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Echinomycin

Alias: Quinomycin A Antibiotic A 654ISK 302BEchinomycin NSC 526417NSC 13502
Cat No.:V9769 Purity: ≥98%
Echinomycin (Quinomycin A) is a potent, cell-penetrating/penetrable, small molecule inhibitor of the DNA-binding activity of hypoxia-inducible factor-1 (HIF-1).
Echinomycin
Echinomycin Chemical Structure CAS No.: 512-64-1
Product category: New1
This product is for research use only, not for human use. We do not sell to patients.
Size Price Stock Qty
1mg
50mg
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Product Description
Echinomycin (Quinomycin A) is a potent, cell-penetrating/penetrable, small molecule inhibitor of the DNA-binding activity of hypoxia-inducible factor-1 (HIF-1). Echinomycin selectively inhibits cancer stem cells with IC50 of 29.4 pM.
Biological Activity I Assay Protocols (From Reference)
ln Vitro
Treatment with echinomycin (0-10 nM; 16 hours; U251 cells) markedly and dose-dependently reduced the production of VEGF mRNA produced by hypoxia. With an EC50 of 1.2 nM, echinomycin highly potently and dose-dependently suppresses the hypoxic stimulation of luciferase expression in U251-HRE [1].
ln Vivo
Through selective depletion of cancer stem cells (CSCs), treatment with Echinomycin (10 μg/kg; i.v.; for 40 days) efficiently eradicates human acute myeloid malignancies and murine lymphoma in xenogeneic models. AML, or leukemia. HIF1α prevents the negative feedback loop in the Notch pathway, which keeps mice lymphoma CSCs alive [2].
Cell Assay
RT-PCR[1]
Cell Types: U251 Cell
Tested Concentrations: 0 nM, 0.625 nM, 1.25 nM, 5 nM, 10 nM
Incubation Duration: 16 hrs (hours)
Experimental Results: Dramatically inhibited hypoxia-induced VEGF mRNA expression in a dose-dependent manner.
Animal Protocol
Animal/Disease Models: NOD-SCID (severe combined immunodeficient) mouse received 1.8Gy irradiation and intravenous (iv) (iv)injection of peripheral blood cells from AML-71 and AML-150 patients [2]
Doses: 10 μg/kg
Route of Administration: intravenous (iv) (iv)injection; intravenous (iv) (iv)injection. Results lasting 40 days: Effective eradication of mouse lymphoma and serially transplantable human AML in xenogeneic models by preferential elimination of CSCs.
References

[1]. Echinomycin, a small-molecule inhibitor of hypoxia-inducible factor-1 DNA-binding activity. Cancer Res. 2005 Oct 1;65(19):9047-55.

[2]. Targeting HIF1α eliminates cancer stem cells in hematological malignancies. Cell Stem Cell. 2011 Apr 8;8(4):399-411.

Additional Infomation
Quinomycin C is a cyclodepsipeptide.
Echinomycin is a cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis.
Echinomycin has been reported in Streptomyces triostinicus, Streptomycetaceae, and Streptomyces echinatus with data available.
Echinomycin is a polypeptide quinoxaline antineoplastic antibiotic isolated from the bacterium Streptomyces echinatus. Echinomycin intercalates into DNA at two locations simultaneously in a sequence-specific fashion, thereby inhibiting DNA replication and RNA synthesis. (NCI04)
A cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis.
See also: Echinomycin (annotation moved to).
These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C51H64N12O12S2
Molecular Weight
1101.265
Exact Mass
1100.42
CAS #
512-64-1
PubChem CID
3197
Appearance
White to off-white solid powder
Density
1.41 g/cm3
Boiling Point
1427.2ºC at 760 mmHg
Flash Point
817ºC
Index of Refraction
1.536
LogP
1.826
Hydrogen Bond Donor Count
4
Hydrogen Bond Acceptor Count
18
Rotatable Bond Count
7
Heavy Atom Count
77
Complexity
2200
Defined Atom Stereocenter Count
0
InChi Key
AUJXLBOHYWTPFV-UHFFFAOYSA-N
InChi Code
InChI=1S/C51H64N12O12S2/c1-25(2)38-49(72)74-22-36(59-42(65)34-21-53-30-17-13-15-19-32(30)57-34)44(67)55-28(6)46(69)63(10)40-48(71)62(9)39(26(3)4)50(73)75-23-35(58-41(64)33-20-52-29-16-12-14-18-31(29)56-33)43(66)54-27(5)45(68)60(7)37(47(70)61(38)8)24-77-51(40)76-11/h12-21,25-28,35-40,51H,22-24H2,1-11H3,(H,54,66)(H,55,67)(H,58,64)(H,59,65)
Chemical Name
N,N'-((1R,4S,7R,11S,14R,17S,20R,24S)-11,24-diisopropyl-2,4,12,15,17,25-hexamethyl-27-(methylthio)-3,6,10,13,16,19,23,26-octaoxo-9,22-dioxa-28-thia-2,5,12,15,18,25-hexaazabicyclo[12.12.3]nonacosane-7,20-diyl)bis(quinoxaline-2-carboxamide)
Synonyms
Quinomycin A Antibiotic A 654ISK 302BEchinomycin NSC 526417NSC 13502
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

Note: Please store this product in a sealed and protected environment (e.g. under nitrogen), avoid exposure to moisture.
Shipping Condition
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
Solubility Data
Solubility (In Vitro)
DMSO : ~5.3 mg/mL (~4.81 mM)
Solubility (In Vivo)
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.

Injection Formulations
(e.g. IP/IV/IM/SC)
Injection Formulation 1: DMSO : Tween 80: Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution 50 μL Tween 80 850 μL Saline)
*Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution.
Injection Formulation 2: DMSO : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO 400 μLPEG300 50 μL Tween 80 450 μL Saline)
Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO 900 μL Corn oil)
Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals).
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Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO 900 μL (20% SBE-β-CD in saline)]
*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.
Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin 500 μL Saline)
Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO 100 μLPEG300 200 μL castor oil 650 μL Saline)
Injection Formulation 7: Ethanol : Cremophor : Saline = 10: 10 : 80 (i.e. 100 μL Ethanol 100 μL Cremophor 800 μL Saline)
Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline
Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH 900 μL Corn oil)
Injection Formulation 10: EtOH : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH 400 μLPEG300 50 μL Tween 80 450 μL Saline)


Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium)
Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose
Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals).
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Oral Formulation 3: Dissolved in PEG400
Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose
Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose
Oral Formulation 6: Mixing with food powders


Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.

 (Please use freshly prepared in vivo formulations for optimal results.)
Preparing Stock Solutions 1 mg 5 mg 10 mg
1 mM 0.9080 mL 4.5402 mL 9.0804 mL
5 mM 0.1816 mL 0.9080 mL 1.8161 mL
10 mM 0.0908 mL 0.4540 mL 0.9080 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.

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Using the equation C1V1 = C2V2, where C1=10 mM, C2=25 μM, V2=25 ml and V1 is the unknown:
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Note: Chemical formula is case sensitive: C12H18N3O4  c12h18n3o4
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In vivo Formulation Calculator (Clear solution)
Step 1: Enter information below (Recommended: An additional animal to make allowance for loss during the experiment)
Step 2: Enter in vivo formulation (This is only a calculator, not the exact formulation for a specific product. Please contact us first if there is no in vivo formulation in the solubility section.)
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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.

Biological Data
  • Lymphoma CSC were abrogated by selectively by an HIF inhibitor. a. Selective ablation of lymphoma CFU by echinomycin. The cultured lymphoma cells were treated with given doses of pharmacologically effective drugs in medium for 24 hours prior to CFU assay. Data shown are means +/−SD of triplicates and have been confirmed by 3 independent experiments. b. Constitutive HIF activity among c-Kit+ cells and its sensitivity to echinomycin. The FACS profiles in the upper and middle panels show the specificity of the GFP reporter by co-expression of GFP expressing cells and c-Kit in WT HRE, but not mutant HRE lentiviral reporters. The dose response to inhibition by echinomycin is shown in the bottom panel. The lymphoma cells transfected with the HRE reporter system were cultured in the presence of different concentration of echinomycin for 12 hours, the % of c-Kit+GFP+ cells was normalized against the untreated group (1.13%, which was defined as 100%). The dose that resulted in 50% reduction of the c-Kit+GFP+ cells is defined as IC50. Detailed description of the reporter and its specificity is presented in supplemental data Fig. S3a. c. Selectivity of HIF inhibitor for CFU of lymphoma CSC over the CFU from hematopoietic progenitor cells (HPC). c-Kit+Sca-1+ cells from either TGB or normal bone marrow were treated with given concentration of echinomycin overnight prior to CFU assay. The data shown were % of untreated controls, and were means +/− S.D. of triplicates. d. ShRNA silencing reduces susceptibility of CFU activity to echinomycin.[2]. Wang Y, et al. Targeting HIF1α eliminates cancer stem cells in hematological malignancies. Cell Stem Cell. 2011 Apr 8;8(4):399-411.
  • HIF1α is a target for therapeutic elimination of human AML in xenogenic mouse model. a. Isolation of 4 subsets of tumor cells in AML samples. Bone marrow cells from AML patient MI-AML-71 were stained for CD34 and CD38 and sorted into 4 subsets for RNA isolation. The presort samples and the gates used for sorting are shown in the left panel and the post-sorted populations are shown in the middle and right panels. The percentages of cells in each gate are provided in the panels. b. Expression of HIF1a (top) and GLUT1 in the subsets. Data shown are means+/−S.D. of transcript levels of the genes, presented as % of βactin from the same samples. Enhanced expression in the CD34+CD38− samples have been observed in all 6 AML samples tested. c. Increased accumulation of HIF1α protein in CD34+CD38− AML cells. CD38+ cells were depleted by negative selection with anti-CD38-conjugated magnetic beads. The remaining cells were further separated into CD38−CD34+ (purity 72–78%) and CD38−CD34− (purity 96–100%) cells by positive selection, Lysates from the two populations were used for Western blot. d. HIF1α activity is essential for AML-CFU. AML-60 and AML-71 were transduced with either scrambled (Sr) or HIF1a shRNA (Sh-2). The CFU of transduced AML cells were counted based on EGFP signal. The transduction efficacy were measured by FACS prior to plating. The % of GFP+ cells for the experiment were: AML60: Sr, 32.6; Sh-2:32.48. AML-71: Sr: 45.70; Sh-2: 40.19. The shRNA used, Sh-2, targets shared sequenced between mouse and human HIF1a genes. Data showing are CFU per 2x105 cells. e. HIF1a silencing increased the resistance to CFU to echinomycin. As in e, except the transduced cells were treated with given concentration of echinomycin. Data shown were % of CFU after normalized to untreated group (defined as 100%). The number of colonies in the control group are shown in Fig. 6d. Data in d and e have been repeated once with the same conclusions. f. AML-CFU in all 7 AML samples are highly sensitive to echinomycin. AML samples (2.5x105/ml) from either peripheral blood (PB) or bone marrow (BM) were pretreated with given concentrations of echinomycin in 2 ml medium for 24 hours. Treated viable cells were then plated at 105/well for CFU assay in triplicates. The colony numbers were counted 7–10 days later. The data shown are % means+/− S.D. of untreated controls. g. Echinomycin selectively eliminates the CD34+CD38− subset of AML cells. Primary AML samples were thawed from liquid nitrogen. After overnight recovery, they were cultured with given doses of echinomycin or vehicle control for 30 hours in RPMI 1640 containing 10% fetal calf serum and human cytokine cocktail consisting of CSF, GM-CSF and IL-3 at a density of 5X105/ml. The cells were stained with antibodies against CD34, CD38 in conjunction with Annexin V and DAPI. Data shown are the % of Annexin V+DAPI+/− cells with the specified markers. The Annexin V+ cells % in vehicle treated group has been subtracted. The filled symbols show the data for the CD34+CD38− subsets, while the open symbols show data for the bulk leukemia cells (CD34+CD38+ for AML9, AML32, AML60 and AML71 and CD34−CD38+ for AML15, AML36 and AML132). These data have been repeated twice. h. Therapeutic effect of human AML in NOD-SCID mice, data shown are % of human CD45 (hCD45)+ cells in the bone marrow of the recipient mice at 40 days after last treatment. The therapeutic effect has been repeated twice.[2]. Wang Y, et al. Targeting HIF1α eliminates cancer stem cells in hematological malignancies. Cell Stem Cell. 2011 Apr 8;8(4):399-411.
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