This compound belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.
External Descriptors
Not available
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.
Certificats (CoA, COO, BSE/TSE et tableau d'analyse)
C of A & Other Certificates(BSE/TSE, COO):
Analytical Chart:
Propriétés chimiques et physiques
Poids moléculaire
622.900 g/mol
XLogP3
5.500
Hydrogen Bond Donor Count
2
Hydrogen Bond Acceptor Count
10
Rotatable Bond Count
12
Exact Mass
622.232 Da
Monoisotopic Mass
622.232 Da
Topological Polar Surface Area
206.000 Ų
Heavy Atom Count
41
Formal Charge
0
Complexity
991.000
Isotope Atom Count
0
Defined Atom Stereocenter Count
3
Undefined Atom Stereocenter Count
0
Defined Bond Stereocenter Count
1
Undefined Bond Stereocenter Count
0
The total count of all stereochemical bonds
1
Covalently-Bonded Unit Count
1
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Application Protocols
Only tested/validated application protocols from product data may be listed here. No application protocols are provided for this item.
General note (not a protocol or specification)
In many research settings, small-molecule probes like largazole are prepared as concentrated DMSO stocks (e.g., millimolar range), aliquoted, and diluted into assay buffers or media to the desired working concentration while keeping final DMSO low (typically ≤0.1–1% v/v). Validate conditions in your own system.
Biological Roles
General/literature (biochemistry; not medical claims)
Origin: Largazole is a marine cyanobacterial natural product (originally isolated from Symploca sp., literature), characterized as a prodrug that releases an active thiol intracellularly.
Molecular function: Serves as a potent inhibitor of zinc-dependent histone deacetylases (HDACs). The released thiolate coordinates to the catalytic Zn2+ ion in the HDAC active site, blocking deacetylation activity (literature).
Selectivity profile: Reported to be highly active against class I HDACs (e.g., HDAC1–3) with varying activity on other isoforms; selectivity and potency depend on assay format and conditions (literature).
Cellular consequences studied in research contexts: increased histone acetylation, modulation of chromatin accessibility, and changes in transcriptional programs (literature). These are mechanistic biochemical observations, not therapeutic claims.
Probe utility: Used as a chemical biology tool for dissecting epigenetic regulation, benchmarking HDAC assay platforms, and informing structure–activity relationship (SAR) efforts through analog development.
Notes
Biological activity can depend on conversion to the thiol, cellular uptake, and efflux. Careful control of dosing vehicle (e.g., DMSO percentage) and time-course is recommended in experimental designs.
Enzyme selectivity and binding constants vary across reports; consult primary literature for isoform-resolved data under conditions matching your assay.
Buffer Applications
Not typically applicable. Largazole is not a buffering agent and is not used to prepare pH-stabilizing buffer systems. For experimental use, it is commonly dissolved in DMSO and then diluted into pre-made biological buffers or media. Ensure the final organic co-solvent level is compatible with your assay system.
Green Alternatives
Applicability: This product is a complex small-molecule probe, not a process solvent or commodity reagent. “Green alternatives” therefore relate to handling and formulation practices rather than substituting the compound itself.
Greener handling strategies (general/literature)
Minimize DMSO content: Use the lowest feasible DMSO percentage in aqueous assays (e.g., 0.1–0.5% v/v) consistent with solubility, to reduce solvent load.
Solvent exchange: For preparative workups, favor EtOAc/EtOH and water where compatible, in place of chlorinated solvents.
Microscale experimentation: Due to potency, micro- to milligram-scale studies reduce solvent consumption and waste.
Inert-atmosphere storage of thiol solutions: Extends solution lifetime and reduces need for re-preparation, lowering waste.
Not typically applicable
There is no direct “green substitute” for largazole itself, as its value lies in its specific structure and target engagement profile. When alternative probes are acceptable for your study design, consult the literature for HDAC inhibitors available in greener formulations.
Pharmaceutical Uses
Not applicable as an excipient. This product is provided for research use only and is not intended for formulation as a drug product. In pharmaceutical research settings, largazole may serve as a reference standard or tool compound in discovery assays and analytical method development. No pharmacopeial status, dosage form guidance, or clinical use is specified for this item.
Physical Properties
Item-specific properties (from Product Data)
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.
General/literature information (for context; not item specifications)
Physical state: typically an off-white to pale solid for purified largazole analogs; exact appearance varies by batch and form (literature).
Solubility: common laboratory stocks are prepared in DMSO (millimolar range); limited aqueous solubility without co-solvent or carrier (literature). Soluble to a lesser extent in MeOH/EtOH and CH3CN; insoluble to sparingly soluble in nonpolar hydrocarbons.
Stability: thioester functionality is moisture/base sensitive; hydrolysis yields the corresponding thiol (literature). The free thiol can air-oxidize to disulfide; handle under inert atmosphere for prolonged work.
Spectroscopy: UV absorption arises from heteroaromatic thiazole and conjugated elements; no item-specific UV cutoff is provided here.
Partitioning: amphiphilic macrocycle; exact logP/logD values vary with ionization state and are not specified here.
Note: All numerical values (bp, mp, density, refractive index, pKa, logP) are not specified for this item; refer to the CoA/Spec Sheet or primary literature for exact values.
Quality and Grades
Item-specific quality data
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
Context and guidance
Research-use compound: In the absence of a declared analytical grade, items in small-molecule libraries are typically provided as research-grade materials suitable for discovery chemistry, screening, and method development. Purity is commonly assessed by HPLC/LC–MS and 1H NMR; confirm with the CoA for this lot.
Documentation: For potency-relevant small molecules, CoAs often include purity by area %, measured water content (e.g., KF), residual solvents, and identity confirmation (MS and/or NMR). None of these are specified here for this item.
Stabilizers: No stabilizer information is provided for this item. If your workflow is sensitive to antioxidants or acid scavengers, verify absence/presence on the CoA.
Lot-to-lot consistency: For SAR or screening campaigns, we recommend documenting lot numbers and, where critical, re-verifying purity/identity by in-house LC–MS.
Fitness for purpose: If you require low-UV or trace-metal specifications (e.g., for bioanalytical assays), consult the CoA/Spec Sheet or contact technical support with your application requirements.
Reaction and Applications
Scope: As a complex natural product, largazole is predominantly used as a biochemical probe and reference standard rather than as a reaction solvent or generic reagent.
Research applications (literature/general)
Epigenetics tool compound: Largazole is a potent, zinc-dependent histone deacetylase (HDAC) inhibitor prodrug; intracellular processing yields the active thiol that coordinates the catalytic Zn2+ in class I HDACs (literature). Used to interrogate transcriptional regulation via histone acetylation.
Chemical biology: Applied in target engagement studies, chemoproteomics, and as a benchmark inhibitor in enzymology assays of HDACs. SAR studies exploit modifications around the thioester side chain and heterocycles.
Analytical reference: Employed as a positive control or reference standard in LC–MS method development and bioanalytical quantification of largazole analogs.
Practical handling tips (literature)
Stock preparation: dissolve in anhydrous DMSO to prepare concentrated stocks; store aliquots to minimize freeze–thaw.
Hydrolysis consideration: avoid strong base or prolonged aqueous exposure prior to use if the intact thioester prodrug is required; conversely, controlled hydrolysis/trans-thioesterification can be used to generate the active thiol when desired.
Redox management: the free thiol (if formed) may oxidize to disulfide; handle under inert atmosphere or include reducing agent for experiments that require the thiol state.
Note: No therapeutic/clinical claims are made; for laboratory research only.
Reaction Conditions
Item-specific reaction parameters are not provided. The following general/literature conditions relate to common chemical manipulations of largazole and its analogs; they are not specifications for this item.
Common transformations (literature)
Thioester to thiol: basic hydrolysis (e.g., Na2CO3–NaHCO3 or NaOH, MeOH/H2O, 0–25 °C) or trans-thioesterification with a soft nucleophile (e.g., cysteamine) under mild conditions. Monitor by LC–MS to avoid overexposure leading to side reactions.
Protection of thiol: if the free thiol is generated, protect as thioacetate or S-alkyl derivatives to prevent oxidation; deprotect under standard conditions prior to assays.
Macrocycle modifications: amide couplings (HATU/EDCI with hindered bases) at side-chain termini; mild conditions (rt to 40 °C) preferred to preserve sensitive motifs.
Hydrogenation/isomerization of the side-chain alkene on suitable precursors using Pd/C (1–10 wt%) at 1 atm H2, rt to 40 °C, solvent EtOH/EtOAc.
General practices
Solvents: anhydrous DMSO, DMF, CH2Cl2, MeCN, or MeOH commonly used depending on step; avoid strong base or prolonged aqueous conditions when the intact thioester must be retained.
Atmosphere: inert gas (N2/Ar) for operations involving the free thiol to mitigate oxidation.
Workup: rapid aqueous quench and extraction with EtOAc; minimize basic aqueous exposure.
Safety and Handling
Item-specific safety data
GHS classification: Not specified for this item; refer to SDS.
Signal word / Pictograms / H-statements: Not specified for this item; refer to SDS.
General laboratory safety guidance (non-authoritative; defer to SDS)
PPE: wear appropriate lab coat, safety glasses, and chemically resistant gloves. Handle powders/solids in a fume hood to avoid inhalation and ensure containment.
Avoid exposure: prevent ingestion, inhalation, and skin/eye contact. Wash thoroughly after handling.
Incompatibilities: strong bases, nucleophiles, and prolonged aqueous exposure can promote thioester hydrolysis to the thiol (literature). Oxidants can convert the thiol (if generated) to disulfides.
Handling risks specific to functional groups (literature):
Thioesters can be irritants; hydrolysis generates free thiols that may have strong odor and can oxidize.
Sensitive to strong base and to extended exposure to moisture; maintain dry conditions for solid handling and solution storage when feasible.
First aid (overview): in case of contact, rinse affected area with water for at least 15 minutes and seek medical attention as needed. If inhaled, move to fresh air. If ingested, rinse mouth; do not induce vomiting; seek medical attention. Always follow institutional SOPs.
Waste: collect unused material and contaminated disposables in appropriate hazardous organic waste streams per local regulations.
Authoritative safety information is provided in the Safety Data Sheet (SDS) for this product.
Solvent Selection
Applicability: Largazole is a complex, largely non-volatile macrocyclic small molecule. Solvent selection pertains to dissolution for stock solutions and assay/media spiking rather than use as a reaction solvent.
Primary stock solvent: DMSO is the standard due to high solvating power for polar, heteroatom-rich natural products and compatibility with screening assays.
Secondary solvents: methanol, ethanol, or acetonitrile can dissolve largazole at lower concentrations; co-solvent strategies (e.g., DMSO to 0.1–1% v/v in aqueous buffers) help achieve working solutions (literature).
Aqueous media: direct aqueous solubility is limited. Use co-solvent or complexing carriers (e.g., cyclodextrins, serum proteins) as permissible for the assay.
Polarity/profile: amphiphilic macrocycle with multiple H-bond donors/acceptors; favors polar aprotic or protic organic solvents.
Comparison (literature)
DMSO: highest solubility; broadly assay-compatible up to 0.1–1% v/v final.
MeOH/EtOH: miscible with water; moderate solubility; volatility can assist solvent exchange.
ACN: good for LC–MS sample prep; moderate solubility; lower viscosity than DMSO.
Practical tips
Filter 0.22 µm if particulate persists; avoid aqueous base that can hydrolyze the thioester.
Minimize freeze–thaw and air exposure for solutions containing the free thiol (if generated) to limit oxidation.
Storage and Reconstitution
Item-specific storage
Storage conditions: Room temperature (as provided in Product Data). Protect from moisture. For long-term solution storage, cooler temperatures may be beneficial; verify stability for your use-case.
Shipped in: Not specified for this item; refer to CoA/Spec Sheet.
Reconstitution (general guidance; not a specification)
Solvents: Dissolve in anhydrous DMSO to prepare a concentrated stock. Alternative solvents include methanol, ethanol, or acetonitrile where compatible.
Concentration: Choose stock concentration to minimize freeze–thaw and to achieve low final co-solvent in assays. Filter-sterilize (0.22 µm) if particulate is observed.
Aliquoting: Dispense single-use aliquots into airtight vials or PCR tubes to limit air/moisture exposure.
Solution handling (literature)
Stability: The thioester group can hydrolyze under basic or aqueous conditions; the free thiol (if formed) may oxidize to disulfide. Store solutions under inert atmosphere and minimize light/air exposure when feasible.
Freeze–thaw: Avoid repeated cycles; thaw on ice or at room temperature and use promptly.
Always consult the CoA and SDS for lot-specific details and stability information.
Structure and Identity
Item-specific identifiers (from Product Data)
SKU: L998561
Product name: Largazole
CAS: 1009815-87-5
PubChem CID: 24757913
InChIKey: 17247 (as provided)
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 description (literature/general)
Largazole is a marine natural-product macrocyclic depsipeptide. The macrocycle contains a peptide–ester linkage (depsipeptide), a thiazole and a thiazoline heteroaromatic/heterocyclic motif, and a pendant thioester side chain that serves as a prodrug for a free thiol.
Stereochemistry: multiple defined stereocenters in the macrocycle and side chain (literature), conferring a well-defined 3D conformation important for target engagement.
Functional groups: thioester (prodrug), amide(s), ester, heteroaromatics (thiazole), heterocycles (thiazoline), and alkene functionality. The thioester can be hydrolyzed or trans-thioesterified to the active thiol (literature).
2D depiction in words: a 16-membered (approx.) macrocyclic ring formed by an ester linkage between a hydroxy acid fragment and a peptide backbone, bearing a thiazole–thiazoline fragment on one segment of the ring and an exocyclic alkenyl thioester arm terminating in a thioester moiety.
Synthetic Utility
Scope: Largazole is principally a target molecule and probe; however, its structure offers several handles for derivatization and SAR exploration (literature/general).
Key functional elements and reactivity (literature)
Thioester prodrug: amenable to exchange/hydrolysis to the corresponding thiol; site for installing alternative promoieties (e.g., carbamates, carbonates, or varied thioesters) to tune permeability and release kinetics.
Heterocycles (thiazole/thiazoline): can be modified via halogenation, metalation, or substitution on precursors during total synthesis to explore electronic effects on binding.
Macrocyclic depsipeptide: the ester linkage can be replaced by amide (lactam) to generate “lactamized” analogs with altered rigidity and metabolic stability.
Side-chain alkene: suitable for hydrogenation, hydroboration–oxidation, or cross-metathesis in precursor stages to adjust geometry and steric profile.
Retrosynthetic value (literature)
Modular assembly: typical routes use fragment coupling (peptide fragment + heterocycle fragment + side-chain thioester), macrolactonization/lactamization, and late-stage acylation to install the thioester.
Tagged analogs: Incorporation of photoaffinity or reporter tags (e.g., diazirines, alkynes) on the side chain enables chemoproteomic profiling while retaining HDAC engagement.
Use as a standard
Employed as a benchmark in analytical methods (LC–MS/HRMS) and to calibrate bioassays when comparing new analogs or batch-to-batch activity.
Target Specificity
Only item-specific target information may be listed here. No target specificity data are provided for this catalog item. Refer to the CoA/Spec Sheet or primary literature for isoform-resolved binding/inhibition data generated under your assay conditions.
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