Nanafrocin
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MedKoo CAT#: 584889

CAS#: 52934-83-5

Description: Nanafrocin is produced by the strain OS-3966 of Streptomyces rosa var. notoensis and is a quinone-related compound.


Chemical Structure

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Nanafrocin
CAS# 52934-83-5

Theoretical Analysis

MedKoo Cat#: 584889
Name: Nanafrocin
CAS#: 52934-83-5
Chemical Formula: C16H14O6
Exact Mass: 302.08
Molecular Weight: 302.282
Elemental Analysis: C, 63.58; H, 4.67; O, 31.76

Price and Availability

Size Price Availability Quantity
1mg USD 450 2 Weeks
5mg USD 950 2 Weeks
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Synonym: Nanafrocin; Nanaomycin A; Antibiotic OS 3966A; OS-3966-A

IUPAC/Chemical Name: (1S,3R)-3,4,5,10-Tetrahydro-9-hydroxy-1-methyl-5,10-dioxo-1H-naphtho-(2,3-c)pyran-3-acetic acid

InChi Key: ZCJHPTKRISJQTN-JGVFFNPUSA-N

InChi Code: InChI=1S/C16H14O6/c1-7-13-10(5-8(22-7)6-12(18)19)15(20)9-3-2-4-11(17)14(9)16(13)21/h2-4,7-8,17H,5-6H2,1H3,(H,18,19)/t7-,8+/m0/s1

SMILES Code: O=C(O)C[C@H]1CC(C(C2=C3C(O)=CC=C2)=O)=C(C3=O)[C@H](C)O1

Appearance: Solid powder

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: Soluble in DMSO

Shelf Life: >3 years if stored properly

Drug Formulation: This drug may be formulated in DMSO

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:

Product Data:
Biological target: Nanaomycin A is the first selective DNMT3B inhibitor with an IC50 of 500 nM.
In vitro activity: This work presents nanaomycin A, initially identified by a virtual screening for inhibitors against DNMT1, as a compound inducing antiproliferative effects in three different tumor cell lines originating from different tissues. Nanaomycin A treatment reduced the global methylation levels in all three cell lines and reactivated transcription of the RASSF1A tumor suppressor gene. Reference: Mol Cancer Ther. 2010 Nov;9(11):3015-23. https://pubmed.ncbi.nlm.nih.gov/20833755/
In vivo activity: TBD

Solubility Data

Solvent Max Conc. mg/mL Max Conc. mM
Solubility
DMSO 55.0 181.95

Preparing Stock Solutions

The following data is based on the product molecular weight 302.28 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
Formulation protocol: 1. Kuck D, Caulfield T, Lyko F, Medina-Franco JL. Nanaomycin A selectively inhibits DNMT3B and reactivates silenced tumor suppressor genes in human cancer cells. Mol Cancer Ther. 2010 Nov;9(11):3015-23. doi: 10.1158/1535-7163.MCT-10-0609. Epub 2010 Sep 10. PMID: 20833755. 2. Tanaka Y, Kamei K, Otoguro K, Omura S. Heme-dependent radical generation: possible involvement in antimalarial action of non-peroxide microbial metabolites, nanaomycin A and radicicol. J Antibiot (Tokyo). 1999 Oct;52(10):880-8. doi: 10.7164/antibiotics.52.880. PMID: 10604757.
In vitro protocol: 1. Kuck D, Caulfield T, Lyko F, Medina-Franco JL. Nanaomycin A selectively inhibits DNMT3B and reactivates silenced tumor suppressor genes in human cancer cells. Mol Cancer Ther. 2010 Nov;9(11):3015-23. doi: 10.1158/1535-7163.MCT-10-0609. Epub 2010 Sep 10. PMID: 20833755. 2. Tanaka Y, Kamei K, Otoguro K, Omura S. Heme-dependent radical generation: possible involvement in antimalarial action of non-peroxide microbial metabolites, nanaomycin A and radicicol. J Antibiot (Tokyo). 1999 Oct;52(10):880-8. doi: 10.7164/antibiotics.52.880. PMID: 10604757.
In vivo protocol: TBD

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1: Kasai M, Shirahata K, Ishii S, Mineura K, Marumo H, Tanaka H, Omura S. Structure of nanaomycin E, a new nanaomycin. J Antibiot (Tokyo). 1979 May;32(5):442-5. PubMed PMID: 528392.

2: Nakashima T, Kimura T, Miyano R, Matsuo H, Hirose T, Kimishima A, Nonaka K, Iwatsuki M, Nakanishi J, Takahashi Y, Ōmura S. Nanaomycin H: A new nanaomycin analog. J Biosci Bioeng. 2017 Jun;123(6):765-770. doi: 10.1016/j.jbiosc.2017.01.011. Epub 2017 Feb 13. PubMed PMID: 28202308.

3: Tanaka H, Minami-Kakinuma S, Omura S. Biosynthesis of nanaomycin. III. Nanaomycin A formation from nanaomycin D by nanaomycin D reductase via a hydroquinone. J Antibiot (Tokyo). 1982 Nov;35(11):1565-70. PubMed PMID: 7161196.

4: Tanaka H, Marumo H, Nagai T, Okada M, Taniguchi K. Nanaomycins, new antibiotics produced by a strain of Streptomyces. III. A new component, nanaomycin C, and biological activities of nanaomycin derivatives. J Antibiot (Tokyo). 1975 Dec;28(12):925-30. PubMed PMID: 1206004.

5: Omura S, Tanaka H, Minami S, Takahashi I. Biosynthesis of nanaomycin. II. Purification and properties of nanaomycin D reductase involved in the formation of nanaomycin A from nanaomycin D1. J Biochem. 1981 Aug;90(2):355-62. PubMed PMID: 7298593.

6: Nakashima T, Boonsnongcheep P, Kimura T, Iwatsuki M, Sato N, Nonaka K, Prathanturarug S, Takahashi Y, Ōmura S. New compounds, nanaomycin F and G, discovered by physicochemical screening from a culture broth of Streptomyces rosa subsp. notoensis OS-3966. J Biosci Bioeng. 2015 Nov;120(5):596-600. doi: 10.1016/j.jbiosc.2015.03.018. Epub 2015 Jun 20. PubMed PMID: 26100318.

7: Caulfield T, Medina-Franco JL. Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A. J Struct Biol. 2011 Nov;176(2):185-91. doi: 10.1016/j.jsb.2011.07.015. Epub 2011 Aug 3. PubMed PMID: 21839172.

8: Kuck D, Caulfield T, Lyko F, Medina-Franco JL. Nanaomycin A selectively inhibits DNMT3B and reactivates silenced tumor suppressor genes in human cancer cells. Mol Cancer Ther. 2010 Nov;9(11):3015-23. doi: 10.1158/1535-7163.MCT-10-0609. Epub 2010 Sep 10. PubMed PMID: 20833755.

9: Marumo H, Kitaura K, Morimoto M, Tanaka H, Omura S. The mode of action of nanaomycin A in Gram-positive bacteria. J Antibiot (Tokyo). 1980 Aug;33(8):885-90. PubMed PMID: 6159343.

10: Liu C, Jiang Y, Lei H, Chen X, Ma Q, Han L, Huang X. Four New Nanaomycins Produced by Streptomyces hebeiensis Derived from Lichen. Chem Biodivers. 2017 Jul;14(7). doi: 10.1002/cbdv.201700057. Epub 2017 Jun 9. PubMed PMID: 28390085.

11: Nakamae S, Toba Y, Takayama K, Sakurai F, Mizuguchi H. Nanaomycin A Treatment Promotes Hepatoblast Differentiation from Human iPS Cells. Stem Cells Dev. 2018 Mar 15;27(6):405-414. doi: 10.1089/scd.2017.0251. Epub 2018 Feb 27. PubMed PMID: 29378471.

12: Kakinuma S, Takada Y, Ikeda H, Tanaka H, Omura S, Hopwood DA. Cloning of large DNA fragments, which hybridize with actinorhodin biosynthesis genes, from kalafungin and nanaomycin A methyl ester producers and identification of genes for kalafungin biosynthesis of the kalafungin producer. J Antibiot (Tokyo). 1991 Sep;44(9):995-1005. PubMed PMID: 1938623.

13: Sperry J, Lorenzo-Castrillejo I, Brimble MA, Machín F. Pyranonaphthoquinone derivatives of eleutherin, ventiloquinone L, thysanone and nanaomycin A possessing a diverse topoisomerase II inhibition and cytotoxicity spectrum. Bioorg Med Chem. 2009 Oct 15;17(20):7131-7. doi: 10.1016/j.bmc.2009.08.064. Epub 2009 Sep 4. PubMed PMID: 19783445.

14: Tanaka Y, Kamei K, Otoguro K, Omura S. Heme-dependent radical generation: possible involvement in antimalarial action of non-peroxide microbial metabolites, nanaomycin A and radicicol. J Antibiot (Tokyo). 1999 Oct;52(10):880-8. PubMed PMID: 10604757.

15: Penter L, Maier B, Frede U, Hackner B, Carell T, Hagemeier C, Truss M. A rapid screening system evaluates novel inhibitors of DNA methylation and suggests F-box proteins as potential therapeutic targets for high-risk neuroblastoma. Target Oncol. 2015 Dec;10(4):523-33. doi: 10.1007/s11523-014-0354-5. Epub 2015 Jan 6. PubMed PMID: 25559288.

16: Chen JL, Ping YH, Tseng MJ, Chang YI, Lee HC, Hsieh RH, Yeh TS. Notch1-promoted TRPA1 expression in erythroleukemic cells suppresses erythroid but enhances megakaryocyte differentiation. Sci Rep. 2017 Feb 21;7:42883. doi: 10.1038/srep42883. PubMed PMID: 28220825; PubMed Central PMCID: PMC5318885.

17: Masuma R, Zhen DZ, Tanaka Y, Omura S. Site of regulation of nanaomycin biosynthesis by inorganic phosphate. J Antibiot (Tokyo). 1990 Jan;43(1):83-7. PubMed PMID: 2307632.

18: Kitaura K, Araki Y, Marumo H. [The therapeutic effect of nanaomycin A against experimental Trichophyton mentagrophytes infection in guinea pigs (author's transl)]. Jpn J Antibiot. 1980 Jul;33(7):728-32. Japanese. PubMed PMID: 7452913.

19: Sztiller-Sikorska M, Koprowska K, Majchrzak K, Hartman M, Czyz M. Natural compounds' activity against cancer stem-like or fast-cycling melanoma cells. PLoS One. 2014 Mar 3;9(3):e90783. doi: 10.1371/journal.pone.0090783. eCollection 2014. PubMed PMID: 24595456; PubMed Central PMCID: PMC3940936.

20: Imai H, Suzuki K, Kadota S, Iwanami M, Saito T. Production of enantiomer of nanaomycin a by Nocardia. J Antibiot (Tokyo). 1989 Jul;42(7):1186-8. PubMed PMID: 2753823.