Oxynitidine , CAS No.548-31-2

CAS: 548-31-2 Cat. No.: O1029646 Formula: C₂₁H₁₇NO₅ Molecular Weight: 363.400

Storage

Room temperature

Specifications

Storage

Room temperature

Action Type

INHIBITOR

Names and Identifiers

Canonical Smiles

CN1C2=C(C=CC3=CC4=C(C=C32)OCO4)C5=CC(=C(C=C5C1=O)OC)OC

IUPAC Name

2,3-dimethoxy-12-methyl-[1,3]benzodioxolo[5,6-c]phenanthridin-13-one

InChIKey

TVYBYUSEIMYSFA-UHFFFAOYSA-N

INCHI

1S/C21H17NO5/c1-22-20-12(5-4-11-6-18-19(7-13(11)20)27-10-26-18)14-8-16(24-2)17(25-3)9-15(14)21(22)23/h4-9H,10H2,1-3H3

Molecular Weight

363.400

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Class Quinolines and derivatives
      • Subclass Benzoquinolines

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Class: Quinolines and derivatives
• Subclass: Benzoquinolines
• Intermediate Tree Nodes: Not available
• Direct Parent: Phenanthridines and derivatives
• Alternative Parents: Hydroquinolones Isoquinolones and derivatives Hydroquinolines Naphthalenes Benzodioxoles Anisoles Pyridinones Alkyl aryl ethers Heteroaromatic compounds Lactams Oxacyclic compounds Acetals Azacyclic compounds Organonitrogen compounds Organopnictogen compounds Hydrocarbon derivatives Organic oxides
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Phenanthridine - Dihydroquinolone - Isoquinolone - Dihydroquinoline - Isoquinoline - Naphthalene - Benzodioxole - Anisole - Alkyl aryl ether - Pyridinone - Benzenoid - Pyridine - Heteroaromatic compound - Lactam - Acetal - Ether - Oxacycle - Azacycle - Hydrocarbon derivative - Organic oxide - Organic nitrogen compound - Organopnictogen compound - Organic oxygen compound - Organooxygen compound - Organonitrogen compound - Aromatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included.
• External Descriptors: Not available

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

Chemical and Physical Properties

• Molecular Weight: 363.400 g/mol
• XLogP3: 3.600
• Hydrogen Bond Donor Count: 0
• Hydrogen Bond Acceptor Count: 5
• Rotatable Bond Count: 2
• Exact Mass: 363.111 Da
• Monoisotopic Mass: 363.111 Da
• Topological Polar Surface Area: 57.200 Ų
• Heavy Atom Count: 27
• Formal Charge: 0
• Complexity: 585.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 0
• Undefined Atom Stereocenter Count: 0
• 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

• Item-specific tested applications and protocols:

  • None are provided in the Product Data for this item. No validated protocols (e.g., WB, IHC, IF, FC) apply to this small molecule.

• General handling suggestions (non-validated, for planning only):

  • For screening use, prepare a DMSO stock after confirming solubility and purity. Dispense using calibrated liquid handlers to ensure accurate molar dosing, and limit final DMSO to ≤1% v/v in biological assays if applicable.
  • For analytical characterization, establish an HPLC method with a C18 column and a water/acetonitrile (+0.1% acid) gradient, verifying single, symmetrical peaks and orthogonal confirmation by MS and NMR.

Please refer to your internal SOPs for any assay-specific procedures. No official protocols are endorsed for this product.

Biological Roles

• Item-specific biological data (from Product Data):

  • None provided. This product is for research use only and is listed within a small-molecule/compound library.

• Literature/general context (no clinical or efficacy claims):

  • Compounds termed “oxynitidine” have been described in the literature as plant-derived alkaloids within, or closely related to, the benzophenanthridine family. Natural products of this class often function in plants as chemical defenses and can exhibit characteristic photophysical properties due to their extended aromatic systems.
  • From a biochemical handling perspective, many alkaloids interact with biomolecules through combinations of aromatic stacking, cation–π interactions (when protonated or quaternary), and hydrogen bonding via oxygen substituents. These properties underpin their frequent inclusion in discovery libraries for target-agnostic screening.

• Research implications (general):

  • Oxynitidine can be leveraged as a molecular probe candidate for non-biological assays (e.g., binding surrogates, chromatography retention index standards) and for comparative studies of polyaromatic binding in model systems (DNA-polyelectrolyte interactions, micelle incorporation), staying within purely research/physicochemical domains.

Note: No biological function, pathway involvement, or therapeutic relevance is claimed for this catalog item. For any biological experiments, define appropriate controls and concentration ranges, and consult the SDS/CoA for solubility and purity considerations.

Buffer Applications

• Applicability to buffers:

  • Oxynitidine is a small organic molecule and is not a conventional buffering agent. It does not define a standard pKa-based buffer system for pH control in aqueous solutions.

• Practical note (general):

  • If Oxynitidine is used in aqueous assays, prepare it in a suitable vehicle (e.g., DMSO stock) and dilute into your existing assay buffer (PBS, HEPES, Tris, etc.) at minimal final organic content to avoid perturbing buffer capacity. Determine solubility and stability at the working pH beforehand.

• Recipe guidance:

  • Not applicable for this item; use established biological or analytical buffers appropriate to your application. Document the final cosolvent percentage and pH to ensure reproducibility.

Green Alternatives

• Context: As a target compound (not a solvent), Oxynitidine itself has no greener “substitute.” However, greener choices can be made for handling, analysis, and purification.

• Greener solvent choices for solution preparation and chromatography (general guidance):

  • Prefer ethanol over methanol where feasible (lower toxicity, renewable sourcing). Validate solubility and assay compatibility.
  • For RP-HPLC, consider water/ethanol gradients or water/acetonitrile with minimized organic content. When acetonitrile is constrained, water/ethanol or water/IPA can sometimes substitute, with adjustments to viscosity and backpressure.
  • For normal-phase work, evaluate 2-MeTHF or EtOAc in place of DCM/CHCl3 when compatible with analyte polarity and stability.

• Workup and waste minimization:

  • Use micro-scale solubility screens to avoid overuse of solvents. Consolidate waste streams (halogenated vs non-halogenated) correctly to facilitate downstream recovery.
  • Favor solid-phase sample cleanup (e.g., SPE) over repeated liquid–liquid extractions where appropriate.

• Comparative snapshot (general):

  • Acetonitrile vs Ethanol: ACN offers lower viscosity and UV cutoff; EtOH is greener but may increase system backpressure and change selectivity.
  • DCM vs 2-MeTHF/EtOAc: DCM has excellent elution power but poor environmental profile; 2-MeTHF/EtOAc are greener with different selectivity—re-optimize gradients accordingly.

Note: Always verify that greener alternatives maintain the required performance for your analytical or preparative workflow.

Pharmaceutical Uses

• Regulatory/grade context (item-specific):

  • No pharmacopeial status or excipient grade is stated for this product. It is labeled for research use only.

• Formulation-related, non-clinical considerations (general):

  • As a small-molecule reference or screening compound, Oxynitidine may be used in pre-formulation research to evaluate solubility, stability, and analytical behavior (e.g., forced-degradation studies) under non-GMP conditions.
  • Salt selection studies (if a free-base form exists) can inform solubility and solid-state properties for purely research purposes. Conversely, if supplied as a defined salt, counterion identity should be recorded for data integrity.

• Analytical development (general):

  • Develop stability-indicating LC methods using gradients of water/acetonitrile (0.1% FA), monitoring multiple wavelengths suitable for polyaromatic chromophores. Assess solution stability in common vehicles (DMSO, MeOH, buffer) and evaluate adsorption losses in plasticware vs glass.

• Important limitations:

  • No therapeutic, diagnostic, or clinical use is implied or permitted. This product is not intended for human or veterinary administration and has no approved pharmaceutical function within this catalog entry.

Physical Properties

• Item-specific properties (from Product Data):

  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular Weight: Not specified for this item; refer to CoA/Spec Sheet.
  • Physical constants (mp/bp/density/refractive index): Not specified for this item; refer to CoA/Spec Sheet.
  • Solubility: Not specified for this item; refer to CoA/Spec Sheet.

• Literature/general expectations for benzophenanthridine alkaloids (non-binding, not the item spec):

  • Often isolated as crystalline solids (free base or as salts). Salt forms can be more water-soluble; free bases tend to be sparingly soluble in water and soluble in polar aprotic solvents (e.g., DMSO, DMF) and polar protic alcohols (MeOH/EtOH).
  • The polyaromatic, rigid framework typically confers relatively high melting points compared with simple aromatics. Exact values vary by substitution and ionic form.
  • Ionization and solubility are pH-dependent if a non-quaternized nitrogen is present; quaternary ammonium salts are permanently charged and may exhibit higher aqueous solubility.

• Practical guidance (general):

  • For assay stock solutions, DMSO is commonly used when water solubility is uncertain. Prepare small test dissolutions to confirm solubility limits before scaling.
  • If a hydrochloride or other mineral acid salt form is supplied, water or aqueous buffer may suffice; verify pH and compatibility with your assay matrix.

Always defer to the product’s CoA/SDS for authoritative physical property data of this specific lot.

Quality & Grades

• Item-specific grade/purity (from Product Data):

  • Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.

• How to interpret grades (general guidance):

  • Analytical/Reference grade: Typically suitable for method development, quantitative reference, and analytical calibration; often accompanied by tight impurity profiling.
  • Screening grade (compound libraries): Suitable for discovery screening and SAR exploration; typically provided with purity by HPLC/UPLC and identity confirmation (MS/NMR). Trace-level specifications (water, residual solvents, inorganics) may be less stringent than analytical reference standards.
  • Pharmacopoeial grades (e.g., USP/EP): Apply to excipients/APIs; not expected for this research-use-only product.

• Stabilizers and form (general considerations):

  • If supplied as a specific salt (e.g., hydrochloride), batch-to-batch consistency in counterion and hydration/solvation state matters for assay reproducibility.
  • If a stabilizer is used (rare for solid small molecules), it will be declared on the CoA; absence of a declaration typically implies none used.

• What is specific to this item:

  • This product is listed under a small-molecule/compound library category and labeled “For research use only.” For numerical purity, residual solvents, water content, and detailed impurity profiles, please consult the item’s CoA/Spec Sheet for the exact lot you receive.

Reaction & Applications

• Manufacturer Applications (from catalog):

  • Not specified beyond inclusion in a small-molecule/compound library. This product is for research use only.

• Research uses (general, non-clinical, and without biological claims):

  • As a structurally defined small molecule, Oxynitidine can serve as a reference material for analytical method development (e.g., LC–MS/MS retention characterization) and as a member of screening decks for structure–activity relationship exploration in chemical biology.
  • Useful in comparative studies of benzophenanthridine-like chromophores (if applicable), including spectroscopic benchmarking (UV/Vis, fluorescence) where allowed by solubility and stability.

• Sample preparation and handling (general):

  • Prepare concentrated DMSO stocks (e.g., 10–50 mM) after confirming solubility; filter through a 0.2 µm PTFE syringe filter if particulate is observed. Record exact concentration by weight-in and adjust for purity per CoA.
  • For LC–MS methods, begin with water/acetonitrile + 0.1% formic acid; optimize gradient and ionization settings empirically. Monitor for potential on-column adsorption common to planar polyaromatics.

• Synthetic chemistry context:

  • Natural-product-like scaffolds such as benzophenanthridines can be used as comparators in photophysical studies and as substrates in derivatization campaigns (O- or N-methylation/acetylation, salt formation) to tune solubility and spectral properties.

Note: No claims are made about biological activity or therapeutic use. All applications should remain within research and method-development contexts.

Reaction Conditions

• Applicability:

  • No specific reactions or conditions are provided for this item. Oxynitidine is not supplied as a reagent and does not have standard “use conditions” analogous to catalysts or solvents.

• General guidance for derivatization studies (literature-informed, not item-specific specs):

  • O-acylation/alkylation: Commonly performed with acyl chlorides/anhydrides or alkyl halides under mild base (e.g., pyridine, DMAP) in aprotic solvents (DCM, MeCN, THF). Monitor for over-alkylation if multiple phenolic sites exist.
  • Salt formation/counterion exchange: Dissolve in minimal solvent and treat with mineral/organic acids or ion-exchange resins; isolate by precipitation or lyophilization. Verify stoichiometry and hydration.
  • Photophysical assays: Prepare micromolar solutions in spectroscopic-grade solvents; minimize light exposure if photolability is suspected.

• Yields/temperatures/times:

  • Highly substrate- and substitution-dependent; consult primary literature for the exact oxynitidine congener and reaction of interest. Pilot small-scale experiments are recommended to define conditions for this specific material.

Note: These are general considerations for analogous scaffolds and are not performance guarantees for this catalog item.

Safety & Handling

• Item-specific hazard information (from Product Data):

  • Signal Word: Not specified for this item; refer to SDS.
  • H-Statements: Not specified for this item; refer to SDS.
  • GHS Classification/Pictograms: Not specified for this item; refer to SDS.

• General laboratory safety guidance (not a substitute for SDS):

  • Handle in a chemical fume hood, avoiding inhalation of dust or aerosols. Prevent skin/eye contact. Use appropriate PPE: lab coat, safety glasses, and suitable chemical-resistant gloves (e.g., nitrile). For weighing fine powders, consider antistatic measures and a balance enclosure.
  • Avoid ingestion and environmental release. Collect waste in properly labeled containers per your institutional protocols.
  • If dissolved in organic solvents (e.g., DMSO, DMF, MeOH), observe the solvent’s hazards and flash points. Many alkaloids are bioactive; minimize exposure and practice good hygiene.

• First-aid overview (general):

  • Eye contact: Rinse cautiously with water for several minutes; remove contact lenses if easy; seek medical attention.
  • Skin contact: Wash with soap and water; remove contaminated clothing.
  • Inhalation: Move to fresh air; seek medical attention if symptoms persist.
  • Ingestion: Rinse mouth; do not induce vomiting; seek medical advice.

• Storage incompatibilities and precautions (general):

  • Keep away from strong oxidizers and strong acids/bases unless the material is a defined salt designed for such media. Protect from excessive heat and light as prudent practice.

Consult the official SDS for definitive hazard classification and emergency measures for this specific product.

Solvent Selection

• Item-specific solubility/vehicle guidance (from Product Data):

  • Not specified for this item; refer to CoA/Spec Sheet.

• Practical selection framework (general, for polyaromatic alkaloids):

  • Primary stock solvent: DMSO is a robust default for discovery screening due to broad solvency and biological assay compatibility at low final %.
  • Protic options: Methanol or ethanol can dissolve many alkaloids; they may be preferable for spectroscopic work (UV/Vis, CD) or when DMSO is incompatible with the assay.
  • Aqueous media: If supplied as a salt (e.g., HCl), water or buffer may suffice; adjust pH to favor the ionized form if a free base is used. Perform small-scale trials to avoid precipitation on dilution.

• Polarity and miscibility (general):

  • Anticipated to have moderate-to-low water solubility in free-base forms and higher solubility in polar organic solvents; quaternary salts are often water-miscible. Always verify with a bench test.

• When to choose alternatives:

  • DMF/NMP: For difficult solubilization where DMSO is insufficient (ensure biocompatibility if used in bioassays).
  • Acidified aqueous co-solvent: A small % of MeOH/EtOH with 0.1–1% acid (e.g., HCl) may enhance solubility of basic alkaloids; validate compatibility with your system.

• Small comparison (general):

  • DMSO: highest solvency; broad assay tolerance at ≤1% v/v.
  • MeOH/EtOH: good solvency; easier evaporation; flammable.
  • Water/buffer: best for biocompatibility if soluble; watch pH and precipitation on dilution.

Storage & Reconstitution

• Item-specific storage/shipping (from Product Data):

  • Storage Conditions: Room temperature.
  • Shipped In: Not specified for this item; refer to CoA/Spec Sheet.

• General storage guidance (small-molecule solids):

  • Keep container tightly closed in a dry, well-ventilated place. Protect from prolonged exposure to light and moisture. If repeated access is expected, consider aliquoting to minimize ambient exposure.
  • Record open date and maintain lot traceability. Avoid cross-contamination by using clean spatulas and antistatic tools when handling powders.

• Reconstitution guidelines (general):

  • Choose solvent based on preliminary solubility testing (DMSO, MeOH, EtOH, or water/buffer if a salt form). Target concentrated stocks (e.g., 10–50 mM) to minimize final vehicle in assays.
  • Warm gently to ambient temperature and vortex/sonicate as needed. Do not overheat. If particulates remain, clarify by 0.2 µm PTFE filtration.
  • Document the exact concentration using weight-in and adjust for lot-specific purity per CoA. Note storage stability of solutions; many small molecules are stable for days at 2–8°C and weeks at −20°C, but confirm empirically.

• Freeze–thaw:

  • For solution stocks, aliquot to avoid repeated freeze–thaw cycles. Inspect for precipitation, color change, or degradation before use.

Always consult the CoA/SDS for lot-specific recommendations and stability data.

Structure & Identity

• Item-specific identifiers (from Product Data):

  • Product Name: Oxynitidine
  • CAS: 548-31-2
  • SKU: O1029646
  • InChIKey: Not specified for this item; refer to CoA/Spec Sheet. (Note: the placeholder “351383” in Product Data is not a valid InChIKey format.)
  • 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.

• Literature/general chemistry context (not item-specific):

  • “Oxynitidine” is reported in the literature as a member of the benzophenanthridine alkaloids, structurally related to nitidine. These frameworks feature a polycyclic, planar aromatic system fused to a cationic or protonatable nitrogen center in many congeners.
  • Typical structural motifs in this family include multiple methoxy/oxy substituents on a tetracyclic scaffold; exact substitution and ionic state depend on the specific salt/free-base form described in a given report.

• Descriptive 2D structural features (literature, general):

  • Core: condensed polyaromatic ring system (benzophenanthridine) that is largely rigid and planar.
  • Heteroatoms: nitrogen in a ring (often quaternized in some congeners), plus oxygen atoms as hydroxy/methoxy substituents in many analogs.
  • Stereochemistry: typically none (planar polyaromatic), unless chiral counterions or atropisomerism are introduced (rare for this class).

Note: Please consult the CoA/Spec Sheet for the definitive structural identifiers (SMILES/InChIKey/formula/MW) of this specific catalog item.

Synthetic Utility

• Item-specific reactivity role:

  • Oxynitidine is offered as a discrete small molecule, not as a general-purpose reagent or catalyst. No specific synthetic-grade role is provided in the Product Data.

• General considerations (literature context for benzophenanthridine-like scaffolds):

  • Such rigid, polyaromatic alkaloids can be starting points for late-stage derivatization to tune physicochemical properties (e.g., O-acylation/alkylation of phenolic groups where present, counterion exchange for salts, or N-methylation/quaternization for free bases).
  • The extended aromatic system can participate in electron-transfer or photophysical studies; derivatization can shift absorption/emission maxima, enabling use as chromophoric probes in materials/analytical chemistry.

• Retrosynthetic value:

  • While total synthesis of benzophenanthridines is a rich academic area, Oxynitidine itself is not typically used as a building block in multistep synthesis outside of derivatization campaigns. For synthetic methodology development, it can serve as a challenging substrate to test chemoselectivity on polyoxygenated, polyaromatic systems.

• Practical notes:

  • If performing transformations, characterize thoroughly (1H/13C NMR, HRMS, HPLC purity) and document counterion and solvate state. Plan purification with RP-HPLC or carefully chosen normal-phase systems to manage strong π–π interactions with stationary phases.

Target Specificity

• Not applicable. Oxynitidine is a small molecule and not an antibody, enzyme, or nucleic acid probe. No antigen/epitope/clone/isotype information applies.

• If used in target-based research assays, any observed selectivity or binding profiles should be generated de novo in your laboratory and documented alongside lot-specific identity/purity from the CoA. No target specificity is provided or implied by the Product Data.