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| Targets |
Cyanosafracin B is a DNA-interacting agent that exhibits potent cytotoxic activity by interfering with DNA synthesis. As a member of the safracin family, it binds to DNA and disrupts replication and transcription processes, leading to cell death. The compound's mechanism of action is similar to that of trabectedin, which binds to the minor groove of DNA and interferes with transcription-coupled nucleotide excision repair. Cyanosafracin B is a precursor to trabectedin and phthalascidin, both of which are DNA binding agents with antitumor activity.
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| ln Vitro |
Cyanosafracin B exhibits potent cytotoxic and antimicrobial properties in vitro by interfering with DNA synthesis. The compound is a precursor to trabectedin (ET-743), which has well-characterized antitumor activity. Cyanosafracin B is a starting material for the synthesis of phthalascidin Pt-650 and ecteinascidin ET-743. The compound's activity has been demonstrated in various in vitro assays for cytotoxicity and antimicrobial activity.
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| ln Vivo |
As a synthetic precursor, cyanosafracin B is not used directly as a therapeutic agent. However, its derivative trabectedin (ET-743) has demonstrated potent antitumor activity in vivo and is approved for the treatment of soft tissue sarcoma. Trabectedin has shown efficacy in patients with previously treated advanced soft tissue sarcoma, including liposarcoma and leiomyosarcoma. The in vivo activity of cyanosafracin B itself has not been extensively characterized as it is primarily used as a starting material for drug synthesis.
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| Enzyme Assay |
Cytotoxicity assays for cyanosafracin B are performed using various cancer cell lines. Cells are seeded in 96-well plates and treated with varying concentrations of cyanosafracin B for 48-72 hours. Cell viability is assessed using MTT, CCK-8, or CellTiter-Glo assays. IC50 values are calculated from concentration-response curves. The compound's antimicrobial activity is assessed using standard broth microdilution assays against various bacterial strains. The mechanism of DNA interaction can be studied using DNA binding assays such as gel shift or fluorescence intercalation assays.
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| Cell Assay |
Cell-based assays for cyanosafracin B employ various cancer cell lines to assess cytotoxicity. Cells are treated with the compound for 24-72 hours, and cell viability is measured. Apoptosis is evaluated by Annexin V/PI staining. Cell cycle analysis is performed by propidium iodide staining. DNA damage is assessed by measuring γ-H2AX foci formation. The compound's effects on DNA synthesis can be assessed by measuring incorporation of labeled nucleotides (e.g., [3H]-thymidine or EdU). Resistance mechanisms can be studied using drug-resistant cell lines.
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| Animal Protocol |
As a synthetic precursor, cyanosafracin B is not typically used in animal efficacy studies. However, its derivative trabectedin has been extensively studied in mouse xenograft models and in clinical trials. In preclinical studies, trabectedin demonstrated antitumor activity in various xenograft models including sarcoma, breast cancer, and ovarian cancer. The compound's efficacy, safety, and pharmacokinetics have been characterized in extensive clinical development programs.
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| ADME/Pharmacokinetics |
Cyanosafracin B has molecular formula C29H35N5O6 and molecular weight 549.62. It is a starting material for the synthesis of phthalascidin Pt-650 and ecteinascidin ET-743 (trabectedin). The compound has limited solubility in water (0.22 g/L at 25°C). The compound is typically used as a research reagent for chemical synthesis and as a reference standard.
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| Toxicity/Toxicokinetics |
Toxicological data for cyanosafracin B itself are limited as it is a synthetic precursor. However, its derivative trabectedin has been extensively characterized in toxicology studies. Trabectedin is associated with hepatotoxicity, myelosuppression, and rhabdomyolysis. The compound should be handled with appropriate laboratory safety precautions due to its cytotoxic properties. As a DNA-interacting agent, it may have genotoxic potential.
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| References | |
| Additional Infomation |
Cyanosafracin B is a natural antibiotic produced by Pseudomonas fluorescens. It is a key starting material for the industrial synthesis of trabectedin (ET-743, Yondelis), an approved anticancer drug for soft tissue sarcoma. The compound is also used in the synthesis of phthalascidin Pt-650. It exhibits potent cytotoxic and antimicrobial properties by interfering with DNA synthesis.
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| Molecular Formula |
C29H35N5O6
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| Molecular Weight |
549.61810708046
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| Exact Mass |
549.258
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| CAS # |
96996-50-8
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| PubChem CID |
11353355
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| Appearance |
Light yellow to yellow solid powder
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| LogP |
0.6
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| Hydrogen Bond Donor Count |
3
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| Hydrogen Bond Acceptor Count |
10
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| Rotatable Bond Count |
5
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| Heavy Atom Count |
40
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| Complexity |
1220
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| Defined Atom Stereocenter Count |
6
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| SMILES |
C([C@H]1C2C(C(=C(C(C=2C[C@H]2[C@@H]3N(C)[C@H]([C@@H](N12)C#N)CC1C=C(C(=C(C3=1)O)OC)C)=O)C)OC)=O)NC(=O)[C@@H](N)C
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| InChi Key |
BHINEHROXMLHMV-BVRLQDJESA-N
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| InChi Code |
InChI=1S/C29H35N5O6/c1-12-7-15-8-17-19(10-30)34-18(23(33(17)4)21(15)25(36)27(12)39-5)9-16-22(20(34)11-32-29(38)14(3)31)26(37)28(40-6)13(2)24(16)35/h7,14,17-20,23,36H,8-9,11,31H2,1-6H3,(H,32,38)/t14-,17-,18-,19-,20-,23-/m0/s1
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| Chemical Name |
(2S)-2-amino-N-[[(1R,2S,10R,12R,13S)-12-cyano-19-hydroxy-7,18-dimethoxy-6,17,21-trimethyl-5,8-dioxo-11,21-diazapentacyclo[11.7.1.02,11.04,9.015,20]henicosa-4(9),6,15(20),16,18-pentaen-10-yl]methyl]propanamide
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month Note: This product requires protection from light (avoid light exposure) during transportation and storage. |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
DMSO : ~25 mg/mL (~45.49 mM)
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| 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
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *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 : PEG300 ：Tween 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). View More
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)] 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). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.8194 mL | 9.0972 mL | 18.1944 mL | |
| 5 mM | 0.3639 mL | 1.8194 mL | 3.6389 mL | |
| 10 mM | 0.1819 mL | 0.9097 mL | 1.8194 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.
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.
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