MedKoo Cat#: 122473 | Name: Zebularine
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Description:

WARNING: This product is for research use only, not for human or veterinary use.

Zebularine is a synthetic cytidine analog that functions as a DNA methylation inhibitor by forming a covalent complex with DNA methyltransferases (DNMTs). It has demonstrated anti-tumor properties in vitro and in vivo, with studies showing its ability to reactivate silenced genes and inhibit tumor growth.

Chemical Structure

Zebularine
Zebularine
CAS#3690-10-6

Theoretical Analysis

MedKoo Cat#: 122473

Name: Zebularine

CAS#: 3690-10-6

Chemical Formula: C9H12N2O5

Exact Mass: 228.0746

Molecular Weight: 228.20

Elemental Analysis: C, 47.37; H, 5.30; N, 12.28; O, 35.05

Price and Availability

Size Price Availability Quantity
500mg USD 450.00 2 Weeks
1g USD 750.00 2 Weeks
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Related CAS #
No Data
Synonym
4-Deoxyuridine; Pyrimidin-2-one ribonucleoside; Pyrimidin-2-one beta-ribofuranoside
IUPAC/Chemical Name
1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one
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
SMILES Code
OC[C@@H]1[C@@H](O)[C@@H](O)[C@H](N2C=CC=NC2=O)O1
Appearance
To be determined
Purity
>98% (or refer to the Certificate of Analysis)
Shipping Condition
Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.
Storage Condition
Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).
Solubility
To be determined
Shelf Life
>2 years if stored properly
Drug Formulation
To be determined
Stock Solution Storage
0 - 4 C for short term (days to weeks), or -20 C for long term (months).
HS Tariff Code
2934.99.9001
More Info

Preparing Stock Solutions

The following data is based on the product molecular weight 228.20 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.

Recalculate based on batch purity %
Concentration / Solvent Volume / Mass 1 mg 5 mg 10 mg
1 mM 1.15 mL 5.76 mL 11.51 mL
5 mM 0.23 mL 1.15 mL 2.3 mL
10 mM 0.12 mL 0.58 mL 1.15 mL
50 mM 0.02 mL 0.12 mL 0.23 mL
1: Lai J, Fu Y, Tian S, Huang S, Luo X, Lin L, Zhang X, Wang H, Lin Z, Zhao H, Lin S, Zhao J, Xu S, Li D, Cai S, Dong L, Qian J, Liang J, Li Q, Zhang Y, Fan J, Balderas R, Chen Q. Zebularine elevates STING expression and enhances cGAMP cancer immunotherapy in mice. Mol Ther. 2021 May 5;29(5):1758-1771. doi: 10.1016/j.ymthe.2021.02.005. Epub 2021 Feb 9. PMID: 33571681; PMCID: PMC8116609. 2: Zeng X, He G, Yang X, Xu G, Tang Y, Li H, Yu B, Wang Z, Xu W, Song K. Zebularine protects against blood-brain-barrier (BBB) disruption through increasing the expression of zona occludens-1 (ZO-1) and vascular endothelial (VE)-cadherin. Bioengineered. 2022 Feb;13(2):4441-4454. doi: 10.1080/21655979.2021.2024323. PMID: 35112992; PMCID: PMC8974047. 3: Prochazkova K, Finke A, Tomaštíková ED, Filo J, Bente H, Dvořák P, Ovečka M, Šamaj J, Pecinka A. Zebularine induces enzymatic DNA-protein crosslinks in 45S rDNA heterochromatin of Arabidopsis nuclei. Nucleic Acids Res. 2022 Jan 11;50(1):244-258. doi: 10.1093/nar/gkab1218. PMID: 34904670; PMCID: PMC8754632. 4: Sass P, Sosnowski P, Kamińska J, Deptuła M, Skoniecka A, Zieliński J, Rodziewicz-Motowidło S, Pikuła M, Sachadyn P. Examination of epigenetic inhibitor zebularine in treatment of skin wounds in healthy and diabetic mice. J Tissue Eng Regen Med. 2022 Dec;16(12):1238-1248. doi: 10.1002/term.3365. Epub 2022 Nov 9. PMID: 36350668. 5: Yoo CB, Cheng JC, Jones PA. Zebularine: a new drug for epigenetic therapy. Biochem Soc Trans. 2004 Dec;32(Pt 6):910-2. doi: 10.1042/BST0320910. PMID: 15506921. 6: Kong J, Garcia V, Zehraoui E, Stammitti L, Hilbert G, Renaud C, Maury S, Delaunay A, Cluzet S, Lecourieux F, Lecourieux D, Teyssier E, Gallusci P. Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells. Genes (Basel). 2022 Jul 15;13(7):1256. doi: 10.3390/genes13071256. PMID: 35886036; PMCID: PMC9316115. 7: Krzeminski P, García-Sanz R, Gutiérrez NC. Zebularine-induced myeloma cell death is accompanied by decreased c-Myc expression. Cell Oncol (Dordr). 2020 Aug;43(4):743-750. doi: 10.1007/s13402-020-00516-6. Epub 2020 May 11. PMID: 32394351. 8: Marquez VE, Kelley JA, Agbaria R, Ben-Kasus T, Cheng JC, Yoo CB, Jones PA. Zebularine: a unique molecule for an epigenetically based strategy in cancer chemotherapy. Ann N Y Acad Sci. 2005 Nov;1058:246-54. doi: 10.1196/annals.1359.037. PMID: 16394141. 9: Yap ZH, Kong WY, Azeez AR, Fang CM, Ngai SC. Anti-Cancer Effects of Epigenetics Drugs Scriptaid and Zebularine in Human Breast Adenocarcinoma Cells. Anticancer Agents Med Chem. 2022;22(8):1582-1591. doi: 10.2174/1871520621666210608103251. PMID: 34102995. 10: Marquez VE, Barchi JJ Jr, Kelley JA, Rao KV, Agbaria R, Ben-Kasus T, Cheng JC, Yoo CB, Jones PA. Zebularine: a unique molecule for an epigenetically based strategy in cancer chemotherapy. The magic of its chemistry and biology. Nucleosides Nucleotides Nucleic Acids. 2005;24(5-7):305-18. doi: 10.1081/ncn-200059765. PMID: 16247946. 11: Chen J, Li QY, Luo YH, Xiao EH. Continuous zebularine treatment enhances hepatic differentiation of mesenchymal stem cells under liver-specific factors induction in vitro. Life Sci. 2018 Dec 15;215:57-63. doi: 10.1016/j.lfs.2018.10.049. Epub 2018 Oct 25. PMID: 30473025. 12: Tang M, Lozano Hernandez L, Reginald-Opara JN, Svirskis D, Leung E, Wang H, Wu Z. Zebularine suppressed gemcitabine-induced senescence and improved the cellular and plasma pharmacokinetics of gemcitabine, augmented by liposomal co- delivery. Int J Pharm. 2021 Jun 1;602:120659. doi: 10.1016/j.ijpharm.2021.120659. Epub 2021 Apr 30. PMID: 33933647. 13: Ye K, Wang S, Wang J, Han H, Ma B, Yang Y. Zebularine enhances apoptosis of human osteosarcoma cells by suppressing methylation of ARHI. Cancer Sci. 2016 Dec;107(12):1851-1857. doi: 10.1111/cas.13088. Epub 2016 Dec 19. PMID: 27685841; PMCID: PMC5198947. 14: Xiong X, Lan D, Li J, Zhong J, Zi X, Ma L, Wang Y. Zebularine and scriptaid significantly improve epigenetic reprogramming of yak fibroblasts and cloning efficiency. Cell Reprogram. 2013 Aug;15(4):293-300. doi: 10.1089/cell.2012.0092. Epub 2013 Jun 22. PMID: 23790013. 15: Orta ML, Pastor N, Burgos-Morón E, Domínguez I, Calderón-Montaño JM, Huertas Castaño C, López-Lázaro M, Helleday T, Mateos S. Zebularine induces replication- dependent double-strand breaks which are preferentially repaired by homologous recombination. DNA Repair (Amst). 2017 Sep;57:116-124. doi: 10.1016/j.dnarep.2017.07.002. Epub 2017 Jul 12. PMID: 28732309. 16: Luo YH, Chen J, Xiao EH, Li QY, Luo YM. Zebularine Promotes Hepatic Differentiation of Rabbit Bone Marrow Mesenchymal Stem Cells by Interfering with p38 MAPK Signaling. Stem Cells Int. 2018 Oct 10;2018:9612512. doi: 10.1155/2018/9612512. PMID: 30405726; PMCID: PMC6199887. 17: Koh ES, Kim S, Son M, Park JY, Pyo J, Kim WY, Kim M, Chung S, Park CW, Kim HS, Shin SJ. The Protective Effect of Zebularine, an Inhibitor of DNA Methyltransferase, on Renal Tubulointerstitial Inflammation and Fibrosis. Int J Mol Sci. 2022 Nov 14;23(22):14045. doi: 10.3390/ijms232214045. PMID: 36430531; PMCID: PMC9697081. 18: Dock H, Theodorsson A, Theodorsson E. DNA Methylation Inhibitor Zebularine Confers Stroke Protection in Ischemic Rats. Transl Stroke Res. 2015 Aug;6(4):296-300. doi: 10.1007/s12975-015-0397-7. Epub 2015 Apr 1. PMID: 25824538. 19: Wang Q, Liang N, Yang T, Li Y, Li J, Huang Q, Wu C, Sun L, Zhou X, Cheng X, Zhao L, Wang G, Chen Z, He X, Liu C. DNMT1-mediated methylation of BEX1 regulates stemness and tumorigenicity in liver cancer. J Hepatol. 2021 Nov;75(5):1142-1153. doi: 10.1016/j.jhep.2021.06.025. Epub 2021 Jul 1. PMID: 34217777. 20: Bryan JN, Kumar SR, Jia F, Balkin ER, Lewis MR. Zebularine significantly sensitises MEC1 cells to external irradiation and radiopharmaceutical therapy when administered sequentially in vitro. Cell Biol Int. 2014 Feb;38(2):187-97. doi: 10.1002/cbin.10215. Epub 2013 Dec 9. PMID: 24323360; PMCID: PMC3947096.