptosis, also called programmed cell death, is generally characterized by distinct morphological characteristics.
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TUNEL staining for apoptotic DNA fragmentation
TUNEL staining detects DNA strand breaks by using terminal deoxynucleotidyl transferase to add labeled nucleotides to exposed 3′-OH DNA termini, generating either microscopic staining in fixed cells or tissue sections, or fluorescence/cytometric signal in cell suspensions. TUNEL positivity reflects DNA fragmentation but should not be interpreted alone as definitive apoptosis, because TUNEL can also label necrotic, autolytic, mechanically damaged, or DNA-repair-associated DNA breaks.
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Ki-67 Immunostaining Proliferation Assay
Ki-67 immunostaining measures the growth fraction of a cell population by detecting Ki-67, a nuclear antigen present in proliferating cells and absent in quiescent G0 cells. The readout is the percentage of Ki-67-positive nuclei among total counted cells, commonly called the Ki-67 labeling index or proliferation index.
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Cell Cytotoxicity Assay
Cytotoxicity assays are usually based on the assessment of cell membrane damage, which can also be indirectly detected by measuring cell viability. Detection methods include MTT assay, CKK-8 assay, LDH assay and ATP assay, etc.
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Annexin V plus membrane-impermeant dye apoptosis staining
Annexin V-based apoptosis assays rely on the detection of phosphatidylserine (PS) externalization from the inner leaflet of the plasma membrane to the outer leaflet, an early biochemical hallmark of apoptosis. Fluorescently labeled Annexin V binds PS in a calcium-dependent manner, enabling identification of early apoptotic cells by flow cytometry or fluorescence microscopy. When combined with a membrane-impermeant DNA-binding dye (e. g. , propidium iodide), this approach allows discrimination between viable (Annexin V−/dye−), early apoptotic (Annexin V+/dye−), and late apoptotic or necrotic (Annexin V+/dye+) cell populations by assessing membrane integrity and PS exposure.
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Apoptosis Solutions
Apoptosis is a regulated, generally non-lytic cell-death pathway that removes unwanted, damaged, infected, or abnormal cells through coordinated morphological changes, caspase activation, DNA fragmentation, and membrane remodeling. The intrinsic apoptosis pathway is controlled mainly by mitochondrial outer membrane permeabilization, BCL-2 family proteins, cytochrome c release, apoptosome formation, caspase-9 activation, and downstream executioner caspase-3/7 activation. The extrinsic apoptosis pathway is initiated by death receptors such as Fas, TNFR, and TRAIL receptors, which recruit adaptor proteins and activate caspase-8 before engaging executioner caspases or mitochondrial amplification through BID cleavage. Apoptosis is linked to many phenotypes, including cancer cell killing, tissue homeostasis, immune regulation, neurodegeneration, infection response, and treatment-induced cytotoxicity; unresolved questions include how apoptosis interacts with necroptosis, pyroptosis, ferroptos
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Breast Cancer Modeling
Breast cancer is a heterogeneous cancer, and it has been distinguished into four subtypes: luminal A, luminal B, HER2-positive and basal-like. Molecular mutations, epigenetic alterations, hormone exposure and immune microenvironment are related to the progression of breast cancer.
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Cell Viability Determination by MTT Colorimetric Assay
The following protocol uses the MTT colorimetric assay as a classic literature-established method for assessing cell viability/metabolic activity in cultured mammalian cells. MTT[3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] is reduced by metabolically active cells to a colored formazan product; the amount of formazan is quantified spectrophotometrically and provides an indirect measure of metabolically active viable cells. Importantly, MTT reduction reflects cellular oxidoreductase/metabolic activity rather than an absolute direct count of living cells, so changes in cellular metabolism can alter the signal independently of cell number.
Purity & Documentation
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Data Sheet (269 KB)
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SDS (252 KB)
- Français - FR (252 KB)
- Deutsch - DE (252 KB)
- Norwegian - NO (252 KB)
- Español - ES (252 KB)
- Swedish - SV (252 KB)
- Italian - IT (252 KB)
- Korean - KR (252 KB)
- Portuguese - PT (252 KB)
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Handling Instructions (2659 KB)
References
Complete Stock Solution Preparation Table
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
| Optional Solvent | Concentration Solvent Mass | 1 mg | 5 mg | 10 mg | 25 mg |
|---|---|---|---|---|---|
| DMSO | 1 mM | 3.1709 mL | 15.8544 mL | 31.7088 mL | 79.2720 mL |
| 5 mM | 0.6342 mL | 3.1709 mL | 6.3418 mL | 15.8544 mL | |
| 10 mM | 0.3171 mL | 1.5854 mL | 3.1709 mL | 7.9272 mL | |
| 15 mM | 0.2114 mL | 1.0570 mL | 2.1139 mL | 5.2848 mL | |
| 20 mM | 0.1585 mL | 0.7927 mL | 1.5854 mL | 3.9636 mL | |
| 25 mM | 0.1268 mL | 0.6342 mL | 1.2684 mL | 3.1709 mL | |
| 30 mM | 0.1057 mL | 0.5285 mL | 1.0570 mL | 2.6424 mL | |
| 40 mM | 0.0793 mL | 0.3964 mL | 0.7927 mL | 1.9818 mL | |
| 50 mM | 0.0634 mL | 0.3171 mL | 0.6342 mL | 1.5854 mL | |
| 60 mM | 0.0528 mL | 0.2642 mL | 0.5285 mL | 1.3212 mL | |
| 80 mM | 0.0396 mL | 0.1982 mL | 0.3964 mL | 0.9909 mL | |
| 100 mM | 0.0317 mL | 0.1585 mL | 0.3171 mL | 0.7927 mL |
HDAC3-IN-2 Related Classifications
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