Decarbamylcefoxitin , CAS No.54333-94-7

CAS: 54333-94-7 Cat. No.: D971665 Summenformel: C₁₅H₁₆N₂O₆S₂ Molekulargewicht: 384.43 PubChem CID: 23620315

Storage

Room temperature

Specifications

Storage

Room temperature

Namen und Kennungen

• Kanonisches Lächeln: COC1(C2N(C1=O)C(=C(CS2)CO)C(=O)O)NC(=O)CC3=CC=CS3
• IUPAC Name: (6R,7S)-3-(hydroxymethyl)-7-methoxy-8-oxo-7-[(2-thiophen-2-ylacetyl)amino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
• InChIKey: ZTFUMAYWSRFLRO-CABCVRRESA-N
• INCHI: 1S/C15H16N2O6S2/c1-23-15(16-10(19)5-9-3-2-4-24-9)13(22)17-11(12(20)21)8(6-18)7-25-14(15)17/h2-4,14,18H,5-7H2,1H3,(H,16,19)(H,20,21)/t14-,15+/m1/s1
• Isomere SMILES: CO[C@@]1([C@@H]2N(C1=O)C(=C(CS2)CO)C(=O)O)NC(=O)CC3=CC=CS3
• PubChem CID: 23620315
• Molekulargewicht: 384.43

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Klasse Lactams
      • Subclass Beta lactams
        • Ebene5 Cephems
          • Ebene6 Cephalosporins
            • Ebene7 Cephamycins

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Klasse: Lactams
• Subclass: Beta lactams
• Intermediate Tree Nodes: Cephems - Cephalosporins
• Direct Parent: Cephamycins
• Alternative Parents: N-acyl-alpha amino acids and derivatives 1,3-thiazines Thiophenes Tertiary carboxylic acid amides Heteroaromatic compounds Secondary carboxylic acid amides Azetidines Thiohemiaminal derivatives Azacyclic compounds Carboxylic acids Dialkylthioethers Monocarboxylic acids and derivatives Carbonyl compounds Organonitrogen compounds Hydrocarbon derivatives Primary alcohols Organic oxides
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Cephamycin - N-acyl-alpha amino acid or derivatives - Alpha-amino acid or derivatives - Meta-thiazine - Heteroaromatic compound - Tertiary carboxylic acid amide - Thiophene - Azetidine - Carboxamide group - Secondary carboxylic acid amide - Azacycle - Dialkylthioether - Hemithioaminal - Thioether - Carboxylic acid derivative - Carboxylic acid - Monocarboxylic acid or derivatives - Organic oxygen compound - Organic oxide - Hydrocarbon derivative - Organonitrogen compound - Alcohol - Carbonyl group - Organic nitrogen compound - Organooxygen compound - Primary alcohol - Aromatic heteropolycyclic compound
• Beschreibung: This compound belongs to the class of organic compounds known as cephamycins. These are compounds containing a the cephalosporin (oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid) nucleus, with an alkyloxy group attached to the C6 carbon atom.
• 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

Chemische und physikalische Eigenschaften

• Molekulargewicht: 384.400 g/mol
• XLogP3: 0.000
• Hydrogen Bond Donor Count: 3
• Hydrogen Bond Acceptor Count: 8
• Rotatable Bond Count: 6
• Exact Mass: 384.045 Da
• Monoisotopic Mass: 384.045 Da
• Topological Polar Surface Area: 170.000 Ų
• Heavy Atom Count: 25
• Formal Charge: 0
• Complexity: 640.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 2
• 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

No tested application protocols (e.g., WB, IHC, IF, FC) are applicable to this small-molecule reagent, and none are provided in the Product Data. For analytical use, consider the following literature-inspired starting points:

• LC–MS reference standard preparation: Dissolve in DMSO (e.g., 10 mg/mL), dilute with water/acetonitrile containing 0.1% formic acid to 10–100 µg/mL working solutions; store aliquots frozen and use promptly after thaw.
• Stability-indicating HPLC method (example framework): C18 column; gradient 5–50% acetonitrile in water (0.1% formic acid or ammonium acetate) over 15–20 min; detect at 230–270 nm; confirm peak identity by MS.
• Enzyme kinetics (PBP/β-lactamase) setup: Prepare fresh buffer (pH 7–7.5), maintain low DMSO content (≤1–2%), run time courses at 25 °C, quench with acidified acetonitrile and analyze by LC–MS.

These are general starting points only; optimize for your instrumentation and verify stability/linearity prior to quantitative use.

Biological Roles

Decarbamylcefoxitin is employed as a research analog of cefoxitin to explore structure–function relationships of cephamycin-type β-lactams (literature). No medical or clinical use is implied.

• Mechanistic probe: Used to evaluate acylation of penicillin-binding proteins (PBPs) and the kinetics of β-lactamase-mediated hydrolysis, clarifying the role of the 3-position carbamoyl group present in cefoxitin (literature).
• Resistance studies: Facilitates investigations into β-lactamase substrate specificity and inhibitor design by contrasting activity between carbamylated and decarbamylated cephamycin cores (research context only).
• Transport/uptake: Changes at the 3-substituent can alter polarity and interactions with porins or transporters in bacterial models; decarbamyl analogs provide comparative data for permeability assessments (literature/general).
• Stability mapping: Serves as a defined product in stress-testing workflows to understand degradation cascades of cephamycins in buffered, oxidative, or photolytic environments.

Guidance for biochemistry workflows:

• Prepare fresh solutions and keep at low temperature during incubations to preserve the β-lactam ring.
• Verify integrity via LC–MS before and after assays, as ring-opened species may confound readouts.
• Use appropriate negative controls (non-β-lactam analogs) to distinguish specific PBP/β-lactamase interactions from nonspecific effects.

Buffer Applications

This product is not a buffering agent. It does not define a pH range or buffering capacity. For experiments requiring buffered environments (e.g., kinetic assays with β-lactamases or PBPs), select an appropriate buffer system separately (HEPES, phosphate, MOPS) and assess compound stability within that buffer (literature guidance).

Green Alternatives

This product is a specialized β-lactam research reagent rather than a process solvent or bulk auxiliary; the “green alternatives” framework is therefore less directly applicable. Nonetheless, greener practices can be applied around its use:

• Solvent choice (literature/guidance): Prefer water, aqueous buffers, or bio-derived solvents when compatible with stability. For nonaqueous stocks, minimize DMSO/DMF volumes and quench into water where feasible.
• Scale minimization: Conduct microscale assays and analytics to reduce chemical use and waste.
• Waste management: Segregate β-lactam-containing aqueous waste and treat as hazardous; avoid discharge to drains. Use high-surface-area sorbents to minimize solvent usage in spill response.
• Energy efficiency: Store at room temperature as specified for this item (Product Data), avoiding unnecessary refrigeration.

Comparison note:

• Because this is not a commodity solvent or reagent with simple functional substitutes, “alternative chemicals” are not generally applicable. Where a cephamycin analog is needed but lower hazard is desired, consider non-β-lactam mechanistic probes; however, binding modes will differ and experimental conclusions may not translate (literature caution).

Pharmaceutical Uses

This item is offered strictly for research use only. It is not an excipient, not manufactured to GMP, and has no assigned pharmacopeial monograph under this catalog entry.

Research/formulation context (non-clinical, literature guidance):

• Analytical reference: Can serve as a reference standard in stability-indicating HPLC/LC–MS methods for cefoxitin-related substances.
• Forced-degradation panels: Included among probable/known degradants when mapping impurity profiles of cephamycin-containing research formulations.
• Preformulation screening: Solubility and stability studies in various pH buffers to inform handling of cephamycin scaffolds in nonclinical research.

No therapeutic, diagnostic, or clinical manufacturing applications are supported or implied for this SKU.

Physical Properties

Item-specific physico-chemical specifications have not been provided for this catalog entry. For exact values that govern acceptance criteria, please consult the item’s CoA/Specification Sheet.

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula: 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 for typical cephamycin solids (decompose before boil; literature, general class guidance).
• Density: Not specified for this item; refer to CoA/Spec Sheet.
• pKa values (literature, class-level): β-Lactam carboxylate pKa typically ~2–3; side-chain/amine functionalities can introduce additional pKa values depending on substituents.
• LogP/logD (literature, class-level): Cephamycins are generally polar/zwitterionic near neutral pH, leading to low logP and higher aqueous compatibility relative to nonpolar organics.
• Solubility (literature, class-level): Often soluble in polar aprotic solvents (DMSO) and aqueous buffers at basic to neutral pH; limited solubility in nonpolar solvents. Exact solubility for this item is not specified; verify experimentally.
• UV characteristics (literature): β-Lactams and oxyimino side chains typically show absorbance in the UV range; exact cutoff/extinction not specified for this item.

Notes for handling measurements:

• Many β-lactams exhibit hydrolytic sensitivity; measure properties rapidly and under controlled pH to avoid degradation artifacts (literature).

Quality and Grades

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet for assay, impurity profile, and acceptance limits.

Guidance on interpreting grades (general):

• Research grade: Typical for discovery and method development; assay and impurity limits defined on CoA.
• Chromatography/HPLC grade (if applicable): Emphasizes low UV background and low nonvolatile residues—relevant when using UV detection.
• Bioactive small-molecule grade: For enzyme binding or microbiology research, focus is on identity (NMR/HRMS), purity by HPLC/UPLC, and residual solvent limits.

Stabilizers/antioxidants:

• Stabilizer content: Not specified for this item; refer to CoA/Spec Sheet. Some β-lactam materials are supplied without stabilizers and rely on controlled moisture; others may include buffering salts—verify before sensitive assays.

Batch-specific documentation:

• Certificate of Analysis will define: identity methods (NMR/MS/IR), assay (%), water content (e.g., KF), residual solvents, and storage guidance. For regulated workflows, request a full specification sheet and methods package.

User notes:

• If employing for quantitative studies (e.g., PBP-binding kinetics), verify purity on receipt and consider preparing fresh solutions to minimize degradation during use.

Reaction and Applications

This compound is primarily used as a research analog/degradation product of cefoxitin for mechanistic and analytical studies (literature). Key application themes include:

• β-Lactamase and PBP probe: Decarbamylcefoxitin can be used to interrogate the role of the 3-position carbamoyl group in binding and turnover, informing structure–activity relationships (SAR) across cephamycins (literature; no clinical claims).
• Degradation pathway mapping: Serves as a reference standard for cefoxitin stress testing (acid/base/hydrolytic), aiding LC–MS method development and stability-indicating analytics.
• Comparative reactivity: Useful in assessing β-lactam ring opening rates and the influence of the 7-α-methoxy substituent on hydrolysis.
• Microbiological research controls: As a decarbamylated analog, it may provide a comparative control in β-lactam exposure studies (research-only context).

Practical notes:

• Handle under dry, cool conditions; prepare solutions immediately before experiments to limit hydrolysis.
• For kinetic studies, buffer at controlled ionic strength; quench and analyze rapidly by LC–MS to avoid post-quench degradation.
• When used in conjugation chemistry (e.g., immobilization for affinity matrices), attach via side-chain handles rather than the β-lactam ring to preserve integrity (literature best practice).

Related named context (literature):

• Studies on class C β-lactamases and PBP acylation/deacylation kinetics with cephamycin cores often cite decarbamyl analogs to dissect substituent effects at C-3 and C-7.

Reaction Conditions

Specific optimized conditions for this exact item are not provided; the following are general, literature-based guidelines for manipulating cephamycin/β-lactam scaffolds while preserving ring integrity.

• Solvents: Dry DMF or DMSO for coupling; aqueous buffers (pH 6.5–7.5) for biochemistry assays. Avoid strong protic acids/bases.
• Temperature: 0–25 °C preferred for derivatizations; brief exposures only. Elevated temperatures accelerate hydrolysis and epimerization.
• Atmosphere: Ambient is acceptable; exclude moisture for anhydrous couplings.
• Couplings at carboxylate: EDC·HCl/NHS or HATU at 0–10 °C, short times (0.5–2 h). Quench promptly and purify at low temperature.
• O-Acylation at C-3 (decarbamyl context): Use mild acyl chlorides or activated carbonates with base scavengers (e.g., pyridine) at ≤0–5 °C; monitor closely by LC.
• Biochemical assays (PBP/β-lactamase kinetics):
  • Buffers: 50 mM HEPES or phosphate, pH 7.0–7.5; ionic strength 0.1–0.2 M (literature general).
  • Stock: 10–50 mM in DMSO; final DMSO ≤1–2% v/v after dilution into buffer.
  • Readouts: UV or LC–MS to track intact compound and hydrolysis products.
• Purification: Reverse-phase preparative HPLC with water/acetonitrile and 0.1% formic acid or ammonium acetate; keep column and fractions cool.

Always verify with small-scale trials and analytical checkpoints; adjust conditions based on observed stability of the specific lot.

Safety and Handling

GHS hazard classification and pictograms are not specified for this item; refer to the product SDS for authoritative safety information.

• Signal word: Not specified for this item; refer to SDS.
• GHS classification/pictograms: Not specified for this item; refer to SDS.
• H-statements: Not specified for this item; refer to SDS.

General safety considerations for β-lactam/cephamycin research chemicals (literature, precautionary):

• Sensitization risk: β-Lactams can act as sensitizers; avoid skin contact and inhalation. Individuals with known β-lactam allergy should not handle without appropriate controls.
• Hydrolysis products: Degradation under basic/acidic conditions can yield reactive fragments; minimize exposure and segregate waste.
• PPE: Use lab coat, nitrile gloves (change regularly), splash goggles; handle powders in a chemical fume hood or ventilated enclosure.
• Incompatibilities: Avoid strong acids/bases (hydrolysis), strong oxidizers, and prolonged exposure to moisture and elevated temperature (literature).
• First aid (overview; follow SDS/site protocols):
  • Skin/eye contact: Immediate decontamination with water for ≥15 minutes; remove contaminated clothing; seek medical evaluation if irritation persists.
  • Inhalation: Move to fresh air; seek medical attention if symptoms occur.
  • Ingestion: Rinse mouth; do not induce vomiting; obtain medical advice.
• Spill/waste: Avoid dust generation; collect with inert absorbent. Dispose of according to local regulations for laboratory chemical waste.

For research use only. Not for human or animal consumption or clinical applications.

Solvent Selection

Decarbamylcefoxitin, as a polar cephamycin analog, typically shows better compatibility with polar solvents. Exact solubility for this SKU is not specified; confirm experimentally on receipt.

General solvent guidance (literature/class-level):

• Preferred solvents: DMSO (high solubility for many β-lactams), DMF; aqueous buffers at neutral to slightly basic pH can dissolve the zwitterionic form. Filter sterilize only if necessary and compatible with chemical stability.
• Conditional solvents: Methanol, ethanol, and water–miscible mixtures (e.g., DMSO→buffer serial dilution) often work for stock solutions destined for biochemical assays.
• Avoid: Nonpolar solvents (hexane, toluene) and strongly acidic/basic media that accelerate β-lactam hydrolysis.

Practical tips:

• Prepare concentrated DMSO stock (e.g., 10–100 mM), then dilute into buffered media immediately before use to limit ring-opening.
• Keep solutions cold and minimize exposure to moisture/heat.
• For chromatographic purification or analytical checks, reverse-phase systems (water/acetonitrile with volatile buffers) are generally effective; monitor at UV 230–270 nm (literature), adjusting for the specific chromophores.

Comparison (literature/general):

• Versus cefoxitin: Decarbamyl variant may be less polar depending on the 3-substituent change; expect modest differences in aqueous solubility and retention time; confirm by small-scale trials.

Storage and Reconstitution

• Storage conditions (as supplied): Room temperature (Product Data). Protect from moisture and excessive heat. Store in the original, tightly closed container.
• Shipped in: Not specified for this item; refer to CoA/Spec Sheet.
• Appearance: Not specified for this item; refer to CoA/Spec Sheet.

Reconstitution and solution handling (general guidance for β-lactams):

• Stock solutions: Prepare in dry DMSO or compatible solvent immediately before use. For aqueous work, dilute DMSO stocks into pre-cooled buffer with gentle mixing.
• Working concentration and stability: Stability is experiment-dependent; prepare only the amount needed for same-day use. Avoid repeated freeze–thaw.
• Aliquoting: If long-term storage of solution is unavoidable, prepare single-use aliquots, flash-freeze, and store at ≤−20 °C protected from light and moisture. Verify integrity by LC–MS before critical experiments.
• Container compatibility: Use glass or high-quality polypropylene. Avoid reactive metals and basic glass surfaces for prolonged contact.

Always defer to the item’s CoA and SDS for definitive guidance. Research use only.

Structure and Identity

Decarbamylcefoxitin is a cephamycin-type β-lactam research reagent closely related to cefoxitin; the “decarbamyl” descriptor denotes loss of the 3-carbamoyl substituent present in cefoxitin (literature). It is typically discussed as a des-carbamoylated transformation product/probe of the cephamycin scaffold.

• CAS: 54333-94-7 (Product Data)
• PubChem CID: 23620315 (Product Data)
• InChIKey: 465888 (as provided; atypical length in Product Data)
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

Structural features (literature, generic for decarbamyl cephamycins):

• Core bicyclic β-lactam system: a fused four-membered β-lactam ring to a dihydrothiazine ring (cephalosporin/cephamycin core).
• 7-α-methoxy substituent typical of cephamycins, which modulates β-lactamase stability and PBP interactions.
• 3-position substituent: decarbamyl variant generally bears a hydroxy or related functionality in place of cefoxitin’s carbamoyloxymethyl group (literature descriptions), altering polarity and reactivity.
• Side chain at C-7 derived from cefoxitin (oxyimino-type acyl side chain); stereochemistry at the β-lactam centers is retained from the cephamycin class (literature).

2D structure (descriptive, literature-based): A bicyclic scaffold with a strained β-lactam amide fused to a six-membered dihydrothiazine containing sulfur; an α-methoxy at C-7 and a modified 3-substituent replacing cefoxitin’s carbamate; an acylamido side chain on the β-lactam nitrogen.

Synthetic Utility

From a synthetic perspective, decarbamylcefoxitin represents a modified cephamycin core that can be used to explore or build β-lactam chemistry.

• Scaffold for SAR: Provides a handle to compare effects of the 3-substituent on reactivity and binding; useful for derivatization at positions that do not compromise the β-lactam ring (literature).
• Functional handles (literature/general):
  • Carboxylate at C-4: Amenable to salt formation or esterification (with care to avoid ring opening).
  • Side-chain amide: Potential site for isotopic labeling or linker attachment via mild coupling.
  • 3-position (decarbamyl): The absence of the carbamoyl group can enable selective O-acylation or carbonate formation under controlled conditions.
• Reaction considerations:
  • Maintain neutral to slightly basic conditions; avoid strong acids/bases which accelerate β-lactam hydrolysis.
  • Use mild coupling reagents (e.g., carbodiimides with additives, uronium reagents) at low temperature and short contact times.
• Retrosynthetic value: Serves as a late-stage intermediate to access libraries of 3-substituted cephamycins by installing alternative carbonate/carbamate moieties, facilitating SAR around sterics/electronics at C-3 (literature).

Analytical control:

• Monitor by RP-HPLC and LC–MS; track β-lactam integrity via characteristic mass and diagnostic fragments. Use orthogonal NMR (1H/13C) to confirm retention of the β-lactam signals (downfield amide proton, characteristic carbonyl shifts).

Target Specificity

No antibody or biological macromolecule targeting data is provided for this item. Decarbamylcefoxitin is a small-molecule β-lactam research reagent, not an affinity reagent or biologic. Any discussion of binding to PBPs or β-lactamases in this listing should be considered general, literature-based context rather than validated, item-specific targeting data.