Rifapentine - Moligand™, 10mM in DMSO , CAS No.61379-65-5

CAS: 61379-65-5 Cat. No.: R409193 Formula: C₄₇H₆₄N₄O₁₂ Peso molecolare: 877.03 Numero EC: 262-743-9 PubChem CID: 135403821

GRADE & PURITY Moligand™, 10mM in DMSO

Synonyms

MDL473 | 3-​[[(4-​cyclopentyl-​1-​piperazinyl)​imino]​methyl]​-rifamycin

Storage

Store at -80°C

Shipped In

Dry ice packs + Cold packs

Panoramica

Information

Rifapentine Rifapentine (MDL473) is an antibiotic, which inhibits DNA-dependent RNA polymerase activity, used to treat tuberculosis.
In vitro

Rifapentine inhibits the function of DNA-dependent RNA polymerase in strains of M. tuberculosis, while inducing no effect on mammalian cells. Both Rifapentine and its active metabolite, 25-desacetylrifapentine, localize within monocyte-derived macrophages, thus allowing for intracellular inhibition of M. tuberculosis at a greater kill rate as compared with that of the parent or metabolite alone. Rifapentine is deacetylated in the liver and induces cytochrome P450 much less than rifampin. Rifapentine has shown higher bacteriostatic and bactericidal activities (MICs and MBCs) than RMP, especially against intracellular bacteria growing in human monocyte-derived macrophages.

In vivo

Rifapentine inhibits bacterial RNA synthesis by binding to the β-subunit of DNA-dependent RNA polymerase in susceptible species. Rifapentine is generally more active than rifampicin against sensitive strains of M. tuberculosis. Rifapentine significantly increases the rate of antipyrine and pentobarbital metabolism in vivo. Rifapentine also increases liver weight, the content of liver microsomal protein and cytochrome P-450, the activity of NADPH-cytochrome C reductase and NADPH oxidase. Rifapentine combined with isoniazid (INH) and pyrazinamide (PZA) administered daily results in an apparent clearance of M.tuberculosis organisms in the lungs and spleens of infected mice after 10 weeks of treatment.
Cell Data

cell lines：HeLa, PC-3, DU-145, MIAPaCa-2, U937, MCF-7, A549, and WiDr cells

Concentrations：

Incubation Time：

Powder Purity:

Specifications

Sinonimi

MDL473 | 3-​[[(4-​cyclopentyl-​1-​piperazinyl)​imino]​methyl]​-rifamycin

Specifiche e purezza

Moligand™, 10mM in DMSO

Meccanismi biochimici e fisiologici

Rifapentine (MDL473) is an antibiotic, which inhibits DNA-dependent RNA polymerase activity, used to treat tuberculosis.

Condizioni di conservazione di stoccaggio

Store at -80°C

Spedito in

Dry ice packs + Cold packs

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

Grado

Moligand™

Proprietà del prodotto

ALogP

6.7

Nomi e identificatori

Isomeri SMILES

C[C@H]1/C=C/C=C(\C(=O)NC2=C(C(=C3C(=C2O)C(=C(C4=C3C(=O)[C@](O4)(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)C)O)O)/C=N/N5CCN(CC5)C6CCCC6)/C

PubChem CID

135403821

Peso molecolare

877.03

Proprietà chimiche e fisiche

• Indice di rifrazione: 1.63
• Punto di fusione (°C): 179-180ºC

Application Protocols

General guidance for research use in screening and analytical workflows (non-clinical):

Preparation of stock solutions:

• Equilibrate vial to room temperature in the dark before opening to avoid condensation.
• Prepare a concentrated stock in anhydrous DMSO (e.g., 10–50 mM). Sonication or brief warming (≤30–35 °C) can aid dissolution. Protect from light (amber vials).
• Verify concentration by UV–Vis or LC–UV if needed; rifamycin chromophores exhibit strong visible absorbance.

Assay dilution:

• Add DMSO stock as the final component to pre-warmed buffer to minimize precipitation.
• Maintain final DMSO ≤1–2% v/v for most biochemical assays; include 0.01–0.05% nonionic surfactant to reduce adsorption.
• Use low-binding tips and plates; pre-rinse tips with solution to minimize loss.

Analytical method development:

• LC: C18 or phenyl-hexyl stationary phases; start with water/ACN + 0.1% formic acid; monitor at visible and UV wavelengths.
• MS: Positive ESI typically suitable; optimize source conditions to prevent in-source fragmentation of the rifamycin core.

Stability handling:

• Minimize light exposure (foil wrap, amber labware).
• Avoid prolonged basic conditions; prepare fresh working solutions daily when possible.

No item-specific tested applications or validated dilutions are provided for this product.

Biological Roles

The following describes biological function/mechanism for rifapentine as a chemical probe; it is provided for research context only and does not imply any clinical use.

• Class: Rifamycin (ansamycin) antibiotic derivative (literature classification).
• Primary biochemical target (literature): Bacterial DNA-dependent RNA polymerase (RNAP), binding to the β-subunit (rpoB) at the rifamycin-binding pocket.
• Mechanistic note (literature): Stabilizes an RNAP conformation that blocks elongation/early transcription by preventing RNA chain extension; does not directly intercalate DNA.
• Spectrum considerations (literature): Active primarily against mycobacteria and some Gram-positives in biochemical assays; potency varies with rpoB mutations.
• Resistance mechanisms (literature): Point mutations in rpoB alter the rifamycin-binding pocket, diminishing affinity.
• Physicochemical/biological handling:
  • High hydrophobicity favors membrane association and nonspecific binding to plastics; include carrier proteins or surfactants in biochemical assay buffers as appropriate.
  • Strong visible absorbance provides a built-in chromophore for tracking compound in spectroscopic assays.

Notes:

• Use in cells or organisms must be confined to research settings consistent with institutional approvals. Do not infer therapeutic performance from in vitro observations.

Buffer Applications

Rifapentine is not a buffering agent and is not used to prepare pH-stabilizing solutions. However, when formulating assay buffers that include rifapentine as a test article, consider the following practical guidance (general/literature):

• Choose biologically relevant buffers (e.g., HEPES, PBS, Tris) appropriate for the target assay; maintain low final DMSO (≤1–2% v/v) to preserve biological activity.
• Include low levels of nonionic surfactant (e.g., 0.01–0.05% Tween-80 or Triton X-100) to mitigate adsorption and precipitation of this hydrophobic compound.
• Pre-wet plasticware or use low-binding tubes/plates; glass vials with silanized surfaces can reduce loss.
• For optical assays, account for the compound’s visible absorbance; use reference wells to correct background.

No standard buffer recipes are specific to rifapentine; tailor the system to the biochemical target and detection method.

Green Alternatives

This product is an active small-molecule tool compound rather than a process solvent or commodity reagent; therefore, “green alternative” selection focuses on solvent/system choices during its use rather than replacing the compound itself.

Greener handling considerations (general):

• Prefer DMSO over DMF for stock solutions where possible due to DMF’s regulatory and toxicity profile.
• Minimize organic solvent volumes by preparing concentrated stocks and performing serial dilutions directly in assay buffers.
• Use aqueous-compatible dispersants (e.g., low levels of nonionic surfactants) to reduce the need for higher co-solvent percentages.
• Select low-waste analytical methods: short LC gradients, smaller-ID columns, and MS with minimal mobile-phase modifiers (e.g., formic acid rather than nonvolatile salts) to reduce solvent consumption and waste.

Illustrative comparison (general):

• DMF vs DMSO for stock preparation:
  • Solubility: Comparable; DMSO often superior for hydrophobic drugs.
  • Worker exposure: DMSO preferred; DMF is a reproductive hazard.
  • Waste: Neutral pH aqueous-compatible DMSO dilutions are simpler to treat.

End-of-life:

• Collect DMSO/organic mixtures for solvent recycling if available.
• Deactivate assay plates with minimal volumes of compatible quench solvents, and segregate halogen-free organic waste.

Pharmaceutical Uses

No clinical or therapeutic claims are made for this product. In a research and quality-control context, rifapentine may be used as follows (general/literature):

• Reference standard or system suitability material in analytical method development (HPLC/UPLC–UV/MS) for rifamycin-class compounds.
• Process/stability studies in preformulation research to understand degradation pathways (e.g., light- or base-catalyzed changes of the ansa/quinone system).
• Spiking studies to validate extraction and quantitation methods from complex matrices in nonclinical settings.

Regulatory/compendial status, excipient roles, impurity thresholds, and release specifications: Not specified for this item; refer to CoA/Spec Sheet and relevant pharmacopeial monographs if applicable to your work.

This catalog item is supplied strictly for research use only.

Physical Properties

Item-specific specification values are not provided for this catalog entry; consult the product CoA/Spec Sheet for definitive specs. The following are literature/general values for rifapentine (for planning only):

• Appearance (literature): Red-orange crystalline solid/powder.
• Molecular weight (literature): ~877.05 g/mol (C47H64N4O12).
• Solubility (literature, qualitative):
  • Practically insoluble in water; limited solubility in alcohols.
  • Soluble in polar aprotic organic solvents (e.g., DMSO, DMF); stocks typically prepared in DMSO for screening.
• logP (literature, approximate): High hydrophobicity relative to rifampin; reported logP in the ~3.5–4.5 range depending on method (consult primary sources for exact value).
• pKa (literature, qualitative): Multiple ionizable phenolic and imide nitrogens; overall amphiprotic with weakly acidic phenols; exact pKa values vary by study.
• UV–Vis (literature, qualitative): Strong absorption in visible region (orange-red chromophore) due to extended conjugation; suitable for UV–Vis/LC–UV detection.
• Stability (literature, qualitative): Light-sensitive; can degrade upon prolonged exposure to light, heat, or strongly acidic/basic conditions.

Not provided for this item (refer to CoA/Spec Sheet): melting point, boiling point, density, refractive index, precise solubility values, water or residual solvent content, peroxide/metal limits, UV cutoff, and chromatographic purity metrics.

Quality and Grades

• Grade/Purity: Moligand™ (item-specific). Moligand™ indicates inclusion in a curated small-molecule/compound library suitable for screening, SAR exploration, and assay development.
• What Moligand™ typically implies (general description):
  • Identity confirmation by modern spectroscopic/analytical methods (e.g., LC–MS, NMR, or HRMS) to support screening use.
  • Packaged and stored to preserve integrity for high-throughput or hit-validation workflows.
  • Documentation available upon request (CoA/Spec Sheet) for lot-specific identity and purity.
• Item-specific purity, stabilizers, counterions/salt form: Not specified for this item; refer to CoA/Spec Sheet.
• UV/fluorescence background, residual solvents, water content, metals, and other analytical specifications: Not specified for this item; refer to CoA/Spec Sheet.

Practical notes for users:

• For screening campaigns, prepare fresh DMSO stocks or verify integrity by quick LC–MS/UPLC prior to use, as rifamycin chromophores can undergo light- or base-promoted changes.
• Follow the specified storage at −80°C to minimize degradation and maintain library performance.

Reaction and Applications

As a complex rifamycin derivative, rifapentine is not typically used as a synthetic reagent or solvent. Its laboratory applications are predominantly in chemical biology and analytical contexts.

Applicable research uses (non-clinical, literature/general):

• Reference material for analytical method development (LC–UV/LC–MS), stability studies, and impurity profiling of rifamycin-class compounds.
• Positive control/benchmark in biochemical assays interrogating bacterial DNA-dependent RNA polymerase (RNAP) inhibition (enzyme or binding assays). Avoid clinical/therapeutic extrapolation.
• Tool compound in target engagement studies (e.g., thermal shift, SPR/BLI with RNAP β-subunit constructs), acknowledging its hydrophobicity and visible absorbance.

Practical tips:

• Protect from light during assays to minimize chromophore degradation; use amber vials/plates.
• Prepare fresh DMSO stocks or verify concentration by UV–Vis/LC–MS; rifamycin chromophores provide strong, characteristic absorbance enabling quick checks.
• When titrating into aqueous systems, ensure gentle mixing and consider inclusion of nonionic surfactant to reduce precipitation and plastic adsorption.

Not typically applicable:

• Named synthetic reactions, catalyst screening, or general organic synthesis roles; see Biological Roles and Application Protocols for more relevant guidance.

Reaction Conditions

This section is not typically applicable because rifapentine is not used as a reagent in named organic reactions. For researchers performing semisynthetic derivatizations (literature guidance only):

• Solvents: Anhydrous DMSO, DMF, or dichloromethane depending on transformation; maintain low light exposure.
• Temperatures: Ambient to 40 °C for acylation/alkylation; avoid elevated temperatures that can degrade the ansa macrocycle.
• Bases: Mild organic bases (e.g., DIPEA) for carbamate/carbonate formation; avoid strong bases that can cause quinone addition or elimination.
• Coupling: CDI, DSC, or NHS-activated esters for phenolic derivatization; EDC/NHS for carboxylate-containing linkers if present.
• Times/Yields: Highly substrate- and site-selective; small-scale method scouting with LC–MS monitoring is recommended. No item-specific yields are provided.

For biochemical/assay use, see Application Protocols for solution preparation and handling rather than synthetic conditions.

Safety and Handling

Hazard information specific to this item is not provided here. Always consult the SDS for authoritative safety data.

• GHS classification, signal word, pictograms, H-statements: Not specified for this item; refer to SDS.
• General hazards (literature/analogous compounds): Organic powder; may cause eye/skin irritation; dust may be harmful if inhaled. Rifamycin-class compounds can cause persistent staining of skin/materials.
• Photosensitivity: Rifamycin derivatives are light-sensitive; minimize light exposure during handling to limit degradation.
• PPE: Laboratory coat, safety goggles, and appropriate chemically resistant gloves. Use in a fume hood to avoid dust/aerosol exposure.
• Incompatibilities (general): Strong oxidizers; strong acids/bases can promote decomposition; avoid prolonged exposure to heat and light.
• First-aid overview (general):
  • Inhalation: Move to fresh air; seek medical attention if symptoms persist.
  • Skin contact: Wash with soap and water; remove contaminated clothing.
  • Eye contact: Rinse cautiously with water for several minutes; remove contact lenses; seek medical advice if irritation persists.
  • Ingestion: Rinse mouth; do not induce vomiting; seek medical attention.
• Waste disposal: Treat as hazardous organic waste; dispose according to institutional and local regulations.

This product is for research use only; not for human or veterinary use.

Solvent Selection

Rifapentine is hydrophobic and amphiprotic with very low aqueous solubility. For laboratory use, solvent choice is crucial to obtain reliable concentrations.

• Primary stock solvent (common practice/literature):
  • DMSO: Preferred for preparing concentrated stocks (e.g., 10–50 mM) owing to good solubility and assay compatibility at low final DMSO percentages.
• Alternative organic solvents (literature/practice):
  • DMF: Good solvating power; consider cytotoxicity in biological assays.
  • Methanol/ethanol: Limited solubility; risk of precipitation upon aqueous dilution.
  • Acetone/ACN: Variable solubility; test at small scale; may precipitate upon dilution.
• Aqueous media:
  • Poor solubility in water and most buffers; if needed, co-solvent strategies (DMSO ≤1–2% v/v) and surfactants (e.g., 0.01–0.05% Tween-80) can help maintain dispersion in biochemical assays (literature guidance).

Selection guidance:

• Use DMSO stocks and dilute into assay buffer last to minimize precipitation.
• Filter sterilize only if required; adsorption to membranes can occur—use low-binding filters (PTFE/RC recommended; avoid nylon for hydrophobic analytes).

Quick comparison (general):

• DMSO: Highest solubility, broad assay compatibility → first choice.
• DMF: Similar solubility, less preferred in cells.
• Alcohols: Convenient but limited solubility and higher precipitation risk on dilution.

Storage and Reconstitution

• Storage conditions (item-specific): Store at −80 °C.
• Shipment (item-specific): Shipped on dry ice packs + cold packs.
• Appearance (item-specific): Not specified for this item; refer to CoA/Spec Sheet.

Reconstitution (general guidance):

• Allow the sealed container to equilibrate to room temperature before opening to prevent moisture condensation.
• Dissolve the material in anhydrous DMSO to prepare a concentrated stock (e.g., 10–50 mM) suitable for aliquoting.
• Mix gently; brief sonication may assist dissolution. Protect from light throughout.

Aliquoting and storage of solutions (general best practices):

• Dispense single-use aliquots into amber, low-binding microtubes.
• Store DMSO stocks at −20 to −80 °C; avoid repeated freeze–thaw cycles. For long-term stability, prefer −80 °C aligned with the solid storage condition.
• Thaw on ice or at room temperature protected from light; use promptly. Discard aliquots showing precipitation, color change beyond the typical orange-red hue, or anomalous LC–MS results.

Constraints and notes:

• Stabilizers, salt form, and hydrates: Not specified for this item; refer to CoA/Spec Sheet.
• For research use only. Always consult the SDS for safe handling during storage and reconstitution.

Structure and Identity

Brief overview: Rifapentine is a rifamycin-class ansamycin macrocycle bearing a cyclopentyl-substituted piperazine imide side chain. It is supplied here as a Moligand™ small-molecule library member for research screening.

• SKU: R409193
• Product name: Rifapentine
• CAS: 61379-65-5
• Category: Small-molecule and compound library (Moligand™)
• InChIKey (item-specific): Not specified for this item; refer to CoA/Spec Sheet.
• SMILES (item-specific): Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula (literature): C47H64N4O12
• Molecular weight (literature): ~877.05 g/mol

Structural features (general/literature description):

• Macrocyclic “ansamycin” scaffold with a naphthoquinone core bridged by an aliphatic ansa chain.
• Multiple hydroxyl and methoxy substituents; conjugated diketone/quinone system.
• Imide-linked piperazine bearing a cyclopentyl group (distinguishing rifapentine from rifampin).
• Numerous stereocenters in the ansa chain; supplied stereochemistry corresponds to natural rifamycin derivatives (literature), but item-specific stereochemical confirmation: Not specified for this item; refer to CoA/Spec Sheet.

2D structure (described in words, literature):

• A fused aromatic ring (naphthalene-like) containing a para-quinone motif is connected via an aliphatic, oxygen-bearing bridge that wraps around to form an ansa macrocycle; pendant imide-piperazine substituent extends from the core, and multiple phenolic/methoxy groups decorate the aromatic ring.

Synthetic Utility

Rifapentine is a highly functionalized natural-product derivative and is not commonly used as a building block in routine synthesis. Nonetheless, for researchers engaged in semisynthetic modification of rifamycins (literature context):

• Functional handles (literature): Phenolic hydroxyls (O-acylation/O-alkylation), imide/piperazine nitrogen (N-acylation/alkylation), and quinone/hydroquinone redox interconversions.
• Typical modifications: Prodrug formation via carbonate/carbamate at phenols; linker installation for conjugates (e.g., biotinylation/fluorophore tagging) at accessible hydroxyls or amines using mild coupling chemistries.
• Chemoselectivity: Conjugated quinone is sensitive to strong nucleophiles/bases; employ protecting groups or mild conditions (e.g., carbonyldiimidazole for carbonate formation, NHS-esters for tagging).
• Analytical control: Due to chromophore complexity, reaction monitoring by LC–UV at visible wavelengths and LC–MS is effective; avoid prolonged exposure to light/heat.

If your goal is general organic synthesis, this compound is not an appropriate reagent. Consider standard building blocks instead; see Reaction & Applications for usage as a biochemical tool.

Target Specificity

This section is intended for biologics (antibodies, proteins) and does not directly apply to a small-molecule compound.

• Antigen/epitope, clone, isotype, species reactivity: Not applicable.

For small-molecule target engagement, see Biological Roles for the literature-described biochemical target (bacterial RNA polymerase β-subunit, rpoB).