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Indoles

Indoles are a diverse class of organic compounds charactreized by a fused benzene and pyrrole ring system.
They are found in a variety of natural sources and have wide-ranging biological activities.
Indoles play crucial roles in various physiological processes and are important scaffolds in medicinal chemistry, with applications in the development of therapeutic agents for conditions such as neurological disorders, cancer, and inflammation.
Researchers can leverage PubCompare.ai's advanced AI-driven platform to efficiently explore the vast literature on indole synthesis protocols, identify optimal procedures, and accelerate their indole-based research endeavors.

Most cited protocols related to «Indoles»

In addition to the secondary metabolite cluster types supported in the original release of antiSMASH (type I, II and III polyketides, non-ribosomal peptides, terpenes, lantipeptides, bacteriocins, aminoglycosides/aminocyclitols, β-lactams, aminocoumarins, indoles, butyrolactones, ectoines, siderophores, phosphoglycolipids, melanins and a generic class of clusters encoding unusual secondary metabolite biosynthesis genes), version 2.0 adds support for oligosaccharide antibiotics, phenazines, thiopeptides, homoserine lactones, phosphonates and furans. The cluster detection uses the same pHMM rule-based approach as the initial release (17 (link)): in short, the pHMMs are used to detect signature proteins or protein domains that are characteristic for the respective secondary metabolite biosynthetic pathway. Some pHMMs were obtained from PFAM or TIGRFAM. If no suitable pHMMs were available from these databases, custom pHMMs were constructed based on manually curated seed alignments (Supplementary Table S1). These are composed of protein sequences of experimentally characterized biosynthetic enzymes described in literature, as well as their close homologs found in gene clusters from the same type. The models were curated by manually inspecting the output of searches against the non-redundant (nr) database of protein sequences. The seed alignments are available online at http://antismash.secondarymetabolites.org/download.html#extras. After scanning the genome with the pHMM library, antiSMASH evaluates all hits using a set of rules (Supplementary Table S2) that describe the different cluster types. Unlike the hard-coded rules in the initial release of antiSMASH, the detection rules and profile lists are now located in editable TXT files, making it easy for users to add and modify cluster rules in the stand-alone version, e.g. to accommodate newly discovered or proprietary compound classes without code changes. The results of gene cluster predictions by antiSMASH are continuously checked on new data arising from research performed throughout the natural products community, and pHMMs and their cut-offs are regularly updated when either false positives or false negatives become apparent.
The profile-based detection of secondary metabolite clusters has now been augmented by a tighter integration of the generalized PFAM (22 (link)) domain-based ClusterFinder algorithm (Cimermancic et al., in preparation) already included in version 1.0 of antiSMASH. This algorithm performs probabilistic inference of gene clusters by identifying genomic regions with unusually high frequencies of secondary metabolism-associated PFAM domains, and it was designed to detect ‘classical’ as well as less typical and even novel classes of secondary metabolite gene clusters. While antiSMASH 1.0 only generated the output of this algorithm in a static image, version 2.0 displays these additional putative gene clusters along with the other gene clusters in the HTML output. A key advantage of this is that these putative gene clusters will now also be included in the subsequent (Sub)ClusterBlast analyses.
Publication 2013
Amino Acid Sequence Aminocoumarins Aminoglycosides Anabolism Antibiotics Bacteriocins Biosynthetic Pathways Childbirth Classes Enzymes Furans Gene Clusters Generic Drugs Genes Genome Genomic Library homoserine lactone Indoles Lactams Melanins Natural Products Oligosaccharides Peptides Phenazines Phosphonates Polyketides Prognosis Protein Domain Proteins Ribosomes Secondary Metabolism Siderophores Terpenes
SCFAs including acetate, propionate, butyrate, isobutyrate, valerate, and isovalerate were analysed as described previously67 (link). To ensure the homogenicity of the intestine content sample, the freeze-dried samples were prepared using a Vacuum freeze-dryer (Hrist ALPHA 2-4/LSC, Germany) at −80 °C. Briefly, freeze-dried samples (0.5–0.6 g) were weighed into 10 ml centrifuge tubes and mixed with 8 ml ddH2O, homogenised, and centrifuged in sealed tube at 7,000 g and 4 °C for 10 min. A mixture of the supernatant fluid and 25% metaphosphoric acid solution (0.9 and 0.1 ml, respectively) was centrifuged at 20,000 g and 4 °C for 10 min after standing in a 2 ml sealed tube at 4 °C for over 2 h. The supernatant portion was then filtered through a 0.45-μm polysulfone filter and analysed using Agilent 6890 gas chromatography (Agilent Technologies, Inc, Palo Alto, CA, USA) with a flame ionisation detector and a 1.82 m × 0.2 mm I.D. glass column that was packed with 10% SP-1200/1% H3PO4 on the 80/100 Chromosorb W AW (HP, Inc., Boise, ID, USA). The concentration of NH3-N in the supernatant fluid was measured at 550 nm using a UV-2450 spectrophotometer (Shimadzu, Kyoto, Japan)68 . The bioamines including 1,7-heptyl diamine, cadaverine, phenylethylamine, putrescine, trytamine, tyramine, spermidine, and spermine, as well as the indoles and skatoles, were analysed as described previously69 .
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Publication 2016
Acetate Butyrates Cadaverine Diamines Flame Ionization Freezing Gas Chromatography Homozygote IGBP1 protein, human Indoles Intestinal Contents metaphosphoric acid Phenethylamines polysulfone Propionate Putrescine Spermidine Spermine Tyramine Vacuum Valerates
Bacterial strains from glycerol stocks were streaked onto either an LB agar plate or a TSA plate, depending on the medium of their original isolation and grown at 28°C. For each strain, a single colony was used to inoculate 6 mL of liquid LB medium, with and without 5 mM L-tryptophan. For DAB 33B and DAB 39B, liquid TSB (with and without 5 mM L-tryptophan) was used instead due to difficulty growing these two strains on LB medium. After 48 h of growing at 28°C with shaking at 240 rpm, 1 mL of culture was centrifuged for 5 min at 14,000 rpm to collect the supernatant. The original Salkowski assay based on the Gordon and Weber protocol was adapted for a 96-well format (Gordon and Weber, 1951 (link)). In a Corning 96-well clear bottom white plate, 100 μL of the supernatant was added to 200 μL of Salkowski reagent (10 mM FeCl3, 97% reagent grade, and 34.3% perchloric acid, ACS grade) in duplicate. After incubating samples with the Salkowski reagent at room temperature for 30 min, the color change was recorded. A BioTek Synergy HT microplate reader was used to determine the absorbance (O.D.) at a single wavelength of 530 nm. To estimate the amount of indole related compounds at 530 nm, an IAA standard curve was generated by suspending IAA (Gibco Laboratories, Life Technologies, Inc., New York, USA) in 100% acetonitrile at a concentration of 1 mg/mL and diluting in LB medium or TSB to a concentration of 100, 50, 20, 10, 5, and 0 μg/mL. Sterile LB medium (with and without 5 mM L-tryptophan) and sterile TSB (with and without 5 mM L-tryptophan) were used as controls. The concentration of indole related compounds at 530 nm of the sterile control sample, either LB or TSB depending on the bacterial medium used, was subtracted from the concentration of indole related compounds at 530 nm of the bacterial samples to obtain a background subtracted concentration.
A full spectrum analysis from 440 to 600 nm, using a 1 nm interval, was performed to identify the wavelength of maximum absorbance. Full spectrum analysis was performed on bacterial samples grown in liquid LB medium supplemented with 5 mM L-tryptophan whereas free indole and free IAA (as references) were suspended in 100% acetonitrile. The wavelength of maximum absorbance (λmax) was calculated between 460 and 600 nm due to the high background signal observed at wavelengths shorter than 460 nm from addition of the Salkowski reagent to LB medium.
For determining the specificity of the Salkowski reagent, we tested IAA, indole-acetamide (IAM), indole-3-pyruvatic acid (IPA), ILA, indole-3-butyric acid (IBA), indole, indoxyl sulfate, tryptophol, and tryptophan. The compounds were suspended in 100% acetonitrile, HPLC grade, before diluting in LB medium, which did not contain 5 mM L-tryptophan due to the high absorbance background tryptophan generates when performing a spectrum analysis from 440 to 600 nm wavelength.
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Publication 2018
acetamide acetonitrile Acids Agar Bacteria Biological Assay Colorimetry Glycerin High-Performance Liquid Chromatographies Indican indole indolebutyric acid Indoles isolation Perchloric Acid Spectrum Analysis Sterility, Reproductive Strains Tryptophan tryptophol tryptophyltryptophan
EAE was induced in eight to ten weeks old mice by subcutaneous immunization with 200 μg MOG35–55 peptide emulsified in complete Freund’s adjuvant (CFA, Difco Laboratories) per mouse, followed by administration of 200 ng pertussis toxin (PTX, List biological laboratories, Inc.) on days 0 and 2 as described26 (link). Clinical signs of EAE were assessed according to the following score: 0, no signs of disease; 1, loss of tone in the tail; 2, hind limb paresis; 3, hind limb paralysis; 4, tetraplegia; 5, moribund. Human Interferon-beta 1a (Rebif, Merck Serono) or vehicle control was administered daily at a dose of 5.000 IU intranasally or intraperitoneally as outlined in the specific experiments. Antibiotics, Trp-indoles, and TnAse were administered daily by oral gavage starting from day 22 after EAE induction at the following doses: Ampicillin 6 mg/20 g body weight (BW), vancomycin 3 mg/20 g BW; indole, indole-3-propionic acid, indole-3-aldehyde at 400 μg/20g BW, TnAse at 200 μg/20 g BW. I3S was administered daily intraperitoneally at a dose of 200 μg/20g BW. All agents were purchased from Sigma Aldrich.
Publication 2016
Ampicillin Antibiotics beta-1a, Interferon Biopharmaceuticals Body Weight Freund's Adjuvant Hindlimb indole indole-3-carbaldehyde Indoles Mice, House Micrococcal Nuclease Paraparesis Peptides Pertussis Toxin propionic acid Quadriplegia Rebif Tail Tube Feeding Vaccination Vancomycin
Persister cell survival was determined by counting the number of colonies that grew on solid media after washing and serially diluting cells exposed to antibiotics, as previously described (Kwan et al. 2013 (link)). Briefly, overnight cultures (16 h) were diluted 1:1000 with fresh LB medium and grown to the desired turbidity (0.8 at 600 nm for the exponential phase and 3–4 at 600 nm for the mid-stationary phase) at 250 rpm. Since pretreatments of bacteriostatic rifampicin (Kwan et al. 2013 (link)) and bactericidal ampicillin and ciprofloxacin (Hu et al. 2015 (link); Kwan et al. 2015 (link)) increased persister cell formation, the three antibiotics have been used in this study. In order to obtain antibiotic-induced persister cultures in buffered LB, cultures were exposed to rifampicin (100 μg mL−1), ampicillin (100 μg mL−1), or ciprofloxacin (0.5 μg mL−1) and incubated for 30 min at 37 °C. Cells were harvested by centrifugation at 4000 rpm for 14 min and washed with fresh LB (turbidity was controlled as 0.5). Cells (0.5 mL) were then transferred to micro-tubes and treated with or without indoles and incubated for 3 h at 37 °C at 250 rpm. DMSO was used as a control. Cell viabilities were determined by serially diluting cells with PBS buffer, plating 100 μL drops on LB agar, and counting colonies.
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Publication 2016
Agar Ampicillin Antibiotics Antibiotics, Antitubercular Buffers Cells Cell Survival Centrifugation Ciprofloxacin Indoles Rifampin Sulfoxide, Dimethyl

Most recents protocols related to «Indoles»

Example 176

1-(4-(2-(2,6-dimethylpyridin-4-yl)-3-isopropyl-1H-indol-5-yl)cyclohexyl)-N,N-di methyl methanamine (1.0 mg, 1% yield) was prepared according to the general procedure described in Examples 6 and 7 using 4-(2-(2,6-dimethylpyridin-4-yl)-3-isopropyl-1H-indol-5-yl)cyclohexyl) methanamine (0.080 g, 0.213 mmol) as the starting intermediate. LCMS retention time 1.814 min [E]. MS m/z: 404.3 (M+H); 1H NMR (400 MHz, METHANOL-d4) δ ppm 7.67 (d, J=8.8 Hz, 3H), 7.38 (d, J=8.6 Hz, 1H), 7.18 (d, J=8.6 Hz, 1H), 3.60-3.46 (m, 2H), 3.08 (d, J=6.6 Hz, 2H), 2.94 (s, 6H), 2.75 (s, 6H), 2.65 (t, J=12.5 Hz, 1H), 2.09-1.92 (m, 5H), 1.76-1.61 (m, 3H), 1.55 (d, J=7.1 Hz, 6H), 1.41-1.24 (m, 4H).

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Patent 2024
1H NMR Indoles inhibitors Lincomycin Methanol methylamine Retention (Psychology)

Example 366

A solution of tert-butyl 2-(2,6-dimethylpyridin-4-yl)-5-(2,4-dioxo-1,3-diazaspiro[4.5]decan-8-yl)-3-isopropyl-1H-indole-1-carboxylate (0.1 g, 0.188 mmol) in dioxane-HCl (2 mL) was stirred for 5 h. The reaction mass was concentrated to afford crude product. The crude samples were purified by reverse phase prep HPLC using method D1. The fractions containing desired compound was combined and evaporated to dryness using Genevac to afford 8-(2-(2,6-dimethylpyridin-4-yl)-3-isopropyl-1H-indol-5-yl)-1,3-diazaspiro[4.5]decane-2,4-dione (0.002 g, 2.56% yield) as a pale white solid. LCMS retention time 1.3 min [E], MS m/z: 431 (M+H): 1H NMR (400 MHz, DMSO-d6) δ ppm 11.10 (s, 1H), 10.80 (s, 1H), 8.79 (s, 1H), 7.63 (s, 1H), 7.26 (d, J=8.00 Hz, 1H), 7.14 (s, 1H), 7.09 (d, J=1.60 Hz, 2H), 4.10-4.21 (m, 2H), 3.32-3.38 (m, 4H), 1.82-1.84 (m, 8H), 1.45 (d, J=4.00 Hz, 6H).

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Patent 2024
1H NMR decane Dioxanes High-Performance Liquid Chromatographies indole Indoles inhibitors Lincomycin Retention (Psychology) Sulfoxide, Dimethyl TERT protein, human

Example 390

To a solution of tert-butyl 4-((2-(3,4-dimethoxyphenyl)-3-ethyl-1H-indol-5-yl) methy 1 piperazine-1-carboxylate (30 mg, 0.063 mmol) in 4M dioxane-HCl (5 mL) was stirred at ambient temperature for 2 h. Concentrated the reaction mass to afford crude compound, the crude samples were purified by reverse phase prep HPLC using method D1. The fractions containing desired compound was combined and evaporated to dryness using Genevac to afford 2-(3,4-dimethoxyphenyl)-3-ethyl-5-(piperazin-1-ylmethyl)-1H-indole (0.005 g, 0.012 mmol, 19%, yield) as a white solid. LCMS retention time 1.91 min [E], MS m/z: 416 (M+H). 1H NMR (400 MHz, DMSO-d6) δ ppm 10.94 (s, 1H), 7.39 (s, 1H), 7.27 (d, J=8.22 Hz, 1H), 7.12-7.18 (m, 2H), 7.07-7.11 (m, 1H), 7.03 (dd, J=8.25, 1.47 Hz, 1H), 3.83 (d, J=12.61 Hz, 6H), 3.50 (s, 2H), 2.84 (q, <J=7.61 Hz, 2H), 2.69-2.74 (m, 4H), 2.27-2.38 (m, 3H), 1.90 (s, 3H), 1.25 (t, J=9.60 Hz, 3H).

The following Example was prepared according to the general procedure described for Example 390.

TABLE 41
Ret
Ex.MolLCMSTimeHPLC
No.StructureWt.MH+(min)Method
391[Figure (not displayed)]
4054061.29E

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Patent 2024
1H NMR dioxane High-Performance Liquid Chromatographies indole Indoles inhibitors Lincomycin Piperazine Retention (Psychology) Sulfoxide, Dimethyl TERT protein, human

Example 257

To a solution of tert-butyl 3-(3-isopropyl-2-(8-methyl-[1,2,4]triazolo[1,5-a]pyridin-6-yl)-1H-indol-5-yl)azetidine-1-carboxylate (190 mg, 0.426 mmol) in DCM (10 mL) were added 4 M dioxane in HCl (2 ml, 8.00 mmol), was stirred at room temperature for 3 h Concentrated the reaction mass, then the residue was washed with diethyl ether (20 mL) to afford 6-(5-(azetidin-3-yl)-3-isopropyl-1H-indol-2-yl)-8-methyl-[1,2,4]triazolo[1,5-a]pyridine (128 mg, 0.363 mmol, 85%). LCMS retention time 1.171 min. MS (E+) m/z: 346.2 (M+H).

The following Examples were prepared according to the general procedure used to prepare Example 257.

TABLE 23
Ret
Ex.MolLCMSTimeHPLC
No.StructureWt.MH+(min)Method
258[Figure (not displayed)]
361.4398.11.402E
259[Figure (not displayed)]
319.4320.20.90E

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Patent 2024
Azetidines Dioxanes Ethyl Ether High-Performance Liquid Chromatographies Indoles inhibitors Lincomycin pyridine Retention (Psychology) TERT protein, human

Example 280

To a solution of 2-chloro-1-(3-(2-(3,4-dimethoxyphenyl)-3-isopropyl-1H-indol-5-yl)-7-azabicyclo[4.1.1]octan-7-yl)ethanone (0.11 g, 0.229 mmol) in THF (2 mL) was added DIPEA (0.080 mL, 0.457 mmol) and dimethylamine (0.172 mL, 0.343 mmol) in THF. The reaction mixture was stirred at room temperature for 12 h. The reaction mixture was diluted with EtOAc (10 mL), washed with water (2×20 mL), dried over sodium sulphate, and concentrated to afford crude product. The crude material was purified by Preparative LCMS using method D2, the fractions containing the product was collected and concentrated to afford 1-(3-(2-(3,4-dimethoxyphenyl)-3-isopropyl-1H-indol-5-yl)-7-azabicyclo[4.1.1]octan-7-yl)-2-(dimethylamino)ethanone (1.5 mg, 1.34%). LCMS retention time 1.45 min (F). MS m/z: 490.4 (M+H). 1H NMR (400 MHz, DMSO-de) δ ppm 10.80 (s, 1H), 7.51 (s, 1H), 7.23 (d, J=8.5 Hz, 1H), 7.11-7.04 (m, 2H), 7.03-6.99 (m, 1H), 6.96 (dd, J=8.3, 1.8 Hz, 1H), 3.82 (d, J=7.0 Hz, 4H), 3.31 (d, J=7.0 Hz, 2H), 3.02-2.93 (m, 2H), 2.90 (s, 6H), 2.26-2.16 (m, 4H), 1.74-1.64 (m, 4H), 1.56-1.50 (m, 2H), 1.46 (d, J=11.0 Hz, 2H), 1.41 (d, J=7.0 Hz, 6H).

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Patent 2024
1H NMR dimethylamine DIPEA Indoles inhibitors Lincomycin Retention (Psychology) sodium sulfate Sulfoxide, Dimethyl

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More about "Indoles"

Indoles are a versatile class of heterocyclic organic compounds featuring a fused benzene and pyrrole ring system.
These nitrogen-containing molecules are found in a wide array of natural sources and exhibit a diverse range of biological activities.
Indole-based structures play crucial roles in various physiological processes, making them important scaffolds in medicinal chemistry.
Researchers leverage these compounds in the development of therapeutic agents for conditions such as neurological disorders, cancer, and inflammation.
Indole derivatives can be synthesized using a variety of protocols, and researchers can utilize PubCompare.ai's advanced AI-driven platform to efficiently explore the vast literature on indole synthesis.
This platform helps identify optimal procedures, accelerating indole-based research endeavors.
Beyond indoles, researchers may also encounter other related terms and concepts in their work, such as XBridge C18 and Kinetex C18 chromatography columns, DMSO as a solvent, DB-1 columns for gas chromatography, Silica Gel F260 TLC plates, CFSE for cell labeling, FlashSmart Elemental Analyzers, Silica gel 60 F254 for purification, and Multiskan EX microplate readers for assays.
By understanding the nuances of these tools and techniques, researchers can further enhance their indole-focused research.
Whether exploring the diverse biological activities of indoles, seeking efficient synthesis protocols, or leveraging complementary analytical methods, researchers can benefit from the wealth of information and AI-driven insights provided by platforms like PubCompare.ai.
This comprehensive approach can help advance the field of indole research and lead to exciting new discoveries.