Saphenamycin , CAS No.634600-55-8

CAS: 634600-55-8 Cat. No.: S1022953 Fórmula: C₂₃H₁₈N₂O₅ Peso molecular: 402.400

Storage

Room temperature

Specifications

Condições de armazenamento de armazenamento

Room temperature

Tipo de ação

INHIBITOR

Nomes e identificadores

• Sorrisos canónicos: CC1=C(C(=CC=C1)O)C(=O)OC(C)C2=C3C(=CC=C2)N=C4C(=N3)C=CC=C4C(=O)O
• IUPAC Name: 6-[1-(2-hydroxy-6-methylbenzoyl)oxyethyl]phenazine-1-carboxylic acid
• InChIKey: AXHGAUSFRHOIGV-UHFFFAOYSA-N
• INCHI: 1S/C23H18N2O5/c1-12-6-3-11-18(26)19(12)23(29)30-13(2)14-7-4-9-16-20(14)24-17-10-5-8-15(22(27)28)21(17)25-16/h3-11,13,26H,1-2H3,(H,27,28)
• Peso molecular: 402.400

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Classe Diazanaphthalenes
      • Subclass Benzodiazines
        • Level5 Quinoxalines
          • Level6 Phenazines and derivatives

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Classe: Diazanaphthalenes
• Subclass: Benzodiazines
• Intermediate Tree Nodes: Quinoxalines
• Direct Parent: Phenazines and derivatives
• Alternative Parents: o-Hydroxybenzoic acid esters Salicylic acid and derivatives Benzoyl derivatives Meta cresols Toluenes 1-hydroxy-2-unsubstituted benzenoids 1-hydroxy-4-unsubstituted benzenoids Pyrazines Dicarboxylic acids and derivatives Vinylogous acids Heteroaromatic compounds Carboxylic acid esters Carboxylic acids Azacyclic compounds Organic oxides Organopnictogen compounds Organonitrogen compounds Organooxygen compounds Hydrocarbon derivatives
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Phenazine - O-hydroxybenzoic acid ester - Salicylic acid or derivatives - Benzoate ester - Benzoic acid or derivatives - Benzoyl - M-cresol - 1-hydroxy-2-unsubstituted benzenoid - Toluene - 1-hydroxy-4-unsubstituted benzenoid - Phenol - Dicarboxylic acid or derivatives - Benzenoid - Pyrazine - Monocyclic benzene moiety - Heteroaromatic compound - Vinylogous acid - Carboxylic acid ester - Carboxylic acid derivative - Carboxylic acid - Azacycle - Organic nitrogen compound - Hydrocarbon derivative - Organic oxide - Organopnictogen compound - Organic oxygen compound - Organooxygen compound - Organonitrogen compound - Aromatic heteropolycyclic compound
• Descrição: This compound belongs to the class of organic compounds known as phenazines and derivatives. These are polycyclic aromatic compounds containing a phenazine moiety, which is a linear tricyclic system that consists of a two benzene rings joined by a pyrazine ring.
• External Descriptors: phenazines

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Propriedades químicas e físicas

• Peso molecular: 402.400 g/mol
• XLogP3: 4.500
• Hydrogen Bond Donor Count: 2
• Hydrogen Bond Acceptor Count: 7
• Rotatable Bond Count: 5
• Exact Mass: 402.122 Da
• Monoisotopic Mass: 402.122 Da
• Topological Polar Surface Area: 110.000 Ų
• Heavy Atom Count: 30
• Formal Charge: 0
• Complexity: 643.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 0
• Undefined Atom Stereocenter Count: 1
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

Application Protocols

No tested application protocols, assay conditions, or recommended concentrations are provided for this item.

General starting points for small-molecule tool compounds (adjust per assay and confirm compatibility):

• Stock solutions: 10–50 mM in DMSO or 1–10 mg/mL in MeOH; store aliquots to avoid repeated freeze–thaw.
• Biochemical assays: Start at 0.1–30 µM dose–response with 0.2–1% DMSO final; include vehicle controls and non-specific cytotoxicity counterscreens.
• Cell-based assays: Begin at 0.03–10 µM with stepwise dilutions; monitor for precipitation and cell health.
• Analytical standards: Prepare 1–100 µg/mL in MeOH/ACN for LC–MS; determine response factors and linearity (R² ≥ 0.995) over your range.

These are generic research guidelines; develop and validate your protocol per your instrument, assay, and regulatory framework. Item-specific protocols: Not specified for this item; refer to CoA/Spec Sheet.

Biological Roles

Item-specific biological function data are not provided in this listing. The following are general considerations for natural-product small molecules used in research.

• Origin (general): Many named natural products originate from microbial secondary metabolism and may exhibit interactions with enzymes, membranes, or nucleic acids. For Saphenamycin, consult primary literature for definitive biosynthetic origin and mode of action.
• Use in research: Employed as a tool compound for probing biological pathways in vitro, as a reference analyte, or for comparative studies in metabolomics and dereplication. Any biological testing must observe the “research use only” restriction.
• Mechanistic caution: Natural products can have polypharmacology; interpret assay results with appropriate controls (vehicle control, orthogonal assays) and confirm target engagement independently.
• ADME considerations (general):
  • Solubility and permeability are often limiting; consider carrier proteins, cyclodextrins, or optimized cosolvents for in vitro systems.
  • Metabolic lability may be high; avoid prolonged incubations without stability verification.
• Off-target and safety (general): Potential for cytotoxicity or mitochondrial interference in cell assays at higher concentrations; always conduct dose–response with non-specific cytotoxicity counterscreens.

Definitive biological roles, targets, and potencies for Saphenamycin should be taken from peer-reviewed sources or the supplier’s CoA where available. No medical or clinical claims are made.

Buffer Applications

Saphenamycin is not a buffering reagent. Therefore, classical buffer formulations (e.g., phosphate, Tris, HEPES) are not directly applicable.

Practical guidance for working with this compound in aqueous buffers (general):

• Prepare a concentrated organic stock (e.g., in DMSO or MeOH), then dilute into the chosen buffer to the working concentration while maintaining a small proportion of the organic cosolvent (typically 0.2–2% v/v).
• Assess stability across relevant pH values (e.g., pH 6–8 for most biochemical assays) using quick LC–UV/LC–MS checks at 0, 4, and 24 h.
• Common assay buffers: PBS, HEPES, or Tris; the optimal choice depends on your biological system and analytical method compatibility.
• Adsorption controls: Some natural products adsorb to plastics; prefer low-bind PP or glass vials/microplates where feasible.

If precipitation or degradation occurs upon dilution:

• Increase organic fraction modestly, change buffer ionic strength, or switch to a different buffer system.
• Filter through 0.22 µm PTFE or PVDF only after confirming no analyte loss to the membrane.

All buffer-related parameters for this item remain: Not specified for this item; refer to CoA/Spec Sheet.

Green Alternatives

Saphenamycin is a natural-product research compound, not a process solvent. “Green alternatives” therefore pertain to how you handle and formulate solutions rather than replacing the compound itself.

Greener handling strategies (general):

• Prefer EtOH or water–EtOH cosolvent systems when compatible with your assay, as EtOH is considered a greener solvent than ACN, DMF, or DMSO. Verify solubility and stability first.
• Minimize DMSO concentration in bioassays (e.g., ≤0.5–1% v/v) to reduce environmental and biological burdens.
• Use microscale operations and pre-aliquoted vials to reduce waste and repeated solvent rinses.
• Choose amber glass and PTFE-lined caps to extend solution shelf-life, lowering the need for remake.

Comparison of common stock solvents (general, literature-informed):

• Ethanol: renewable feedstock, good safety profile; moderate solvency; may affect some assays.
• Methanol: good solvency; higher toxicity; suitable for LC–MS.
• DMSO: excellent solvency and stability; high boiling point complicates removal; moderate EHS profile.
• Acetonitrile: LC-friendly, low viscosity; derived from petrochemical sources; toxicity considerations.

Waste considerations:

• Collect all solutions as halogen-free organic waste unless mixed with halogenated solvents.
• Use aqueous workups only after confirming no hazardous degradation products are formed.

Where feasible, select greener solvent systems balanced against assay compatibility and compound stability.

Pharmaceutical Uses

No pharmacopeial status or excipient/formulation role is provided for this item. This product is supplied strictly for research use only and is not intended for human or veterinary use.

General, non-clinical notes for small-molecule natural products in formulation research:

• Can serve as a reference standard in analytical method development (e.g., HPLC assay validation, stability-indicating methods) within a preclinical discovery setting.
• Solubility enhancement strategies (research phase): cyclodextrin inclusion, co-solvent systems (EtOH, PEG 400, DMSO), or lipid-based carriers for in vitro dosing; any such approaches must be verified for compatibility with the intended assay.
• Solid-state studies: Where material is available, DSC/TGA and XRPD can be used to investigate polymorphism or amorphous content (if relevant), informing storage and handling.

Item-specific pharmaceutical-grade attributes (residual solvents, elemental impurities, bioburden/endotoxin) are not specified for this item; refer to CoA/Spec Sheet. No therapeutic, diagnostic, or clinical use is claimed or implied.

Physical Properties

Item-specific physicochemical specifications are not included in the current record. Where a numerical value is not present below, defer to the CoA/SDS or primary literature.

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• Melting point: Not specified for this item; refer to CoA/Spec Sheet.
• Boiling point: Not applicable/rarely specified for complex natural products; decomposition may precede boiling (literature, general observation).
• Density: Not specified for this item; refer to CoA/Spec Sheet.
• Refractive index: Not applicable (typically reported for liquids; most NP standards are solids).
• pKa/logP: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility (practical guidance):
  • For screening/stock prep, begin with DMSO (analytical grade) small-scale tests (1–10 mg/mL), then dilute into aqueous buffers with co-solvent (≤1–5% v/v DMSO) to reduce precipitation.
  • Alternative organic cosolvents to test sequentially: MeOH, EtOH, ACN. Avoid strong bases/acids until stability is known.
• Spectroscopy (general):
  • UV–vis detection is often feasible for polyaromatic/heteroaromatic natural products; determine λmax empirically by scanning 200–400 nm in a low-UV solvent (literature, general practice).

Note: Do not treat the above as specifications; they are practical, literature-style guidelines for handling a natural-product small molecule.

Quality and Grades

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet. If this material is supplied as a screening standard, it is typically intended for research use (analytics, assay development, HTS), not for GMP manufacturing.
• Research Use Note: For research use only (non-clinical, non-diagnostic).

Understanding typical grades for natural-product standards (general guidance):

• Research/analytical grade: Emphasis on structural identity and purity suitable for LC–MS/UPLC and NMR verification. Impurities may include closely related congeners or residual solvents; the CoA will list HPLC area% or qNMR content.
• Screening library grade: Packaged for hit finding/assay; may prioritize practicality (mass, format, solvated stocks) over exhaustive trace-metal/UV-cutoff characterization.

What to check on the CoA for this item:

• Verified identity (NMR, MS, and/or HRMS), lot-specific purity (% area by HPLC or qNMR), residual solvent levels, and water content if measured.
• Any stabilizers or formulation (e.g., supplied as a solid or DMSO stock). If a stabilizer is present, verify its impact on UV detection or bioassays.

Packaging/format (typical):

• Small vials suitable for analytical use. If in solution, expect reporting of solvent, concentration, and allowable storage variance. All item-specific values remain: Not specified for this item; refer to CoA/Spec Sheet.

Reaction and Applications

This product is primarily positioned as a research compound/screening standard rather than a synthetic reagent. No manufacturer applications are specified.

Typical research applications for natural-product small molecules (general):

• Reference material for LC–MS/NMR method development, retention-time matching, and spectral libraries.
• Assay development/HTS: evaluation in biochemical or cell-based assays as a positive control or test article (observing “research use only”).
• Dereplication workflows: match against crude extract profiles to identify known metabolites.

If using Saphenamycin in chemistry workflows:

• Derivatization studies (general): functional-group mapping (acetylation, methylation, hydrogenation) to probe structure–activity relationships; verify compatibility via small-scale tests.
• Stability/stress testing: subject to pH 2–10, oxidative (H2O2 trace), reductive (Na2S2O4), and thermal conditions to map degradation.

Practical tips:

• Prepare master stocks in DMSO or MeOH and aliquot to avoid repeated freeze–thaw or air exposure.
• Employ amber vials if UV-labile; purge with inert gas if oxidation is observed by LC–MS.

Note: No item-specific reactivity or bioactivity claims are made here. For concrete synthetic transformations involving Saphenamycin itself, consult primary literature specific to its scaffold.

Reaction Conditions

No item-specific reaction conditions are provided because Saphenamycin is not primarily a reagent for named organic reactions. The following general guidance applies to small-scale modifications or stability studies of natural products.

• Solvents: Begin with anhydrous MeOH, EtOH, ACN, or DCM for neutral reactions; use DMSO/DMF for higher polarity. Confirm stability via test reactions (0.5–5 mg scale).
• Temperature: Conduct initial trials at 20–25 °C; escalate to 40–60 °C only after establishing stability to avoid decomposition.
• Atmosphere: For oxidation-sensitive scaffolds, use argon/nitrogen and add 0.01–0.1% BHT only if known to be compatible with your analytics.
• Acylation/alkylation (general): Base catalysts such as Et3N or pyridine at 0–25 °C; monitor by LC–MS every 15–30 min.
• Redox: Mild hydrogenation (e.g., H2/Pd-C, 1–3 bar, RT) on analytical scale can probe unsaturation; peroxides/strong oxidants should be avoided until stability is known.
• Aqueous conditions: For bioconjugation or enzymatic assays, buffer at pH 6–8 and keep organic cosolvent ≤5% unless required.

Expected yields and times: Highly scaffold-dependent; for analytical-scale derivatizations, aim for 30–80% isolated after micro-purification (flash/semiprep HPLC). Treat these as literature-style benchmarks only; optimize based on the validated structure of Saphenamycin.

Safety and Handling

Safety data are incomplete in this listing; consult the SDS for authoritative information before use.

• GHS classification: Not specified for this item; refer to SDS.
• Signal word / H-statements / pictograms: Not specified for this item; refer to SDS.
• General hazards (literature/general): Natural products of microbial origin can present risks of acute toxicity, skin/eye irritation, and environmental hazard. Handle as a potentially bioactive small molecule.
• PPE: Laboratory coat, safety glasses, and nitrile gloves. Use in a fume hood to avoid inhalation of dust or solvent vapors.
• Handling guidance:
  • Avoid aerosol/dust formation; open vials carefully.
  • Use dedicated tools to weigh small quantities; minimize exposure time outside the hood.
  • For solutions, cap tightly to limit evaporation and oxidative degradation.
• Incompatibilities (general): Strong oxidizers and strong acids/bases until chemical stability is known. Avoid prolonged exposure to light and elevated temperatures.
• First aid (overview; defer to SDS):
  • Skin/eye contact: Rinse with water for ≥15 min; remove contaminated clothing; seek medical attention if irritation persists.
  • Inhalation: Move to fresh air; seek medical attention if symptoms occur.
  • Ingestion: Rinse mouth; do not induce vomiting; seek medical attention.
• Waste: Collect solutions and solids as hazardous organic waste. Prevent release to environment.

Always prioritize the SDS for lot-specific hazard and first-aid details.

Solvent Selection

Because item-specific solubility data are not provided, select solvents using a tiered, small-scale screening approach common to natural-product standards.

• Primary stock solvent (general best-practice): DMSO due to broad solvency and assay compatibility at low % v/v.
• Secondary solvents to test: MeOH, EtOH, ACN, and, if needed, DMF or acetone. Begin at 1–10 mg/mL and adjust.
• Aqueous work: Prepare cosolvent mixtures (e.g., 0.5–2% DMSO or MeOH in buffered saline) to mitigate precipitation on dilution.
• Polarity considerations (general): Natural products can be amphipathic; if precipitation occurs, increase organic fraction stepwise or add neutral surfactant compatible with your assay (e.g., 0.01% Tween-20) after verifying no assay interference.
• Stability checks:
  • Run quick LC–UV or LC–MS stability screens in each solvent over 24–48 h at room temperature and 4 °C.
  • Assess light sensitivity; wrap amber foil if UV-active.
• Volatility and dryness: Use anhydrous grades when water sensitivity is suspected; ensure vials are sealed with PTFE-lined caps to limit solvent loss and oxygen ingress.

Comparison (general):

• DMSO vs MeOH: DMSO maximizes solvency and long-term stock stability; MeOH offers easier evaporation and LC compatibility but may reduce stability for some NP scaffolds.
• ACN vs EtOH: ACN provides lower viscosity and strong elution power in LC; EtOH is greener and often more biocompatible, but with narrower solvency for highly lipophilic compounds.

Storage and Reconstitution

• Storage conditions: Room temperature (as provided in product data). For best practice with natural-product standards, consider storing protected from light in a desiccator. If long-term storage is anticipated, 2–8 °C or −20 °C may enhance stability, subject to compound-specific data.
• Shipped in: Not specified for this item; refer to CoA/Spec Sheet.
• Appearance: Not specified for this item; refer to CoA/Spec Sheet.

Reconstitution (general guidance):

• For analytical stocks, dissolve in DMSO or MeOH to prepare a concentrated solution (e.g., 10–50 mM or 1–10 mg/mL). Vortex and, if necessary, sonicate briefly. Filter only if verified non-adsorptive.
• For aqueous assays, dilute the organic stock into buffer while stirring to avoid local supersaturation. Maintain 0.2–2% organic cosolvent as needed.
• Aliquoting: Prepare single-use aliquots to avoid repeated freeze–thaw and headspace oxygen exposure.

Stability checks (recommended):

• Assess short-term stability at room temperature and under light vs dark using LC–UV/LC–MS.
• Record pH and solvent composition on vials; use amber containers for UV-sensitive compounds.

All item-specific stability limits, re-test periods, and solution shelf-life remain: Not specified for this item; refer to CoA/Spec Sheet.

Structure and Identity

Brief overview: Saphenamycin is listed as a small-molecule research compound. Item-specific structural identifiers are limited in the present record.

• Product name: Saphenamycin (SKU: S1022953)
• CAS: 634600-55-8
• PubChem CID: 134184 (identifier provided; confirm against latest databases)
• InChIKey: Not specified for this item; refer to CoA/Spec Sheet. (Provided string "17297" is not a standard InChIKey.)
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

Structural features (general/literature guidance):

• Saphenamycin is described in the literature as a natural-product small molecule isolated from microbial sources; specific ring systems, stereocenters, and functional groups should be verified from a trusted structural database or the supplied CoA/SDS for this lot.

2D structure description (general):

• Without a verified SMILES/InChI, a reliable 2D description cannot be provided. Please consult the certificate of analysis or authoritative databases for the definitive structure prior to method development or spectral assignment.

Synthetic Utility

Saphenamycin, as a named natural product, is more commonly used as a research standard than as a building block. Without confirmed structural details in this listing, specific transformations cannot be enumerated. The following are general considerations if derivatization is pursued for SAR or analytical purposes.

• Functional group mapping (general): Identify nucleophilic, electrophilic, and redox-sensitive moieties via small-scale reactions (acylations, alkylations, reductions/oxidations) followed by LC–MS/NMR characterization.
• Protecting-group strategies: If phenolic or amine functions are present (to be confirmed from structure), transient protection (e.g., Boc, Ac, Bn) can aid purification or selective modification.
• Isotopic labeling: Preparation of **13C/15N-**enriched analogs can support quantitative LC–MS assays and metabolic tracing.
• Conjugation handles: Installation of tags (e.g., alkynes/azides for click chemistry) may facilitate target-ID workflows, provided the pharmacophore is preserved.
• Analytical derivatization: If volatility is desired for GC analysis, silylation (e.g., BSTFA) or methylation may be explored after confirming compatibility.

Caveat: All of the above are general strategies for natural products. For Saphenamycin specifically, consult peer-reviewed literature for verified functional groups and reactivity before planning synthesis or semisynthesis.

Target Specificity

No target, enzyme, receptor, or pathway specificity is provided for this item. This product is sold for research use only, with no claims of biological target engagement.

Guidance for determining target specificity (general):

• Perform orthogonal assays (biochemical binding + cell-based function) and include counter-screens to exclude assay artifacts.
• Use thermal shift or DSF, SPR/ITC, and chemoproteomics where applicable.
• Validate on- vs off-target effects with structure–activity relationships (analogs) and genetic perturbation (knockdown/knockout) controls.

All target-specific attributes for Saphenamycin remain: Not specified for this item; refer to CoA/Spec Sheet and primary literature.