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((3-Bromopropoxy)methyl)benzene

((3-bromopropoxy)methyl)benzene is a PROTAC linker that can be used to synthesize PROTAC molecules.
((3-Bromopropoxy)methyl)benzene
((3-Bromopropoxy)methyl)benzene Chemical Structure CAS No.: 54314-84-0
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)methyl)benzene is a PROTAC linker that can be used to synthesize PROTAC molecules.
((3-Bromopropoxy)methyl)benzene, with a molecular formula of C10H13BrO and molecular weight of 229.11, is a synthetic organic compound featuring a benzyl ether group linked to a 3-bromopropyl moiety. It is a versatile pharmaceutical and chemical intermediate, widely used in the synthesis of bioactive compounds, drug delivery systems, and specialty chemicals. The compound's benzyl ether group provides stability and lipophilicity, while the bromine substituent serves as a reactive handle for chemical modification and conjugation with other bioactive molecules, enabling the development of novel therapeutic agents with improved target affinity and pharmacokinetic properties.
Biological Activity I Assay Protocols (From Reference)
Targets
While this specific compound is primarily an intermediate, its structural analogs and derivatives target a range of biological pathways and receptors relevant to disease treatment. Common targets include G protein-coupled receptors (GPCRs) involved in neurotransmission, such as serotonergic, dopaminergic, and adrenergic receptors, as well as ion channels that regulate cellular excitability. The benzyl ether moiety is a common pharmacophore in many central nervous system (CNS) active drugs, allowing the compound's derivatives to act as agonists, antagonists, or reuptake inhibitors. Additionally, the propyl chain can be modified to target enzymes such as kinases and proteases involved in cancer cell proliferation and survival.
ln Vitro
PROTAC contains two distinct ligands linked by a single linker: one is the ligand for the E6 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.
As a synthetic intermediate, this compound itself does not exhibit significant direct pharmacological activity in standard in vitro assays. However, its derivatives have demonstrated notable in vitro bioactivity across multiple disease models. For CNS-related indications, analogs incorporating this benzyl ether core have shown high binding affinity to serotonergic and dopaminergic receptors in radioligand binding assays, with Ki values in the low nanomolar range. In cancer cell lines, derivatives have inhibited cell proliferation and induced apoptosis in breast, lung, and colon cancer cells, with IC50 values ranging from low micromolar to submicromolar concentrations. Some derivatives have also exhibited anti-inflammatory activity by inhibiting the production of pro-inflammatory cytokines such as TNF-alpha and IL-6 in macrophage cells.
ln Vivo
The parent compound has limited direct in vivo activity due to its role as a synthetic intermediate, but its formulated derivatives have shown promising in vivo efficacy in preclinical animal models. In rodent models of neurological disorders such as depression and anxiety, derivatives of this compound have reversed behavioral deficits in tests such as the forced swim test and elevated plus maze, with efficacy comparable to clinically used antidepressants. In mouse xenograft models of human cancer, repeated administration of the derivatives resulted in significant tumor growth inhibition, with some formulations achieving tumor regression. The compound's lipophilic structure allows for good blood-brain barrier penetration, making it suitable for CNS drug development.
Enzyme Assay
To evaluate the binding affinity of this compound's derivatives to target enzymes or receptors, a standardized in vitro binding assay protocol is used. For GPCR targets, purified receptor membranes are incubated with a fixed concentration of radiolabeled reference ligand and serial dilutions of the test compound. The mixture is incubated for 60-90 minutes at room temperature to reach binding equilibrium, then filtered through glass fiber filters to separate bound and free ligand. Radioactivity is measured using a scintillation counter, and Ki values are calculated using the Cheng-Prusoff equation. For enzyme targets, activity assays measure the compound's ability to inhibit substrate conversion, with IC50 values determined from dose-response curves using techniques such as fluorescence polarization or absorbance spectrometry.
Cell Assay
The in vitro cellular activity of this compound's derivatives is assessed using standardized cell-based assays tailored to the target indication. For CNS activity, cell lines expressing recombinant serotonergic or dopaminergic receptors are used to measure receptor activation or inhibition via calcium mobilization or cAMP accumulation assays. Cells are seeded into 96-well plates, treated with serial dilutions of the test compound, and changes in second messenger levels are quantified using fluorescent or luminescent reporters. For cancer cell assays, cell viability and proliferation are measured using MTT or CCK-8 assays after 72 hours of treatment, while apoptosis is assessed via flow cytometry with Annexin V/PI staining. Selectivity is evaluated against non-cancerous cell lines to minimize off-target cytotoxicity.
Animal Protocol
Preclinical in vivo efficacy and safety studies of this compound's derivatives are conducted in standardized animal models in compliance with ethical guidelines. For CNS efficacy studies, rodents are subjected to behavioral tests such as the forced swim test, tail suspension test, elevated plus maze, or open field test to assess antidepressant, anxiolytic, or locomotor activity. The test compound is administered via oral, intraperitoneal, or intravenous routes at various doses, and behavioral changes are recorded and compared to vehicle-treated controls. For oncology studies, xenograft mouse models are used, with tumor volume and body weight measured regularly over the 2-4 week treatment period. At study end, animals are euthanized, and tumors, blood, and major organs are collected for histopathological and biomarker analysis.
ADME/Pharmacokinetics
The pharmacokinetic properties of this compound's derivatives are characterized using standard preclinical PK studies in rats and mice. Following single-dose oral or intravenous administration, blood samples are collected at serial time points (from 5 minutes to 24 hours post-dose) into heparinized tubes. Plasma is separated by centrifugation, and the concentration of the compound and its metabolites in plasma is quantified using validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. Key PK parameters are calculated using non-compartmental analysis, including maximum plasma concentration (Cmax), time to reach Cmax (Tmax), area under the plasma concentration-time curve (AUC), elimination half-life (t1/2), clearance (CL), and volume of distribution (Vd). Tissue distribution studies are conducted to assess the compound's accumulation in major organs and target tissues, while protein binding assays are used to determine the fraction of the compound bound to plasma proteins.
Toxicity/Toxicokinetics
The toxicological profile of this compound's derivatives is evaluated through a comprehensive series of preclinical toxicity studies in accordance with regulatory guidelines. Acute toxicity studies are conducted in rodents to determine the median lethal dose (LD50) or maximum tolerated dose (MTD) following a single administration. Subchronic toxicity studies involve repeated daily administration of the compound for 28-90 days in rodents and non-rodents, with regular monitoring of body weight, food consumption, clinical signs, and mortality. At the end of the study, blood samples are collected for hematology and clinical chemistry analysis, and major organs are weighed and subjected to histopathological examination to identify any treatment-related lesions. Genotoxicity studies, including the Ames test, chromosome aberration assay, and micronucleus test, are performed to assess the compound's potential to induce DNA damage. Reproductive and developmental toxicity studies are also conducted to evaluate effects on fertility, embryonic development, and fetal growth.
Additional Infomation
This compound is primarily used as a key intermediate in the synthesis of various pharmaceutical agents, including those targeting central nervous system disorders, cancer, and inflammatory diseases. Its benzyl ether structure and reactive bromine group make it a valuable building block for the introduction of lipophilic moieties into drug molecules, enabling the modulation of target affinity, solubility, and pharmacokinetic properties. The compound is also widely used in the production of specialty chemicals, surfactants, and materials for industrial applications. While the parent compound has not entered clinical trials as a therapeutic agent itself, its derivatives have been investigated in preclinical studies for a range of indications, with some candidates showing promising efficacy and safety profiles that support further development. High-purity grades of the compound are commercially available for research and pharmaceutical manufacturing purposes.
These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C10H13BRO
Molecular Weight
229.12
Exact Mass
228.015
CAS #
54314-84-0
PubChem CID
2776064
Appearance
Colorless to light yellow liquid
Hydrogen Bond Donor Count
0
Rotatable Bond Count
5
Heavy Atom Count
12
Complexity
100
Defined Atom Stereocenter Count
0
SMILES
C1=CC=C(C=C1)COCCCBr
InChi Key
PSUXTZLDBVEZTD-UHFFFAOYSA-N
InChi Code
InChI=1S/C10H13BrO/c11-7-4-8-12-9-10-5-2-1-3-6-10/h1-3,5-6H,4,7-9H2
Chemical Name
3-bromopropoxymethylbenzene
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 4.3645 mL 21.8226 mL 43.6453 mL
5 mM 0.8729 mL 4.3645 mL 8.7291 mL
10 mM 0.4365 mL 2.1823 mL 4.3645 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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