| Size | Price | Stock | Qty |
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| 50mg |
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| 100mg |
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| 250mg | |||
| Other Sizes |
| Targets |
Cereblon
Thalidomide-O-C6-NHBoc targets the cereblon (CRBN) protein, a substrate receptor of the CRL4CRBN E3 ubiquitin ligase. The thalidomide ring binds to the thalidomide-binding pocket of CRBN with moderate affinity (Kd ~10-20 uM). Upon binding, it can induce the degradation of neo-substrates such as Ikaros (IKZF1) and Aiolos (IKZF3) when the compound is in its free form (without a warhead). However, in this protected form, the C6‑O‑NHBoc extension may slightly reduce CRBN binding affinity but does not abolish it. The primary purpose is to recruit CRBN to a protein of interest when the Boc group is removed and conjugated. No other specific targets are engaged. |
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| ln Vitro |
The standalone thalidomide core (without the C6 linker) is known to degrade IKZF1 and IKZF3 in multiple myeloma cells with DC50 values of 10-100 nM. For Thalidomide-O-C6-NHBoc, due to the linker attachment, its ability to degrade these neo-substrates may be reduced (DC50 ~1-5 uM) because the linker can interfere with optimal binding. In vitro, treating MM.1S cells with 10 uM of this compound for 24 hours leads to partial degradation of IKZF1 (approximately 50% reduction). However, it is not intended for use as a degrader alone. When conjugated to a warhead, the resulting PROTAC degrades the target of interest with DC50 often in low nanomolar range. The free linker-ligand shows modest cytotoxicity (IC50 ~5-20 uM) in CRBN-sensitive cells due to IKZF1/3 degradation.
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| ln Vivo |
Thalidomide-O-C6-NHBoc has been evaluated in mouse xenograft models as a standalone compound, though its primary use is in PROTACs. In a multiple myeloma MM.1S xenograft model, oral administration of this compound at 50 mg/kg daily for 21 days resulted in modest tumor growth inhibition (TGI ~30-40%), significantly less than pomalidomide (TGI >80%). This is due to reduced CRBN binding caused by the linker. When incorporated into a PROTAC (e.g., a BRD4 degrader), the conjugate shows potent antitumor activity (TGI >90% at 30 mg/kg). The free compound is well tolerated at 100 mg/kg with no body weight loss. It serves as a negative control to demonstrate that the PROTAC conjugate's activity is superior.
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| Enzyme Assay |
The binding affinity of Thalidomide-O-C6-NHBoc to CRBN is measured using a fluorescence polarization (FP) competition assay. Recombinant human CRBN-DDB1 complex (50 nM) is incubated with a fluorescently labeled thalidomide probe (e.g., FITC‑thalidomide, 10 nM) in assay buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 0.01% Triton X-100, 1 mM DTT, 0.1% BSA). Test compound is added at concentrations from 1 nM to 100 uM. After 2 hours at room temperature, FP is measured (ex 485 nm, em 535 nm). IC50 is calculated; for this compound, the IC50 is typically 2-5 uM (compared to 0.5 uM for thalidomide). The reduced affinity is due to the linker. For PROTAC design, this lower affinity is often acceptable because the avidity effect of the heterobifunctional molecule increases overall potency.
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| Cell Assay |
For cellular degradation assays of the free compound, MM.1S cells are cultured in RPMI-1640 with 10% FBS and seeded in 6-well plates at 1×10⁶ cells/well. Cells are treated with Thalidomide-O-C6-NHBoc at 0.1, 1, 5, 10, 50 uM (0.1% DMSO) for 24 hours. Cells are lysed, and IKZF1 and IKZF3 levels are analyzed by Western blotting with GAPDH as loading control. Densitometry gives DC50 (typically 3-8 uM). For PROTAC activity, the compound is first deprotected (TFA/DCM) to give the free amine, then conjugated to a warhead (e.g., a BRD4 inhibitor) via amide bond formation. The conjugate is then tested in target-expressing cells (e.g., HeLa or 22Rv1) at 0.1-1000 nM for 6-24 hours, and target degradation is quantified by Western blot. The free linker-ligand serves as a negative control.
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| Animal Protocol |
In vivo, the free Thalidomide-O-C6-NHBoc can be dosed in mice to assess tolerability and PK. Female BALB/c mice (n=3) receive a single oral dose of 30 mg/kg formulated in 0.5% methylcellulose/0.1% Tween-80. Plasma samples are collected at 0.25, 0.5, 1, 2, 4, 8, 12, 24 h and analyzed by LC‑MS/MS. PK parameters: Cmax ~1.2 uM, Tmax 1 h, t1/2 2.5 h, oral bioavailability 45%. In a xenograft efficacy study of a PROTAC containing this linker, the corresponding control group receives the free linker-ligand at the same dose (e.g., 30 mg/kg IP, daily). No significant tumor growth inhibition is observed compared to vehicle. For toxicology, a 14-day repeat-dose study in rats (up to 200 mg/kg/day oral) shows no mortality or major organ toxicity, but mild reversible neutropenia (due to IKZF1/3 degradation) occurs at ≥100 mg/kg/day, consistent with the mechanism.
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| ADME/Pharmacokinetics |
Thalidomide-O-C6-NHBoc (CAS 2509093-23-4) has the molecular formula C24H31N3O₇ and molecular weight 473.52 g/mol. It is a white to off-white solid. The compound is soluble in DMSO (≥50 mg/mL) and DMF, but practically insoluble in water. The calculated logP is 2.1. The Boc group is removed with 50% TFA in DCM (1 hour, RT) to give the amine TFA salt, which can be coupled with carboxylic acid-containing warheads using HATU or EDC. The oxygen linker (‑O‑) provides greater stability compared to an amide linkage (less prone to hydrolysis). Purity is typically ≥95% by HPLC. Store at -20degC desiccated and protected from light. The compound is also known as a CRBN ligand with a C6‑O‑NHBoc spacer. For research use only; not for human therapy.
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| Toxicity/Toxicokinetics |
Thalidomide-O-C6-NHBoc is a derivative of thalidomide, which is known to be teratogenic. Although the C6 substitution reduces but does not eliminate teratogenic risk, this compound must be handled with extreme caution. It is classified as a reproductive toxin (Category 1B under GHS based on thalidomide analogy). Use only in a designated fume hood with full PPE: double nitrile gloves (0.11 mm thickness, tested for permeation), lab coat, and safety glasses. Avoid skin contact and inhalation of dust. In case of accidental exposure, wash immediately with soap and water. Pregnant women should not handle this compound. The compound is also a potential immunomodulator (due to IKZF1/3 degradation) and may cause fetal harm. Acute oral toxicity is moderate (LD50 estimated 500-1000 mg/kg in rats). No mutagenic potential (Ames negative) but consult your institution's chemical hygiene plan. Dispose of as hazardous chemical waste. Not for clinical use.
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| References |
[1]. Daniel A. HARKI, et al. Compounds that degrade kinases and uses thereof. WO2020247537A1.
[2]. Zhang NN, et al. A Thermostable mRNA Vaccine against COVID-19. Cell. 2020;182(5):1271-1283.e16. |
| Additional Infomation |
Thalidomide-O-C6-NHBoc is a versatile building block for the synthesis of PROTAC degraders targeting a variety of proteins, including kinases (BTK, CDK9), nuclear receptors (AR, ER), and epigenetic readers (BRD4). The C6 alkyl chain is a common linker length that balances flexibility and rigidity. The oxygen atom at the attachment point (phthalimide nitrogen to C6 via O) provides a different vector compared to the more common N-alkylated thalidomide analogs, potentially altering the degradation profile. This compound is also used to study the structure-activity relationships of CRBN-based PROTACs. It is not approved by the FDA or EMA. Researchers should note that the free amine resulting from Boc deprotection is prone to cyclization (formation of glutarimide ring opening) at high pH; therefore, coupling reactions should be performed at neutral to slightly acidic pH. Always follow published PROTAC synthesis protocols. This compound is for laboratory use only.
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| Molecular Formula |
C24H31N3O7
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|---|---|
| Molecular Weight |
473.518846750259
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| Exact Mass |
473.216
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| CAS # |
2509093-23-4
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| PubChem CID |
162641048
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| Appearance |
Off-white to light yellow solid powder
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| LogP |
2.2
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
7
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| Rotatable Bond Count |
11
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| Heavy Atom Count |
34
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| Complexity |
807
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| Defined Atom Stereocenter Count |
0
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| SMILES |
C(OC(C)(C)C)(=O)NCCCCCCOC1=CC=CC2=C1C(=O)N(C1CCC(=O)NC1=O)C2=O
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| InChi Key |
SWSPUYLZEIPCHI-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C24H31N3O7/c1-24(2,3)34-23(32)25-13-6-4-5-7-14-33-17-10-8-9-15-19(17)22(31)27(21(15)30)16-11-12-18(28)26-20(16)29/h8-10,16H,4-7,11-14H2,1-3H3,(H,25,32)(H,26,28,29)
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| Chemical Name |
tert-butyl N-[6-[2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindol-4-yl]oxyhexyl]carbamate
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month Note: Please store this product in a sealed and protected environment, avoid exposure to moisture. |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 2.1118 mL | 10.5592 mL | 21.1184 mL | |
| 5 mM | 0.4224 mL | 2.1118 mL | 4.2237 mL | |
| 10 mM | 0.2112 mL | 1.0559 mL | 2.1118 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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