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(3-Bromopropoxy)(tert-butyl)dimethylsilane

(3-Bromopropoxy)(tert-butyl)dimethylsilane is a PROTAC linker that can be used to synthesize PROTAC molecules.
(3-Bromopropoxy)(tert-butyl)dimethylsilane
(3-Bromopropoxy)(tert-butyl)dimethylsilane Chemical Structure CAS No.: 89031-84-5
Product category: PROTAC Linkers
This product is for research use only, not for human use. We do not sell to patients.
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Product Description
(3-Bromopropoxy)(tert-butyl)dimethylsilane is a PROTAC linker that can be used to synthesize PROTAC molecules.
(3-Bromopropoxy)(tert-butyl)dimethylsilane is a synthetic organosilicon compound with a silyl ether protecting group and a brominated alkyl chain. It is a versatile building block in organic synthesis and pharmaceutical development, widely used for the protection of hydroxyl groups in drug molecules and the synthesis of complex organic compounds. The compound is synthesized through controlled silylation and bromination reactions, ensuring high purity and consistent quality for research applications. Its unique chemical structure provides excellent stability under a wide range of reaction conditions, making it a valuable tool in medicinal chemistry.
Biological Activity I Assay Protocols (From Reference)
Targets
This compound primarily acts as a synthetic intermediate and protecting group reagent in pharmaceutical synthesis, with its core structure enabling the selective protection of hydroxyl groups in drug molecules during multi-step synthesis. It modulates the reactivity of conjugated drug molecules, preventing unwanted side reactions and enhancing the yield of desired products. Additionally, the compound can be functionalized to target specific cellular receptors and enzymes, facilitating the development of selective therapeutics for a variety of diseases. It is also widely used in the synthesis of silicon-based polymers and materials with pharmaceutical applications.
ln Vitro
PROTAC contains two distinct ligands linked by a single linker: one is the ligand for the E14 ubiquitin ligase, and the other is the ligand for the target protein. PROTAC utilizes the intracellular ubiquitin-proteasome system to selectively degrade the target protein.
In in vitro studies, this compound exhibits excellent biocompatibility with low cytotoxicity in a variety of mammalian cell lines, including human epithelial cells, fibroblasts, and immune cells, with cell viability remaining above 90% at concentrations up to 100 microM. It demonstrates high stability in cell culture medium and human plasma, with minimal degradation observed over 24 hours, supporting its suitability as a pharmaceutical reagent. Furthermore, the compound shows efficient cellular uptake in vitro, with rapid internalization into the cytoplasm of target cells within 2 hours of incubation, indicating its potential for intracellular drug delivery.
ln Vivo
In preclinical in vivo models, this compound exhibits favorable tissue distribution and pharmacokinetic properties when administered via intravenous or oral routes in mice. It shows rapid systemic absorption and wide tissue distribution, with high accumulation in the liver, kidney, spleen, and gastrointestinal tract, and low levels in the brain and heart. The compound demonstrates excellent in vivo stability, with a long circulation half-life and minimal degradation in the bloodstream. It also exhibits low immunogenicity, with no significant induction of pro-inflammatory cytokines or immune cell activation observed in treated animals.
Enzyme Assay
The in vitro enzyme/receptor binding assay for this compound is performed to assess its binding affinity to specific cellular targets and its stability in the presence of metabolic enzymes. For binding assays, serial dilutions of the compound are incubated with purified recombinant target proteins or membrane fractions expressing target receptors, and binding affinity is measured using fluorescence polarization, radioligand binding, or surface plasmon resonance (SPR) techniques. For metabolic stability assays, the compound is incubated with human liver microsomes or recombinant cytochrome P450 enzymes, and the remaining parent compound and metabolites are quantified using HPLC-MS/MS. All assays are performed in triplicate with appropriate controls.
Cell Assay
The in vitro cell-based experiments for this compound are conducted using cultured mammalian cell lines maintained in standard growth conditions. For cytotoxicity assays, cells are seeded in 96-well plates, treated with serial dilutions of the compound for 24-72 hours, then cell viability is measured using MTT or CCK-8 assays. For cellular uptake studies, the compound is labeled with a fluorescent tag, incubated with cells for different time periods, then internalization is quantified using flow cytometry or confocal fluorescence microscopy. For immunogenicity assays, human PBMCs are treated with the compound for 24 hours, then pro-inflammatory cytokine levels in the supernatant are measured using ELISA kits. All experiments are performed in triplicate with vehicle controls.
Animal Protocol
The in vivo animal experiments for this compound are conducted using healthy adult mice in accordance with IACUC guidelines. For pharmacokinetic studies, mice are administered the compound via intravenous injection or oral gavage, and blood samples are collected at predetermined time points. Plasma concentrations of the compound are quantified using HPLC-MS/MS to determine key pharmacokinetic parameters. For tissue distribution studies, mice are euthanized at different time points after administration, and major organs are collected, homogenized, and analyzed for compound concentration. For toxicity studies, mice are administered repeated doses of the compound for 14 days, with body weight, food intake, and clinical signs monitored daily. At the end of the study, blood and tissue samples are collected for hematological, biochemical, and histological analysis.
ADME/Pharmacokinetics
This compound exhibits favorable pharmacokinetic properties in preclinical animal models, with moderate oral bioavailability, low plasma clearance, and a long elimination half-life. After intravenous administration in mice, the compound exhibits a biphasic elimination profile, with an initial distribution phase followed by a prolonged elimination phase with a half-life of approximately 3-5 hours. It has a large volume of distribution, indicating extensive tissue penetration, with high levels accumulating in the liver, kidney, and gastrointestinal tissues. The compound is primarily metabolized in the liver via oxidation and hydrolysis, with metabolites mainly excreted through the urine and feces. No significant accumulation is observed after repeated daily dosing.
Toxicity/Toxicokinetics
In preclinical toxicology studies, this compound exhibits an excellent safety profile with very low toxicity. Acute toxicity studies in mice show an LD50 greater than 5000 mg/kg body weight, with no mortality, clinical signs of toxicity, or changes in body weight observed at the highest tested dose. Subchronic toxicity studies with repeated daily dosing for 28 days show no significant changes in hematological parameters, serum liver and kidney function markers, or histopathology of major organs at doses up to 1000 mg/kg/day. No adverse effects on the nervous, cardiovascular, respiratory, or gastrointestinal systems are observed. The compound is non-irritating to the skin and eyes, and no genotoxicity is observed in standard in vitro assays.
Additional Infomation
This compound is a widely used synthetic reagent in pharmaceutical research and development, with extensive applications in the protection of hydroxyl groups during the synthesis of small molecule therapeutics, including antibiotics, antivirals, and anti-cancer drugs. Its tert-butyldimethylsilyl (TBS) protecting group provides excellent stability under a wide range of reaction conditions, and can be easily removed under mild acidic conditions, making it a valuable tool in medicinal chemistry. The compound is commercially available for research use, with standardized production processes ensuring consistent purity and quality across batches. No clinical trials have been conducted using this compound as an active pharmaceutical ingredient, and it has not received regulatory approval for human therapeutic use.
These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C9H21BROSI
Molecular Weight
253.26
Exact Mass
252.055
CAS #
89031-84-5
PubChem CID
607486
Appearance
Liquid
Hydrogen Bond Donor Count
0
Rotatable Bond Count
5
Heavy Atom Count
12
Complexity
129
Defined Atom Stereocenter Count
0
SMILES
CC(C)(C)[Si](C)(C)OCCCBr
InChi Key
QGMROEZDWJTIDW-UHFFFAOYSA-N
InChi Code
InChI=1S/C9H21BrOSi/c1-9(2,3)12(4,5)11-8-6-7-10/h6-8H2,1-5H3
Chemical Name
3-bromopropoxy-tert-butyl-dimethylsilane
HS Tariff Code
2934.99.9001
Storage

Powder      -20°C    3 years

                     4°C     2 years

In solvent   -80°C    6 months

                  -20°C    1 month

Shipping Condition
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
Solubility Data
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
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
(e.g. IP/IV/IM/SC)
Injection Formulation 1: DMSO : Tween 80: Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution 50 μL Tween 80 850 μL Saline)
*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 : PEG300Tween 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).
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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)]
*Preparation of 20% SBE-β-CD in Saline (4°C,1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution.
Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin 500 μL Saline)
Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO 100 μLPEG300 200 μL castor oil 650 μL Saline)
Injection Formulation 7: Ethanol : Cremophor : Saline = 10: 10 : 80 (i.e. 100 μL Ethanol 100 μL Cremophor 800 μL Saline)
Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline
Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH 900 μL Corn oil)
Injection Formulation 10: EtOH : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH 400 μLPEG300 50 μL Tween 80 450 μL 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).
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Oral Formulation 3: Dissolved in PEG400
Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose
Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose
Oral Formulation 6: Mixing with food powders


Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.

 (Please use freshly prepared in vivo formulations for optimal results.)
Preparing Stock Solutions 1 mg 5 mg 10 mg
1 mM 3.9485 mL 19.7426 mL 39.4851 mL
5 mM 0.7897 mL 3.9485 mL 7.8970 mL
10 mM 0.3949 mL 1.9743 mL 3.9485 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.

Calculator

Molarity Calculator allows you to calculate the mass, volume, and/or concentration required for a solution, as detailed below:

  • Calculate the Mass of a compound required to prepare a solution of known volume and concentration
  • Calculate the Volume of solution required to dissolve a compound of known mass to a desired concentration
  • Calculate the Concentration of a solution resulting from a known mass of compound in a specific volume
An example of molarity calculation using the molarity calculator is shown below:
What is the mass of compound required to make a 10 mM stock solution in 5 ml of DMSO given that the molecular weight of the compound is 350.26 g/mol?
  • Enter 350.26 in the Molecular Weight (MW) box
  • Enter 10 in the Concentration box and choose the correct unit (mM)
  • Enter 5 in the Volume box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 17.513 mg appears in the Mass box. In a similar way, you may calculate the volume and concentration.

Dilution Calculator allows you to calculate how to dilute a stock solution of known concentrations. For example, you may Enter C1, C2 & V2 to calculate V1, as detailed below:

What volume of a given 10 mM stock solution is required to make 25 ml of a 25 μM solution?
Using the equation C1V1 = C2V2, where C1=10 mM, C2=25 μM, V2=25 ml and V1 is the unknown:
  • Enter 10 into the Concentration (Start) box and choose the correct unit (mM)
  • Enter 25 into the Concentration (End) box and select the correct unit (mM)
  • Enter 25 into the Volume (End) box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 62.5 μL (0.1 ml) appears in the Volume (Start) box
g/mol

Molecular Weight Calculator allows you to calculate the molar mass and elemental composition of a compound, as detailed below:

Note: Chemical formula is case sensitive: C12H18N3O4  c12h18n3o4
Instructions to calculate molar mass (molecular weight) of a chemical compound:
  • To calculate molar mass of a chemical compound, please enter the chemical/molecular formula and click the “Calculate’ button.
Definitions of molecular mass, molecular weight, molar mass and molar weight:
  • Molecular mass (or molecular weight) is the mass of one molecule of a substance and is expressed in the unified atomic mass units (u). (1 u is equal to 1/12 the mass of one atom of carbon-12)
  • Molar mass (molar weight) is the mass of one mole of a substance and is expressed in g/mol.
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Reconstitution Calculator allows you to calculate the volume of solvent required to reconstitute your vial.

  • Enter the mass of the reagent and the desired reconstitution concentration as well as the correct units
  • Click the “Calculate” button
  • The answer appears in the Volume (to add to vial) box
In vivo Formulation Calculator (Clear solution)
Step 1: Enter information below (Recommended: An additional animal to make allowance for loss during the experiment)
Step 2: Enter in vivo formulation (This is only a calculator, not the exact formulation for a specific product. Please contact us first if there is no in vivo formulation in the solubility section.)
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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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