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3-Chloroindole

3-Chloroindole (ZINC6117681) is a natural product derived from marine sources, specifically found in Ptychodera flava.
3-Chloroindole
3-Chloroindole Chemical Structure CAS No.: 16863-96-0
Product category: Microorganisms
This product is for research use only, not for human use. We do not sell to patients.
Official Supplier of:
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Product Description
3-Chloroindole (ZINC6117681) is a natural product derived from marine sources, specifically found in Ptychodera flava.
3-Chloroindole (C₈H₆ClN, CAS 16863-96-0) is a halogenated indole derivative that occurs naturally in marine organisms, specifically in the acorn worm Ptychodera flava. It is a pale yellow to yellow-brown crystalline solid with a melting point of 94-95degC and a predicted LogP of 3.04. This compound serves as a privileged chemical scaffold in medicinal chemistry and as a key synthetic intermediate for developing novel therapeutic agents, particularly indole-imidazole hybrids for tackling antibiotic resistance.
Biological Activity I Assay Protocols (From Reference)
Targets
No specific biological target. 3-Chloroindole is a synthetic intermediate and a natural product, not a drug. Its biological activity, if any, is not well characterized. However, indole derivatives are known to interact with various biological targets, including serotonin receptors, tubulin, and DNA. The chlorine atom at the 3-position provides a reactive site for further functionalization to create more complex bioactive molecules.
ln Vitro
Not applicable, as 3-chloroindole is not a drug candidate with intrinsic activity. The compound is used as a starting material in the synthesis of various biologically active molecules, including antibacterial agents (indole-imidazole hybrids), anticancer agents, and antivirals. The potency of the resulting derivatives depends on the nature and position of the substituents added to the indole core.
ln Vivo
Not applicable; no in vivo studies of 3-chloroindole as a drug candidate have been reported. The compound may be used in animal studies as a reference or as a precursor to labeled compounds for metabolic studies, but its own in vivo behavior has not been extensively characterized.
Enzyme Assay
Not applicable, as 3-chloroindole does not act via a specific enzyme or receptor. For the characterization of new 3-chloroindole-based enzyme inhibitors, the compound is used as a starting material. The enzymatic assay would depend on the target enzyme. For example, if a 3-chloroindole derivative is a monoamine oxidase B (MAO-B) inhibitor, the enzyme is incubated with the derivative in buffer at 37degC, and the production of a fluorescent product is measured.
Cell Assay
In cell culture, 3-chloroindole is typically tested as a part of a more complex derivative, not as a free compound. For general cytotoxicity screening, cells (e.g., HeLa, MCF-7) are treated with 3-chloroindole (1-100 uM) for 48-72 hours. Cell viability is measured by MTT or CellTiter-Glo assays. The compound is typically non-cytotoxic at concentrations up to 50 uM.
Animal Protocol
Not applicable, as 3-chloroindole is not a drug candidate for in vivo testing. If used as a reference compound in a pharmacokinetic study, it would be administered to mice or rats by oral gavage or intravenous injection. Blood samples are collected at various time points, and the concentration of 3-chloroindole and its metabolites (primarily hydroxylated derivatives at the 5- or 6-position of the indole ring) is measured by HPLC-UV or LC-MS.
ADME/Pharmacokinetics
No pharmacokinetic data is available for 3-chloroindole specifically. However, as a small, neutral, lipophilic aromatic molecule (MW 151.59, LogP 3.04), it is predicted to have moderate oral bioavailability, a short plasma half-life (1-3 hours) due to rapid phase I oxidation (primarily at the 5- and 6-positions on the indole ring) and phase II glucuronidation, and high plasma protein binding (>90%).
Toxicity/Toxicokinetics
The acute oral toxicity of 3-chloroindole is unknown. Based on its similarity to other halogenated indoles, it is likely to be moderately toxic. Indole itself has an oral LD50 of 1,000-2,000 mg/kg in rats. 3-Chloroindole may cause skin, eye, and respiratory tract irritation. Standard laboratory safety precautions (gloves, lab coat, goggles, fume hood) should be used when handling this compound.
Additional Infomation
Reports indicate that 3-chloro-1H-indole has been found in chokeberry, and relevant data is available for reference.
Not applicable. 3-Chloroindole is a research chemical, not a drug. It has no FDA approval for any therapeutic use. It is widely used as a building block in medicinal chemistry for the design of bioactive compounds. Indoles are a privileged structure in drug discovery, and many FDA-approved drugs contain an indole moiety, including the antiemetic ondansetron (5-HT3 antagonist), the anti-migraine drug sumatriptan (5-HT1B/1D agonist), and the anti-inflammatory drug indomethacin (COX inhibitor). 3-Chloroindole is a valuable synthetic intermediate for accessing these and other biologically active indole derivatives.
These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Exact Mass
151.019
CAS #
16863-96-0
PubChem CID
177790
Appearance
Solid Powder
Density
1.3±0.1 g/cm3
Boiling Point
293.0±13.0 °C at 760 mmHg
Flash Point
158.9±5.4 °C
Vapour Pressure
0.0±0.6 mmHg at 25°C
Index of Refraction
1.688
LogP
3.04
Hydrogen Bond Donor Count
1
Rotatable Bond Count
0
Heavy Atom Count
10
Complexity
126
Defined Atom Stereocenter Count
0
InChi Key
GVSMQKKMAYLKMM-UHFFFAOYSA-N
InChi Code
InChI=1S/C8H6ClN/c9-7-5-10-8-4-2-1-3-6(7)8/h1-5,10H
Chemical Name
3-chloro-1H-indole
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

Note: (1). 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)
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.)
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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