Tomaymycin DM - ≥98% , CAS No.945490-09-5

CAS: 945490-09-5 Cat. No.: T647435 Formule: C₁₄H₁₄N₂O₃ Poids moléculaire: 258.27

QUALITÉ & PURETÉ ≥98%

Storage

Store at -20°C,Argon charged

Shipped In

Ice chest + Ice pads

Vue d’ensemble

Tomaymycin DM, a DNA alkylator, is a derivative of Tomaymycin, it is a PBD dimer, which is attached to tumor targeting antibodies to create antibody-drug conjugates ( ADCs ).

Form:Solid

IC50& Target:Pyrrolobenzodiazepines

Spécifications

Spécifications et pureté

≥98%

Mécanismes biochimiques et physiologiques

Tomaymycin DM, a DNA alkylator, is a derivative of Tomaymycin, it is a PBD dimer, which is attached to tumor targeting antibodies to create antibody-drug conjugates ( ADCs ).

Conditions de stockage de stockage

Store at -20°C,Argon charged

Expédié en

Ice chest + Ice pads

Ce produit nécessite l'expédition en chaîne froide. Les services terrestres et autres services économiques ne sont pas disponibles.

Pureté

≥98%

Noms et identifiants

Sourires canoniques

O=C1N2[C@](CC(C2)=C)([H])C=NC3=CC(O)=C(OC)C=C13

Poids moléculaire

258.27

Propriétés chimiques et physiques

• Solubilité: DMSO : 100 mg/mL (387.19 mM; Need ultrasonic)

Application Protocols

No manufacturer-validated application protocols are supplied for this item. The following are general laboratory workflows for small-molecule library standards in discovery and analytical contexts.

Preparing stock solutions

• Weigh the required amount quickly in a ventilated enclosure to minimize moisture uptake. Dissolve in anhydrous DMSO to prepare a concentrated stock (e.g., 10–50 mM, as solubility permits). Mix gently until fully dissolved. Protect from light as needed.
• Aliquot into low-bind microtubes under inert gas (argon or nitrogen) to minimize headspace oxygen/moisture, consistent with the item’s storage guidance.

Assay dilution

• Immediately before use, dilute the DMSO stock into pre-equilibrated assay buffer or media with thorough mixing. Maintain a consistent final DMSO concentration across wells or samples. Inspect for precipitation; if present, adjust co-solvent fraction within assay limits.

Analytical method setup

• LC–MS: Begin with water/MeOH or water/MeCN gradients using acidic modifiers (e.g., 0.1% formic acid) unless pH sensitivity dictates neutral conditions. Validate a stability-indicating method by spiking stressed samples.

Stability checks

• Perform a short-term bench-top stability assessment (e.g., 4–24 h at room temperature vs. 4°C) and a freeze–thaw test on aliquots to set handling limits.

Documentation

• Record lot number, preparation date, stock concentration, and storage conditions for traceability. Consult the CoA/SDS before initiating experiments.

Biological Roles

Item-specific biological data

• None provided for this entry. This product is for research use only and is not intended for human or veterinary applications.

Literature/general context on the tomaymycin family

• Tomaymycin is a member of the pyrrolo[1,4]benzodiazepine (PBD) natural product family produced by Streptomyces species. PBDs are renowned for sequence-selective DNA minor-groove binding. Certain PBDs can form covalent adducts with DNA via an electrophilic center, often contributing to potent cytotoxic activity in cell-based assays.
• Structure–activity relationships: Substituents on the PBD core modulate DNA affinity, sequence selectivity (commonly favoring GC-rich sites), and reactivity. Stereochemistry of the tricyclic core is critical for groove fit.
• Cellular consequences (research literature): DNA adduct formation can trigger replication stress, cell cycle arrest, and apoptosis in cultured cells. Such effects are model- and concentration-dependent and pertain to research observations, not to clinical claims.

Use in research workflows

• Chemical biology: Probe compound for studying DNA minor-groove recognition, alkylation kinetics, and repair pathway engagement.
• Omics integration: Employed in chemoproteomics or adductomics to map DNA interaction sites, using LC–MS/MS of nucleoside adducts.

Caveat

• "Tomaymycin DM" specifies an analog, but its exact functional modifications are not provided here. Biological behavior can vary substantially across PBD derivatives; confirm experimentally under your system’s conditions.

Buffer Applications

Not a buffering agent

• Tomaymycin DM is not used to establish pH or ionic strength and has no canonical role as a buffer component.

Practical notes for buffered systems (general guidance)

• Solubilization: Prepare a concentrated DMSO stock, then dilute into your chosen buffer (e.g., phosphate-, HEPES-, or Tris-based) with mixing to mitigate local supersaturation. Keep final DMSO ≤1% v/v where biological tolerance is required.
• Precipitation checks: After dilution, inspect for turbidity/precipitate. If observed, increase co-solvent slightly (e.g., 0.2–0.5% additional DMSO) or add a compatible solubilizer (e.g., low % Tween-80 or PEG-400) as your assay allows.
• pH considerations: PBD-like compounds may undergo acid- or base-catalyzed degradation. Maintain near-neutral pH unless your protocol specifies otherwise, and keep exposure times short at elevated temperatures.
• Adsorptive losses: To reduce nonspecific binding at low concentrations, use low-bind plastics or pre-condition glassware with dilute DMSO-containing buffer.

For electrophoresis or chromatography buffers

• When developing analytical methods (e.g., CE or LC with aqueous-rich eluents), confirm stability in the running buffer and limit light/oxygen exposure during long sequences.

Item-specific buffer recommendations are not available; consult your assay SOPs and verify compatibility empirically.

Green Alternatives

Because Tomaymycin DM is a research standard rather than a process solvent or bulk reagent, green chemistry considerations focus on solvent and process choices during its handling and analysis.

Greener handling strategies (general)

• Prefer water-miscible, lower-toxicity solvents where compatible: ethanol or isopropanol can sometimes partially substitute for acetonitrile/methanol during cleanup steps or for intermediate dilutions, though final solubility must be verified.
• Minimize DMSO volumes while retaining solubility: prepare higher-concentration stocks to reduce per-assay DMSO percentages; validate biological tolerance.
• Chromatography: Evaluate MeOH–water gradients before MeCN–water if sensitivity allows; MeOH has a more favorable life-cycle profile in many settings. Consider reducing flow rates and scaling down column dimensions to decrease solvent consumption.
• Workup/waste: Consolidate halogenated and non-halogenated waste streams correctly; switch to non-halogenated solvents for rinses when feasible.

Illustrative comparison (general; not item-specific)

• DMSO vs. DMF/NMP: DMSO generally preferred for worker safety and environmental profile compared with DMF/NMP while maintaining strong solvation for polar organics.
• MeOH vs. MeCN (LC mobile phases): MeOH is more benign and cost-effective; MeCN often offers lower backpressure and different selectivity—choose based on performance.

Tradeoffs

• Solubility and stability constraints of PBD-like scaffolds can necessitate high-performance polar aprotic solvents. Apply microscale operations and closed systems to minimize exposure and waste while maintaining data quality.

Pharmaceutical Uses

This product is supplied strictly for research use only.

Item-specific regulatory/formulation status

• No pharmacopeial monograph or excipient designation is provided for this entry. It is not manufactured under GMP and is not intended for diagnostic, therapeutic, or veterinary use.

Relevant research/formulation context (general)

• Reference standard: In discovery environments, tomaymycin-class compounds may be employed as reference materials to benchmark assays, evaluate structure–activity relationships, or develop analytical methods (e.g., LC–MS stability-indicating assays) that could later support preclinical research.
• Formulation explorations: Researchers may explore enabling formulations (cyclodextrin inclusion, lipid-based carriers, polymeric micelles) to enhance solubility for in vitro work. These activities remain within non-clinical research boundaries.
• Quality attributes for research lots: Identity, purity, and stability are primary quality attributes. Where dose-response precision is needed, pay attention to counterion, residual solvent content, and water content as reported in the CoA.

Compliance and handling

• Labeling and chain of custody should align with institutional policies for potent small molecules. For any work approaching translational studies, procure appropriate-grade material under applicable regulations.

Summary

• No pharmaceutical or clinical claims apply to this item. Use solely in laboratory research by qualified personnel.

Physical Properties

Item-specific properties

• Appearance: 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/unknown for a complex organic solid; refer to CoA/Spec Sheet.
• Density: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility: Not specified for this item; refer to CoA/Spec Sheet.
• LogP, pKa, refractive index: Not specified for this item; refer to CoA/Spec Sheet.

Handling conditions (from Product Data)

• Storage: Store at −20°C, argon charged.
• Shipping: Ice chest + ice pads.

Literature/general expectations for tomaymycin-class compounds

• Physical state: Typically isolated as off-white to pale solids with low volatility (general expectation; not item-specific).
• Solubility behavior: PBD-type molecules often exhibit limited aqueous solubility; DMSO is commonly used to prepare concentrated stocks, with subsequent dilution into buffered media containing co-solvent or surfactant as needed. Methanol or acetonitrile can serve as intermediate solvents for HPLC sample prep (general guidance; verify item-specific compatibility).
• Stability considerations: PBD electrophilic centers and imine-like functionalities can be moisture- and acid/base-sensitive. Protection from moisture, strong acids/bases, and prolonged light exposure is prudent. Inert atmosphere storage (as specified for this item) is consistent with preserving integrity.

Notes

• For numerical property values suitable for method development (e.g., LC retention, UV–vis features), consult the CoA/SDS or perform small-scale analytical characterization under your laboratory’s validated conditions.

Quality and Grades

Item-specific quality information

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

How to interpret grade and documentation (general guidance)

• CoA (Certificate of Analysis): Provides lot-specific assay, identity confirmation (e.g., NMR/LC–MS/HRMS), and impurity profile where applicable. For structure-confirmation and potency-critical applications, review spectral data alongside acceptance criteria.
• Research grade vs. analytical/clinical grade: This catalog entry is for research use only. Research grade materials prioritize suitability for discovery, screening, and method development. They are not produced under GMP and are not intended for human or veterinary use.
• HPLC/LC–MS suitability: When grades are not explicitly labeled (e.g., “HPLC grade” is typically a solvent designation), rely on the CoA for UV background, residual solvent profile, and chromatographic purity if relevant to your method.

Best practices for incoming QC (user side)

• Identity check: LC–MS with exact mass (if available), retention time versus reference, and orthogonal NMR confirmation for critical studies.
• Purity check: Analytical HPLC with both UV and MS detection; consider ELSD/charged aerosol detection for non-chromophoric impurities.
• Stability check: Short-term stress test (e.g., 24–48 h at bench in common assay matrix) to assess degradation pathways before scale-up studies.

Documentation

• If any specification is required for regulatory submissions in research contexts, request the current CoA/Spec Sheet from Aladdin Scientific before use.

Reaction and Applications

Item context

• Tomaymycin DM is offered as a research-use small molecule standard within a compound library. No manufacturer application text is provided for this entry beyond research-use designation.

Discovery and screening applications (general/literature)

• Reference scaffold: Tomaymycin belongs to the PBD family known for DNA minor-groove interaction. Analog studies often explore substituent effects on sequence selectivity and reactivity. Tomaymycin DM can serve as a reference/benchmark molecule in screening panels, target deconvolution workflows, and mechanistic studies of DNA-binding electrophiles.
• Analytical method development: Useful as a probe compound to develop LC–MS/MS methods for PBD-like chemotypes, including stability-indicating methods and metabolite identification protocols.

Synthetic/derivatization use (general)

• Conjugation studies: If functional handles are present (information not specified here), researchers may derivatize PBD analogs to generate bioconjugates, prodrugs, or affinity reagents to study DNA interaction and cellular uptake.

Practical tips

• Prepare fresh DMSO stocks and minimize aqueous residence time before assays to limit hydrolysis of labile centers.
• For mechanistic assays (e.g., DNA adduct formation), control pH and ionic strength; include appropriate negative/positive controls.
• Employ light and oxygen exclusion during prolonged incubations if degradation is observed.

Note: Specific reactivity and application scope depend on the exact substitution pattern of Tomaymycin DM, which is not provided here. Consult CoA/Spec Sheet and perform pilot experiments.

Reaction Conditions

This product is a complex small molecule standard; it is not primarily intended as a general-purpose reagent. When researchers perform derivatizations or conjugations on tomaymycin-class scaffolds, the following literature-informed practices may be useful. These are general guidelines, not item-specific instructions.

General conditions (literature/context)

• Atmosphere: Inert (argon or nitrogen), aligning with the storage recommendation for this item (−20°C, argon charged).
• Solvents: Dry DMSO, DMF, or dichloromethane/ethyl acetate mixtures depending on functional groups present. For polar modifications, DMSO or DMF are commonly chosen.
• Temperature: 0–25°C for transformations involving labile imine/electrophilic centers; elevated temperatures can accelerate degradation and are best avoided until stability is established.
• Bases/Acids: Use mild, non-nucleophilic bases (e.g., DIPEA) for acylations/carbamates; avoid strong acids/bases that may cleave or rearrange the PBD core.
• Timescales: Short reaction times (minutes to a few hours) with continuous LC–MS monitoring are recommended due to potential lability.

Analytical control

• Employ LC–MS with stability-indicating gradients to follow both parent and potential decomposition products. Record UV spectra to assist in purity tracking.

Yields

• Highly substitution-dependent; literature for PBD analog derivatizations often reports modest to moderate isolated yields due to sensitivity of the scaffold.

Note

• The exact functional groups of Tomaymycin DM are not specified; tailor conditions after small-scale scouting experiments and consult the CoA for any functional group warnings.

Safety and Handling

Authoritative safety information is provided in the SDS. The following guidance summarizes known best practices and item-specific storage from Product Data.

Item-specific safety details

• GHS Classification, Signal Word, H-Statements, Pictograms: Not specified for this item; refer to SDS.
• Storage: Store at −20°C under argon. Shipments are provided cold (ice chest + ice pads).

General laboratory precautions for tomaymycin-class compounds (literature/context; not specific to this item)

• Hazard profile: Tomaymycin belongs to the PBD family, which are potent DNA minor-groove binders capable of covalent interaction in some analogs. Handle as a potentially bioactive, cytotoxic small molecule. Avoid inhalation, ingestion, and skin contact. Use in a certified chemical fume hood or appropriate containment.
• PPE: Lab coat, nitrile gloves (double-gloving recommended for solution handling), safety glasses or splash goggles. Change gloves frequently and immediately if contaminated.
• Engineering controls: Work within a fume hood; for powder weighing, consider a ventilated balance enclosure. Use closed containers for stock solutions. Avoid aerosolization.
• Incompatibilities: Avoid strong acids/bases and oxidants that may degrade the scaffold. Prevent moisture ingress to limit hydrolysis of electrophilic centers. Protect from light where feasible.
• First aid (general): In case of skin contact, wash with soap and water; for eye exposure, rinse with water for several minutes and seek medical attention. If inhaled, move to fresh air; if ingested, rinse mouth and seek medical attention. Always follow institutional exposure response procedures.

Waste disposal

• Collect solid/liquid waste as hazardous organic waste. Decontaminate surfaces with suitable organic solvent followed by detergent rinse, per institutional EHS guidance.

Solvent Selection

This entry is a complex small molecule standard rather than a solvent. Selection here refers to dissolving and handling Tomaymycin DM for assays and analytics.

General solvent guidance (literature/context)

• Primary stock solvent: DMSO is commonly used for PBD-family compounds due to good solvating power and assay compatibility at ≤1% v/v in biological media. Prepare concentrated stocks (e.g., 10–50 mM) as solubility allows; verify empirically.
• Alternative solvents: DMF and NMP offer strong solvation but may be less desirable in bioassays. For analytical sample prep, methanol or acetonitrile are often appropriate; water-miscible binary systems (MeCN/H2O, MeOH/H2O) aid LC injection.
• Aqueous use: For working solutions, dilute DMSO stocks into buffered media with gentle mixing. Consider solubilizers (PEG-400, cyclodextrins) or small amounts of co-solvent if precipitation occurs.
• Stability considerations: Avoid strong acids/bases that can degrade electrophilic centers. Maintain inert atmosphere for longer-term solutions if feasible, consistent with the argon storage recommendation for the solid.

Comparison (typical choices)

• DMSO: Best overall solubility and bioassay compatibility; hygroscopic, keep dry.
• MeCN/MeOH: Good for LC; may not maintain high concentrations in aqueous buffers without co-solvent.
• DMF/NMP: Excellent solvation; higher boiling points and potential assay interference; reserve for analytical or synthetic manipulations.

Always confirm solvent effects on your specific assay endpoints and analytical detection.

Storage and Reconstitution

Item-specific storage and shipping

• Storage Conditions: Store at −20°C, Argon charged (per Product Data).
• Shipped In: Ice chest + Ice pads (per Product Data).

General best practices for this compound class

• Atmosphere: Maintain inert gas headspace (argon or nitrogen) in both solid and solution states to limit oxidative degradation, in alignment with the item-specific argon recommendation.
• Light and moisture: Protect from light and moisture. Use desiccant in secondary containment. Allow vials to reach room temperature under inert atmosphere before opening to minimize condensation.

Reconstitution guidance

• Solvent choice: Reconstitute in anhydrous DMSO as a primary stock solvent. If alternative solvents are desired (DMF, MeOH, MeCN), verify solubility and stability on a small scale first.
• Concentration: Prepare the highest practical concentration to minimize per-assay solvent volumes, subject to solubility limits and assay tolerance. Filter through a low-protein-binding 0.2 µm PTFE filter if particulate is observed.
• Aliquoting: Dispense into single-use aliquots to avoid repeated freeze–thaw cycles. Clearly label with lot number, concentration, solvent, and date.

In-use stability

• Keep working solutions on ice or at 4°C during extended setup. Discard solutions showing precipitation, discoloration, or unexpected LC–MS profiles.

Records and references

• For lot-specific stability and any additional handling notes, consult the CoA and SDS. Adhere to institutional chemical hygiene plans for potent small molecules.

Structure and Identity

Concise overview of identity and structural context for a research-only small molecule listed in our Small Molecules & Compound Libraries category.

• SKU: T647435
• Product Name: Tomaymycin DM
• CAS: 945490-09-5
• Category Path: 全部 / 可售 / 小分子和化合物库
• Research Use Note: For research use only

Item-specific identifiers

• Molecular Formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular Weight: Not specified for this item; refer to CoA/Spec Sheet.
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• InChIKey: Not specified for this item; refer to CoA/Spec Sheet.

Structural features (literature/general context)

• The parent natural product tomaymycin is a member of the pyrrolo[1,4]benzodiazepine (PBD) family, characterized by a fused tricyclic PBD core capable of minor-groove DNA interaction. PBD scaffolds typically include: an electron-deficient imine or related electrophilic center at the N10–C11 region, a diazepine ring fused to an aromatic system, and a pendant pyrrolo substituent that influences sequence selectivity.
• The suffix “DM” denotes a derivative or analog of tomaymycin; however, the precise substitution pattern for this catalog item is not specified here. Consult the CoA/Spec Sheet for definitive structure.

2D structure description (literature/general)

• PBDs present a planar/aromatic face aligned to the DNA minor groove, a curved tricyclic framework, and one or more substituents that project to the groove floor or rim, governing binding and reactivity. Stereochemical configuration at the tricyclic system is frequently important for biological recognition.

Synthetic Utility

Item perspective

• Tomaymycin DM is supplied as a discrete small molecule standard rather than as a synthetic reagent. Nevertheless, understanding the reactivity of the tomaymycin/PBD scaffold can aid in designing derivatives and analytical transformations.

Reactivity of PBD-like scaffolds (literature/general)

• Electrophilic center: Many PBDs feature an imine-like electrophile at the N10–C11 position that can undergo nucleophilic addition (e.g., with amines or DNA bases). Control of pH and nucleophile strength is pivotal in derivatization and stability studies.
• Functional handles: Hydroxyls, amines, or halides (when present in a given analog) enable acylation, carbamate/urea formation, carbonate installation, or etherification to modulate physicochemical properties.
• Protecting-group strategy: If synthesis/derivatization is attempted, temporary protection of sensitive centers (acylals, carbamates, silyl ethers) may be required to prevent decomposition.

Analytical derivatization

• For LC–MS method development, mild derivatization can enhance ionization or stabilize labile centers, provided it does not confound the research objective.

Constraints

• The exact substitution pattern of Tomaymycin DM is not provided in this listing; thus, specific synthetic routes or transformations cannot be prescribed. Verify structure by CoA and evaluate functional group compatibility before designing chemistry.

Practical notes

• Conduct reactions under inert atmosphere and anhydrous conditions to preserve sensitive motifs. Monitor closely by LC–MS and stop reactions at low conversion to prevent overreaction or scaffold degradation.

Target Specificity

Item-specific target data

• Not provided for this product. No antibody/biologic information is applicable; this is a small molecule standard.

Literature/general context on PBD/tomaymycin scaffolds

• Molecular target class: DNA in the minor groove. PBDs exhibit sequence-selective binding, frequently favoring GC-rich sequences. Some analogs can form covalent adducts with guanine at the N2 position via an electrophilic center.
• Determinants of selectivity: Substituent patterns on the PBD core influence curvature and hydrogen-bonding potential, which in turn dictate sequence preference and binding kinetics.

Caveat

• “Tomaymycin DM” denotes a specific analog, but the exact modifications are not listed here. Binding selectivity and covalency are highly structure-dependent. Users should determine target engagement under their experimental conditions using appropriate biophysical or biochemical assays (e.g., thermal shift, footprinting, adduct mapping) and controls.

Foire aux questions

What is the purity of this product?

This product is supplied at ≥98% purity (chemical assay). Lot-specific values are stated on the Certificate of Analysis.

How should this product be stored?

Store at ?20 °C under argon. It is supplied under an argon blanket; reseal under inert gas after each use.

How is this product shipped?

This product ships in an insulated container with ice pads. Unpack on arrival and transfer it to the storage condition stated above.

What are the CAS number, molecular formula and molecular weight?

The CAS Number is 945490-09-5, the molecular formula is C14H14N2O3, and the molecular weight is 258.27 g/mol.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.