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Zebularine (formerly 4-Deoxyuridine; NSC-309132) is a selective and potent inhibitor of DNA methylation/methyltransferase with anticancer activity. It inhibits DNA methylation by forming a covalent complex with DNA methyltransferases. zebularine is a stable cytidine analog that also inhibits cytidinedeaminase with a Ki of 2 μM in a cell-free assay.
Physicochemical Properties
| Molecular Formula | C9H12N2O5 | |
| Molecular Weight | 228.2 | |
| Exact Mass | 228.074 | |
| CAS # | 3690-10-6 | |
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| PubChem CID | 100016 | |
| Appearance | White to off-white solid powder | |
| Density | 1.7±0.1 g/cm3 | |
| Boiling Point | 499.0±55.0 °C at 760 mmHg | |
| Melting Point | 160-162?C | |
| Flash Point | 255.6±31.5 °C | |
| Vapour Pressure | 0.0±2.9 mmHg at 25°C | |
| Index of Refraction | 1.697 | |
| LogP | -1.31 | |
| Hydrogen Bond Donor Count | 3 | |
| Hydrogen Bond Acceptor Count | 5 | |
| Rotatable Bond Count | 2 | |
| Heavy Atom Count | 16 | |
| Complexity | 343 | |
| Defined Atom Stereocenter Count | 4 | |
| SMILES | C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O |
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| InChi Key | RPQZTTQVRYEKCR-WCTZXXKLSA-N | |
| InChi Code | InChI=1S/C9H12N2O5/c12-4-5-6(13)7(14)8(16-5)11-3-1-2-10-9(11)15/h1-3,5-8,12-14H,4H2/t5-,6-,7-,8-/m1/s1 | |
| Chemical Name | 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one | |
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| 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 |
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| Shipping Condition | Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs) |
Biological Activity
| ln Vitro | ZebuLarine accomplishes its demethylating effect by stabilizing DNMT binding to DNA, inhibiting methylation and minimizing dissociation, so trapping the enzyme and preventing turnover even at other locations. zebuLarine improves the chemo- and radiosensitivity of tumor cells and possesses antimitotic and vasculostatic action [1]. ZebuLarine inhibits DNA methylation and reactivates genes previously silenced by methylation. ZebuLarine generates a myogenic phenotype in 10T1/2 cells, a feature unique to DNA methylation inhibitors. ZebuLarine reactivates the silenced p16 gene and demethylates its promoter region in T24 bladder cancer cells [2]. ZebuLarine administration suppressed cell proliferation in a dose- and time-dependent manner, with IC50s of ∼100 μM and 150 μM for MDA-MB-231 and MCF-7 cells, respectively, after 96 hours of exposure. At high dosages, zebuLarine promotes alterations in apoptotic proteins in a cell line-specific way, manifesting as changes in caspase-3, Bax, Bcl2, and PARP cleavage [3]. ZebuLarine is also a powerful competitive inhibitor of CR deaminase. The Ki of zebuLarine is 0.95 μM[4]. | ||
| ln Vivo | ZebuLarine shown minimal cytotoxicity in animals harboring tumors. When mice were administered high dosages of zebularine orally or via intraperitoneal injection, their tumor volumes were much lower than those of control animals [2]. Zebularine also increased the length of time that L1210 leukemic mice receiving 5-AZA-CdR survived. Compared to mice treated with 5-AZA-CdR alone, about 27% of mice treated with this combination of drugs lived longer. | ||
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| References |
[1]. Mechanistic insights on the inhibition of c5 DNA methyltransferases by zebularine. PLoS One. 2010 Aug 24;5(8):e12388. [2]. Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J Natl Cancer Inst. 2003 Mar 5;95(5):399-409. [3]. Effects of a novel DNA methyltransferase inhibitor zebularine on human breast cancer cells. Breast Cancer Res Treat. 2010 Apr;120(3):581-92. [4]. Inhibition of cytidine deaminase by zebularine enhances the antineoplastic action of 5-aza-2'-deoxycytidine. Cancer Chemother Pharmacol. 2009 Feb;63(3):411-6. |
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| Additional Infomation |
Zebularine is a member of pyrimidine ribonucleosides. A chemically stable, cytidine analog that displays anti-tumor properties. It acts as a transition state analog inhibitor of cytidine deaminase by binding to the active site as covalent hydrates. Also shown to inhibit DNA methylation and tumor growth both in vitro and in vivo. Zebularine is a synthetic cytidine analogue and a cytidine deaminase inhibitor with anticancer activity. Following metabolic activation by phosphorylation and incorporation into DNA, zebularine inhibits DNA methyltransferase through covalent complex formation between the enzyme and zebularine-substituted DNA, hence resulting in non-specific, genome-wide induction of demethylation including the removal of aberrant methylation of promoter regions of genes critical for normal cellular functions. |
Solubility Data
| Solubility (In Vitro) |
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (10.96 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 (10.96 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. Solubility in Formulation 3: ≥ 2.5 mg/mL (10.96 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 25.0 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly. Solubility in Formulation 4: Saline: 30mg/mL Solubility in Formulation 5: 100 mg/mL (438.21 mM) in PBS (add these co-solvents sequentially from left to right, and one by one), clear solution; with ultrasonication. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 4.3821 mL | 21.9106 mL | 43.8212 mL | |
| 5 mM | 0.8764 mL | 4.3821 mL | 8.7642 mL | |
| 10 mM | 0.4382 mL | 2.1911 mL | 4.3821 mL |