Rifalazil - ≥99% , DNA-directed RNA polymerase inhibitor, CAS No.129791-92-0, DNA-directed RNA polymerase inhibitor

CAS: 129791-92-0 Cat. No.: R651163 Formula: C₅₁H₆₄N₄O₁₃ Peso molecolare: 941.07 PubChem CID: 135431094

GRADE & PURITY ≥99%

Synonyms

Q-103229 | 2,7-(Epoxy[1,11,13]pentadecatrienoimino)-6H-benzofuro[4,5-a]phenoxazine-1,6,15(2H)-trione, 25-(acetyloxy)-5,12,21,23-tetrahydroxy-27-methoxy-2,4,16,20,22,24,26-heptamethyl-10-[4-(2-methylpropyl)-1-piperazinyl]-, (2S,16Z,18E,20S,21S,22R,23R,24R,

Storage

Store at 2-8°C,Desiccated

Shipped In

Wet ice

Panoramica

Rifalazil (KRM-1648; ABI-1648), a rifamycin derivative, inhibits the bacterial DNA-dependent RNA polymerase and kills bacterial cells by blocking off the β-subunit in RNA polymerase Rifalazil (KRM-1648; ABI-1648) is an antibiotic , exhibits high potency against mycobacteria, gram-positive bacteria, Helicobacter pylori , C. pneumoniae and C. trachomatis with MIC values from 0.00025 to 0.0025 μg/ml Rifalazil (KRM-1648; ABI-1648) has the potential for the treatment of Chlamydia infection, Clostridium difficile associated diarrhea (CDAD), and tuberculosis (TB)

In Vitro

Rifalazil exhibits antimicrobal activity against Gram-positive enteric bacteria, inhibits Clostridium difficile , Clostridium perfringens , Bacteroides fragilis with MIC 50 value of 0.0015, 0.0039, 0.0313 µg/ml, respectively. Rifalazil exhibits antimicrobal activity against Gram-negative enteric bacteria, inhibits Escherichia coli and Klebsiella pneumoniae with MIC 50 value of 16 and 16 µg/ml, respectively. Rifalazil exhibits antimicrobal activity against non-enteric Gram-positive bacteria, inhibits Methicillin-susceptible Staphylococcus aureus , Methicillin-resistant S. aureus , Methicillin- and quinolone-resistant S. aureus , Staphylococcus epidermidis , Streptococcus pyogenes , Streptococcus pneumoniae with MIC 50 value of 0.0078, 0.0078, 0.0078, 0.0078, 0.0002, 0.0001 µg/ml, respectively. Rifalazil exhibits antimicrobal activity against Helicobacter pylori , Chlamydia pneumoniae and Chlamydia trachomatis with MIC 50 value of 0.004, 0.000125 and 0.00025 µg/ml, respectively. MCE has not independently confirmed the accuracy of these methods. They are for reference only.

In Vivo

Rifalazil (oral gavage; 20, 25, and 150 mg/kg; 6-8 weeks) combines with isoniazid (INH) for 6 weeks or greater significantly reduced the number of mice per group in which M. tuberculosis is detected in both spleens and lungs compared to the reductions for the early and late controls. And the addition of Pyrazinamide (PZA) does not significantly improve RLZ-INH therapy at any time point. MCE has not independently confirmed the accuracy of these methods. They are for reference only. Animal Model: Female CD-1 mice infected with 5.2 × 10 7 viable mycobacteriaDosage: 20, 25, and 150 mg/kg; 6-8 weeks Administration: Oral gavage Result: Combined with isoniazid (INH) showed its potential for short-course treatment of Mycobacterium tuberculosis infection.

Form:Solid

IC50& Target:IC50: RNA polymerase

Specifications

Sinonimi

Q-103229 | 2,7-(Epoxy[1,11,13]pentadecatrienoimino)-6H-benzofuro[4,5-a]phenoxazine-1,6,15(2H)-trione, 25-(acetyloxy)-5,12,21,23-tetrahydroxy-27-methoxy-2,4,16,20,22,24,26-heptamethyl-10-[4-(2-methylpropyl)-1-piperazinyl]-, (2S,16Z,18E,20S,21S,22R,23R,24R,

Specifiche e purezza

≥99%

Meccanismi biochimici e fisiologici

Rifalazil (KRM-1648; ABI-1648), a rifamycin derivative, inhibits the bacterial DNA-dependent RNA polymerase and kills bacterial cells by blocking off the β-subunit inxa0RNA polymerase. Rifalazil (KRM-1648; ABI-1648) is an antibiotic , exhibits high p

Condizioni di conservazione di stoccaggio

Store at 2-8°C,Desiccated

Spedito in

Wet ice

Questo prodotto richiede spedizione a catena fredda. I servizi di terra e altri servizi economici non sono disponibili.

Tipo di azione

INHIBITOR

Meccanismo d'azione

DNA-directed RNA polymerase inhibitor

Purezza

≥99%

Proprietà del prodotto

ALogP

3.3

Nomi e identificatori

Sorrisi canonici

CC1C=CC=C(C(=O)NC2=C3C(=C4C(=C(C(=C5C4=C(C(O5)(OC=CC(C(C(C(C(C(C1O)C)O)C)OC(=O)C)C)OC)C)O)C)O)C2=O)N=C6C(=CC(=CC6=O)N7CCN(CC7)CC(C)C)O3)C

IUPAC Name

[(7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,6,15,17-tetrahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-30-[4-(2-methylpropyl)piperazin-1-yl]-23,32,37-trioxo-8,27,38-trioxa-24,34-diazahexacyclo[23.11.1.14,7.05,36.026,35.028,33]octatriaconta-1,3,5,9,19,21,25,28,30,33,35-undecaen-13-yl] acetate

InChIKey

IXSVOCGZBUJEPI-HTQYORAHSA-N

INCHI

1S/C51H64N4O13/c1-24(2)23-54-16-18-55(19-17-54)32-21-33(57)39-35(22-32)67-48-40(52-39)36-37-44(60)30(8)47-38(36)49(62)51(10,68-47)65-20-15-34(64-11)27(5)46(66-31(9)56)29(7)43(59)28(6)42(58)25(3)13-12-14-26(4)50(63)53-41(48)45(37)61/h12-15,20-22,24-25,27-29,34,42-43,46,58-60,62H,16-19,23H2,1-11H3,(H,53,63)/b13-12+,20-15+,26-14-/t25-,27+,28+,29+,34-,42-,43+,46+,51-/m0/s1

Isomeri SMILES

C[C@H]1/C=C/C=C(\C(=O)NC2=C3C(=C4C(=C(C(=C5C4=C([C@](O5)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]1O)C)O)C)OC(=O)C)C)OC)C)O)C)O)C2=O)N=C6C(=CC(=CC6=O)N7CCN(CC7)CC(C)C)O3)/C

CAS alternativo

129791-92-0

PubChem CID

135431094

Termini MeSH

3'-hydroxy-5'-(4-isobutylpiperazinyl)benzoxazinorifamycin;ABI 1648;ABI-1648;ABI1648;benzoxazinorifamycin;KRM 1648;KRM-1648;rifalazil

Peso molecolare

941.07

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Classe Benzoxazines
      • Subclass Phenoxazines

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Classe: Benzoxazines
• Subclass: Phenoxazines
• Intermediate Tree Nodes: Not available
• Direct Parent: Phenoxazines
• Alternative Parents: N-arylpiperazines Naphthols and derivatives Dialkylarylamines N-alkylpiperazines Ketals Vinylogous amides Vinylogous acids Heteroaromatic compounds Cyclic carboximidic acids Trialkylamines Secondary alcohols Carboxylic acid esters Amino acids and derivatives Propargyl-type 1,3-dipolar organic compounds Polyols Oxacyclic compounds Monocarboxylic acids and derivatives Dialkyl ethers Azacyclic compounds Organopnictogen compounds Organic oxides Hydrocarbon derivatives Carbonyl compounds
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Phenoxazine - N-arylpiperazine - 1-naphthol - Naphthalene - Dialkylarylamine - Tertiary aliphatic/aromatic amine - Ketal - N-alkylpiperazine - Benzenoid - Piperazine - 1,4-diazinane - Heteroaromatic compound - Vinylogous amide - Vinylogous acid - Cyclic carboximidic acid - Tertiary aliphatic amine - Tertiary amine - Secondary alcohol - Carboxylic acid ester - Amino acid or derivatives - Oxacycle - Azacycle - Organic 1,3-dipolar compound - Propargyl-type 1,3-dipolar organic compound - Polyol - Monocarboxylic acid or derivatives - Ether - Dialkyl ether - Carboxylic acid derivative - Acetal - Organic nitrogen compound - Organic oxygen compound - Organopnictogen compound - Organic oxide - Hydrocarbon derivative - Organooxygen compound - Organonitrogen compound - Carbonyl group - Amine - Alcohol - Aromatic heteropolycyclic compound
• Descrizione: This compound belongs to the class of organic compounds known as phenoxazines. These are polycyclic aromatic compounds containing a phenoxazine moiety, which is a linear tricyclic system that consists of a two benzene rings joined by a 1,4-oxazine ring.
• 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

Obiettivi associati (umani)

NR1I2 Tchem Pregnane X receptor (6667 Activities)

Discover Target: NR1I2

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Homo sapiens (32628 Activities)

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Obiettivi associati (non umani)

Chlamydia pneumoniae (241 Activities)

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Helicobacter pylori (3113 Activities)

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Staphylococcus aureus (210822 Activities)

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Clostridioides difficile (2968 Activities)

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Mycobacterium tuberculosis (203094 Activities)

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Mycobacterium leprae (477 Activities)

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Meccanismi d'azione

Proprietà chimiche e fisiche

• Solubilità: DMSO : 8.33 mg/mL (8.85 mM; Need ultrasonic)
• Peso molecolare: 941.100 g/mol
• XLogP3: 3.300
• Hydrogen Bond Donor Count: 5
• Hydrogen Bond Acceptor Count: 16
• Rotatable Bond Count: 6
• Exact Mass: 940.447 Da
• Monoisotopic Mass: 940.447 Da
• Topological Polar Surface Area: 226.000 Ų
• Heavy Atom Count: 68
• Formal Charge: 0
• Complexity: 2510.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 9
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 3
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 3
• Covalently-Bonded Unit Count: 1

Application Protocols

No tested application protocols, dilutions, or assay validations are provided for this item. For research use, typical small-molecule handling practices apply (general guidance; not product specifications):

• Stock solutions: Prepare in anhydrous DMSO at an application-appropriate concentration (e.g., 10–50 mM), protect from light, and store aliquots to avoid repeat freeze–thaw.
• Working dilutions: Add DMSO stocks to assay media as the final step, keeping final DMSO ≤1–2% v/v to limit precipitation and biological interference (optimize per assay).
• Analytical QC: Verify concentration by UV–Vis or quantitative NMR where feasible; monitor stability by LC–MS before critical experiments.

For any biological assay or screening application, develop and validate an internal protocol specific to your system. Refer to the SDS for handling and the CoA for lot-specific identity/purity before use.

Biological Roles

The following describes literature knowledge about the rifamycin class to contextualize rifalazil’s use as a research tool compound; these are not medical/clinical claims.

• Mechanistic class (literature): Rifamycins target the bacterial DNA-dependent RNA polymerase (RNAP), binding within the β-subunit tunnel and sterically blocking nascent RNA chain elongation. Rifalazil, a benzoxazinorifamycin, retains this core mechanism while exhibiting increased lipophilicity compared to rifampin.
• Structure–property relationship: The benzoxazine fusion can enhance membrane association and modulate protein binding kinetics. Multiple hydroxyls and the quinone/hydroquinone pair contribute to redox behavior and visible coloration.
• Research applications:
  • Probe for transcription studies in bacteria, enabling interrogation of RNAP function, resistance mutations, and fitness costs in model systems.
  • Tool in structure–activity relationship (SAR) mapping for ansamycin derivatives, informing modifications on the ansa chain and phenolic positions.
  • Benchmark in efflux and permeability assays due to its higher hydrophobicity within the rifamycin class.
• Metabolic considerations (general, literature): Rifamycins can undergo deacetylation, oxidation/reduction of the quinone, and conjugation reactions in biological matrices; these pathways inform bioanalytical method design (e.g., MRM transitions for intact compound vs metabolites).

Note: Specific potency values, spectra, and ADME parameters for this item are not provided here. Consult primary literature and perform in-house characterization for your experimental system.

Buffer Applications

This compound is not a buffering reagent and is not typically used to prepare pH buffer systems. Due to its poor aqueous solubility (literature, rifamycin class), aqueous buffers generally require co-solvent strategies (e.g., low-percent DMSO) if rifalazil must be delivered into an aqueous environment for research assays. For solution preparation guidance, see Solvent Selection and Storage & Reconstitution.

Green Alternatives

While rifalazil itself is a fixed scaffold, greener choices can be made for its handling and analysis by selecting more sustainable solvents and processes. The following points are general, literature-based considerations and not item-specific specifications.

• Preferred greener solvents for stock/dilution (where feasible):

  • Replace DMF with DMSO when solubility allows; DMSO has a better environmental profile and lower worker exposure concerns.
  • For chromatography, consider ethanol–water or acetonitrile–water; avoid chlorinated solvents.
  • For workup/extractions, ethyl acetate and 2-MeTHF can substitute for dichloromethane, balancing performance and environmental impact.

• Stability tradeoffs:

  • Rifalazil’s lipophilicity may demand higher organic content; greener options may require slightly elevated temperatures or sonication to dissolve, which should be balanced against degradation risk.
  • Avoid prolonged heating; use gentle warming and protect from light to reduce redox degradation of the rifamycin chromophore.

• Comparison snapshot (general):

  • DMF vs DMSO: DMSO is greener and often equally effective for dissolution; DMF offers lower viscosity but has more stringent hazard classification.
  • DCM vs EtOAc/2-MeTHF: EtOAc/2-MeTHF reduce halogenated waste; verify rifalazil solubility empirically.

• Process suggestions:

  • Miniaturize screening assays to reduce solvent consumption.
  • Use amber vials to extend solution life and reduce repeat preparations.

Always validate solvent changes for solubility and assay compatibility.

Pharmaceutical Uses

No excipient or formulation-grade information is provided for this catalog item. This product is supplied strictly for research use only.

General, literature-based context (not a claim for this product):

• Rifalazil is a rifamycin-class small molecule sometimes studied as a reference compound in preformulation research due to its high lipophilicity and chromophore, which influence solid-state and dissolution behavior.
• Typical formulation investigations for rifamycin analogs include: solubilization strategies (co-solvents, cyclodextrins), solid dispersions, and stabilization against redox degradation under light/oxygen.

For this specific listing:

• Pharmacopeial status: Not specified for this item; no USP/EP/JP monograph is implied.
• GMP/clinical suitability: Not specified for this item; not for human or veterinary use.
• If applying in preformulation studies, independently establish purity, polymorph, and stability using your own methods or the lot-specific CoA.

Physical Properties

Item-specific specifications are not provided for this catalog entry. Do not treat the following as product specifications; they are general literature characteristics for rifalazil to aid method development.

• Appearance: 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.
• Melting point: Not specified for this item; consult SDS/CoA.
• Boiling point: Not applicable for this macrocyclic solid; decomposition expected (literature, general for rifamycins).
• Density: Not specified for this item.
• pKa: Rifamycin phenols typically pKa ~7–8 and secondary alcohols significantly higher; exact values for rifalazil not established here (literature, class-level guidance).
• LogP: Rifalazil is reported to be highly lipophilic with an elevated logP relative to rifampin (literature, qualitative assessment for benzoxazinorifamycins); numeric value not provided here.
• Solubility (literature, qualitative):
  • Water: Very low solubility typical for rifalazil.
  • Polar aprotic: Soluble in DMSO and DMF; often used for stock solutions.
  • Alcohols: Limited to moderate solubility in methanol/ethanol depending on water content.
  • Nonpolar/EtOAc: Variable; increased solubility versus rifampin noted anecdotally for ethyl acetate and other medium-polarity organics.
• UV–Vis: Rifamycin chromophores show strong visible absorption (orange-red hues) due to naphthoquinone; precise maxima for rifalazil are not provided here.

Always verify working values empirically for your lot.

Quality and Grades

• Grade/purity: Not specified for this item; refer to CoA/Spec Sheet for assay, related substances, and impurity profiles.
• What grade typically implies (general guidance): For research-use small molecules, assay is commonly reported by HPLC area% or qNMR. Trace solvent content, water (KF), and residual inorganic content may be provided on the lot-specific CoA.
• Stabilizers: Not specified for this item. Many rifamycin derivatives are supplied neat without stabilizers; if any stabilizers or counter-ions are used, they will be listed on the CoA.
• Color and polymorphism: Not specified for this item. Rifamycin analogs often display orange-red coloration due to the quinone chromophore; polymorph information, if relevant, will be disclosed on the lot CoA.
• Suggested verification upon receipt (best practices for this scaffold):
  • Confirm identity by HRMS and 1H/13C NMR in anhydrous DMSO-d6 or CDCl3, protecting from light.
  • Assess purity by HPLC/UPLC with diode-array detection (DAD) to monitor for quinone/hydroquinone interconversion.
  • If using in screening libraries, consider LC-MS and stability-indicating methods after thaw cycles.
• Regulatory/compliance: Research use only (as provided). No pharmacopeial monograph is implied for this catalog item.

Reaction and Applications

This product is listed within a small-molecule/compound library context. As a complex natural-product derivative, rifalazil is primarily used as:

• A reference standard and tool compound for biochemical and microbiological research on transcriptional machinery (literature: rifamycins bind the β-subunit of bacterial RNA polymerase). No medical/clinical uses are claimed for this catalog item.
• A scaffold for SAR exploration: The benzoxazinorifamycin framework tolerates modifications at selective positions on the ansa chain and around phenolic/quinone sites.

Synthetic and analytical applications (literature/general):

• Derivatization for probe development: Installation of photoaffinity tags or fluorophores via carbonate/carbamate linkages on secondary alcohols, or etherification of phenolic OH.
• Prodrug exploration: Esterification of alcohols to modulate lipophilicity and stability.
• Stability studies: Redox interconversion between hydroquinone/quinone forms can be monitored by UV–Vis and LC–MS; light and oxygen exclusion improves reproducibility.
• Method development: Reversed-phase LC with gradient elution (high organic content) and MS detection in APCI or ESI (positive) modes are commonly used; multiple adducts may appear due to polyoxygenation.

Practical tips:

• Maintain anhydrous, oxygen- and light-limited conditions during solution prep.
• Use glassware protected from light; minimize basic residues on glass which may catalyze degradation.
• If performing coupling reactions on this scaffold, protect sensitive phenols and control temperature to avoid macrocycle opening.

Reaction Conditions

No item-specific reactivity data are provided. The following general, literature-based conditions are commonly applied to rifamycin/ansamycin scaffolds and may guide method development for rifalazil derivatives:

• Carbonate/carbamate formation on alcohols/phenols:

  • Reagents: p-nitrophenyl chloroformate or carbonyldiimidazole (CDI), followed by amine/alcohol coupling.
  • Solvents: Anhydrous DCM, THF, or acetonitrile; avoid prolonged basic conditions.
  • Temperature: 0–25°C; protect from light; short reaction times (0.5–4 h) preferred.

• Etherification of phenols:

  • Mitsunobu (DIAD/PPh3) or alkyl halide with weak base (e.g., K2CO3) under phase-transfer or DMF; monitor closely to prevent elimination/over-alkylation.

• Ester hydrolysis/exchange (where applicable):

  • Mild basic methanolysis or enzymatic methods; avoid strong base and elevated temperatures.

• Redox adjustments of the quinone/hydroquinone:

  • Reduction: Sodium dithionite or ascorbate under anaerobic conditions.
  • Oxidation: Silver oxide, ferricyanide, or air oxidation under controlled light/oxygen.

• Purification:

  • Flash chromatography on silica/alumina with minimal exposure to light and air; include antioxidant (e.g., 0.1% BHT) where compatible.
  • Preparative HPLC with high-organic mobile phases and amber glassware is often superior for stability.

Expected yields vary widely (20–80%) depending on site selectivity and protection strategy. Always verify conditions on micro-scale before scale-up.

Safety and Handling

• GHS classification, signal word, pictograms, and H-statements: Not specified for this item; consult the product SDS for authoritative hazard information.
• General hazards (literature/class-level for rifamycins; not item-specific):
  • May cause irritation to skin, eyes, and respiratory tract upon exposure.
  • Colored rifamycin chromophores can strongly stain skin, textiles, and lab surfaces.
  • Macrocyclic quinone/hydroquinone motifs can undergo redox transformations; avoid strong oxidizers and prolonged light exposure.
• Incompatibilities: Strong oxidizers, strong acids/bases (may promote degradation), and reactive acylation/alkylation reagents that could modify phenolic/alcoholic sites.
• Handling recommendations (good laboratory practice):
  • Work in a chemical fume hood; avoid inhalation of dust or aerosols.
  • Wear appropriate PPE: lab coat, safety glasses, and chemically resistant gloves (e.g., nitrile). Consider double-gloving for extended handling due to staining.
  • Minimize light exposure; use amber glassware or foil wrap where practical.
  • Prepare solutions with anhydrous solvents to limit hydrolysis/oxidation pathways.
• First aid (overview; defer to SDS):
  • Skin/eye contact: Rinse with water for at least 15 minutes; 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 solids/solutions as hazardous organic waste; follow institutional and regulatory requirements.

Solvent Selection

Rifalazil is a highly lipophilic, polyoxygenated macrocycle. Effective solvent choice is essential for stock preparation and analytical work.

• Polarity and miscibility (literature, class-level):

  • Polar aprotic: DMSO and DMF typically provide the best solubility and solution stability; suitable for high-concentration stocks (e.g., 10–50 mM) used in screening workflows.
  • Alcohols: Methanol and ethanol can dissolve rifalazil to a lesser extent; water content reduces solubility and may accelerate degradation.
  • Moderate polarity organics: Acetone and ethyl acetate show variable solubility; test empirically.
  • Aqueous buffers: Poor solubility; use co-solvent strategies (DMSO or cyclodextrins) if aqueous delivery is needed.

• Practical recommendations:

  • Prepare a primary stock in anhydrous DMSO under subdued light; dilute into assay media last to minimize precipitation.
  • For chromatographic analyses, acetonitrile/water or methanol/water with acidic modifiers (e.g., 0.1% formic acid) are typical; protect autosampler vials from light.
  • Avoid prolonged exposure to strong bases/acids in solution.

• Comparison (general):

  • Rifampin (less lipophilic) is more ethanol/water compatible; rifalazil requires stronger organic co-solvent content, reflecting its benzoxazinyl modification.

Always verify solubility and stability for your specific lot; item-specific solvent specifications are not provided here.

Storage and Reconstitution

• Storage conditions (from Product Data):

  • Store at 2–8°C, desiccated.
  • Shipped on wet ice.

• Light/atmosphere: Given the rifamycin chromophore, protect from light; keep tightly closed to limit oxygen and moisture exposure (general best practice for this class).

• Reconstitution (general, literature-based guidance; not item-specific specifications):

  • Dissolve the solid in anhydrous DMSO to make a concentrated primary stock (e.g., 10–50 mM). Gentle warming (≤30°C) and vortex/sonication can assist dissolution; avoid prolonged heating.
  • Filter sterilization (0.22 µm PTFE) may be used for cell-based assay stocks if required by your workflow.
  • For aqueous applications, dilute the DMSO stock into buffer immediately before use to minimize precipitation; consider co-solvents or carriers (e.g., cyclodextrins) if higher aqueous concentrations are needed.

• Aliquoting and freeze–thaw:

  • Prepare single-use aliquots in amber vials or foil-wrapped microtubes.
  • Store aliquots at 2–8°C for short term per item guidance; for extended storage, many users keep DMSO stocks at −20°C protected from light (literature practice). Avoid repeated freeze–thaw cycles.

• Stability checks: Periodically assess by HPLC/LC–MS for degradation (quinone/hydroquinone interconversion) and by UV–Vis for spectral changes.

Always defer to the lot-specific CoA/SDS for definitive instructions.

Structure and Identity

Rifalazil is a rifamycin-class ansamycin macrocycle used as a research small molecule in compound libraries.

• Item-specific identifiers (from Product Data):

  • CAS: 129791-92-0
  • CID: 135431094
  • InChIKey: 153227 (as provided)
  • SMILES: Not specified for this item; refer to CoA/Spec Sheet.

• Literature structural features (for context; not item-specific specifications):

  • Chemotype: Rifamycin/ansamycin derivative featuring a naphthoquinone/hydroquinone core bridged by a long aliphatic ansa chain.
  • Fused heterocycle: Rifalazil bears a benzoxazinyl moiety fused to the rifamycin core (benzoxazinorifamycin scaffold), increasing lipophilicity.
  • Functional groups: Multiple secondary and tertiary alcohols, phenolic hydroxyl(s), enone/quinone motifs, ether linkages, and an aliphatic macrocyclic chain. Several stereocenters define a rigid three-dimensional macrocycle.
  • 2D description (words): A polyoxygenated, extended macrocycle arcs over a naphthalenoid core; one edge of the aromatic core is fused to a benzoxazine ring, while the opposite edge is spanned by the ansa chain that terminates near an acylated/oxy-functionalized region. Numerous hydroxyl-bearing stereocenters populate the ansa segment.

• Molecular formula and molecular weight: Not specified for this item; see literature values below or consult CoA/Spec Sheet.

Synthetic Utility

As a complex, highly functionalized ansamycin, rifalazil serves primarily as a reference scaffold rather than a routine building block. Nevertheless, literature demonstrates several productive transformations for probe and SAR generation (general guidance; not item-specific specifications):

• Phenolic/allylic functionalization: Etherification or carbonate/carbamate formation at phenolic and secondary alcohol positions to install handles (e.g., click tags, fluorophores, photoaffinity groups). Mild conditions are favored to preserve the macrocycle.
• Redox manipulations: Controlled oxidation/reduction of the hydroquinone/quinone system to access defined redox states for mechanistic studies or crystallography with RNAP.
• Acyl substitutions: Selective acyl exchange or hydrolysis on labile ester sites to generate analogs or prodrugs with tuned lipophilicity.
• Conjugation chemistry: NHS-carbonate/urethane strategies to append PEG segments or affinity labels, improving solubility or enabling target engagement assays.
• Analytical derivatization: Formation of UV-strong or MS-friendly derivatives to improve quantitation in complex matrices.

Practical considerations:

• Protect from base; many transformations proceed best under neutral to mildly acidic conditions with dehydrating agents and non-nucleophilic bases (if any).
• Use anhydrous, oxygen-limited, and light-protected setups; silica gel chromatography should be brief and shielded from light to minimize degradation.
• Validate structural integrity by 2D NMR and HRMS after each step due to the density of stereocenters and potential for subtle rearrangements.

Target Specificity

Item-specific biological target data (e.g., antigen/epitope, species reactivity, clone/isotype) are not provided for this product and are not applicable to this small-molecule compound. For literature context, rifamycin-class compounds bind the β-subunit of bacterial RNA polymerase; however, no target qualification is claimed for this specific catalog lot.