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.
Indoles
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»
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.
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.
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).
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).
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.
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.
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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More about "Indoles"
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.