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Indole; Refer to the product ′s Certificate of Analysis for more information on a suitable instrument technique. Contact Technical Service for further support.

Indole analytical standard 120-72-9

Indole

Discrimination of teas with different degrees of fermentation by SPME-GC analysis of the characteristic volatile flavour compounds.

Experimental design to optimise the analysis of organic volatile compounds in cow slurry by headspace solid-phase microextraction-gas chromatography-mass spectrometry.

Analysis of crab meat volatiles as possible spoilage indicators for blue crab (Callinectes sapidus) meat by gas chromatography-mass spectrometry.

Analysis of malodorous volatile substances of human waste: feces and urine.

Synthesis and antiinflammatory activity of heterocyclic indole derivatives.

The chemo-, regio-, and stereoselectivities of multicomponent [4 + 2]/[3 + 2] domino cycloaddition reactions involving nitroindole derivatives with vinylethers and acrylates are studied computationnally and compared to experimental results. In this process, the nitroarene first reacts as an electron-deficient heterodiene with the electron-rich alkene following an inverse electron-demand [4 + 2] process, leading to a nitronate intermediate in a fully selective way. This intermediate exclusively interacts, in a second step, with the electron-deficient alkene and undergoes a chemo- and regioselective [3 + 2] cycloaddition. The density functional theory calculations reported in this Article fully account for the selectivities observed experimentally. Electronic displacements along the reaction path are examined using a topological analysis of the electron-localization function (ELF). The first [4 + 2] reaction follows a classical concerted, although asynchronous process, which is reliably described by the frontier molecular-orbital (FMO) model. In contrast, the electronic displacements observed during the second [3 + 2] step are unexpected, involving an electron donation by the electron-deficient reaction partner.

Selectivities of multicomponent [4 + 2]/[3 + 2] cycloadditions of 3-nitroindole with substituted alkenes: a DFT analysis.

The phytotoxin coronatine (COR) promotes various aspects of Pseudomonas syringae virulence, including invasion through stomata, growth in the apoplast, and induction of disease symptoms. COR is a structural mimic of active jasmonic acid (JA) conjugates. Known activities of COR are mediated through its binding to the F-box-containing JA coreceptor CORONATINE INSENSITIVE1. By analyzing the interaction of P. syringae mutants with Arabidopsis thaliana mutants, we demonstrate that, in the apoplastic space of Arabidopsis, COR is a multifunctional defense suppressor. COR and the critical P. syringae type III effector HopM1 target distinct signaling steps to suppress callose deposition. In addition to its well-documented ability to suppress salicylic acid (SA) signaling, COR suppresses an SA-independent pathway contributing to callose deposition by reducing accumulation of an indole glucosinolate upstream of the activity of the PEN2 myrosinase. COR also suppresses callose deposition and promotes bacterial growth in coi1 mutant plants, indicating that COR may have multiple targets inside plant cells.

The coronatine toxin of Pseudomonas syringae is a multifunctional suppressor of Arabidopsis defense.

Bacteria can utilize signal molecules to coordinate their behavior to survive in dynamic multispecies communities. Indole is widespread in the natural environment, as a variety of both Gram-positive and Gram-negative bacteria (to date, 85 species) produce large quantities of indole. Although it has been known for over 100 years that many bacteria produce indole, the real biological roles of this molecule are only now beginning to be unveiled. As an intercellular signal molecule, indole controls diverse aspects of bacterial physiology, such as spore formation, plasmid stability, drug resistance, biofilm formation, and virulence in indole-producing bacteria. In contrast, many non-indole-producing bacteria, plants and animals produce diverse oxygenases which may interfere with indole signaling. It appears indole plays an important role in bacterial physiology, ecological balance, and possibly human health. Here we discuss our current knowledge and perspectives on indole signaling.

Indole as an intercellular signal in microbial communities.

Indole-diterpenes are a structurally diverse group of secondary metabolites with a common cyclic diterpene backbone derived from geranylgeranyl diphosphate and an indole group derived from indole-3-glycerol phosphate. Different types and patterns of ring substitutions and ring stereochemistry generate this structural diversity. This group of compounds is best known for their neurotoxic effects in mammals, causing syndromes such as 'ryegrass staggers' in sheep and cattle. Because many of the fungi that synthesise these compounds form symbiotic relationships with plants, insects, and other fungi, the synthesis of these compounds may confer an ecological advantage to these associations. Considerable recent progress has been made on understanding indole-diterpene biosynthesis in filamentous fungi, principally through the cloning and characterisation of the genes and gene products for paxilline biosynthesis in Penicillium paxilli. Important insights into how the indole-diterpene backbone is synthesised and decorated have been obtained using P. paxilli mutants in this pathway. This review provides an overview of these recent developments.

The genetic basis for indole-diterpene chemical diversity in filamentous fungi.

Total synthesis of the tremorgenic indole diterpene paspalinine.

Genetically reducing boar taint using low-taint lines is considered the most sustainable and economic long-term alternative to surgical castration of male pigs. Owing to the high heritability of the main boar taint components (androstenone, skatole and indole), breeding is an excellent tool for reducing the number of tainted carcasses. To incorporate boar taint into breeding programmes, standardized performance testing is required. The objective of this study was to develop and formally present a performance test for the main boar taint compounds on live breeding candidates. First, a standardized performance test for boar taint was established. A biopsy device was developed to extract small tissue samples (200 to 300 mg) from breeding candidates. Quantification of boar taint components from these small samples using specialized chemical extraction methods proved accurate and repeatable (r = 0.938). Following establishment of the method, biopsy samples of 516 live boars (100 to 130 kg live weight) were collected in the second step. Various mixed linear models were tested for each boar taint compound; models were ranked in terms of their information content. Pedigree information of 2245 ancestors of biopsied animals was included, and genetic parameters were estimated using univariate and multivariate models. Androstenone (in μg/g liquid fat (LF): mean = 0.578, σ = 0.527), skatole (in μg/g LF: mean = 0.033, σ = 0.002) and indole (in μg/g LF: mean = 0.032, σ = 0.002) levels obtained by biopsy were plausible. Heritability estimates for androstenone calculated with univariate (0.453) and multivariate (0.452) analyses were comparable to those in the literature. Heritabilities for skatole (0.495) and indole (0.550) were higher than that for androstenone. Genetic and phenotypic correlations were similar to those published previously. Our results show that data on boar taint compounds from small adipose samples obtained by biopsy provide similar genetic parameters as that described in the literature for larger samples and are therefore a reliable performance test for boar taint in live breeding candidates.

A performance test for boar taint compounds in live boars.

Important biologically active indole alkaloids are decorated with prenyl (3,3-dimethylallyl) and tert-prenyl (1,1-dimethylallyl) groups. Covering the literature until the end of 2010, this review article comprehensively summarises and discusses the currently available technologies of prenylation and tert-prenylation of indoles, which have been applied in natural products total syntheses or could be applied there in the near future. We focus on those procedures which introduce the C(5) units in one step, organised according to the indole position to be functionalised. Key strategies include electrophilic and nucleophilic prenylation and tert-prenylation, prenyl and tert-prenyl rearrangements, transition metal-mediated reactions and enzymatic methods.

Indole prenylation in alkaloid synthesis.

Several 5,10-dihydroindeno[1,2-b]indole derivatives incorporating methoxy, hydroxyl, and halogen (F, Cl, and Br) moieties on the indene fragment of the molecule were prepared and tested against five carbonic anhydrase (CA, EC 4.2.1.1) isoforms. The inhibitory potencies of these compounds against the human (h) isoforms hCA I, II, IV, VI and bovine (b) isoform bCA III were assessed. Most of them exhibited low micromolar inhibition of these enzymes. K(I) values of these compounds against hCA I and hCA II were in the range of 2.14-16.32 μM, and 0.34-2.52 μM, respectively. Isozyme hCA IV was inhibited with K(I)-s in the range of 0.435-5.726 μM, while hCA VI with K(I)-s of 1.92-12.84 μM bCA III was inhibited with K(I)-s in the range of 2.13-17.83 μM. The structurally related compounds, 1,2-dimethoxybenzene, catechol and indole were also tested in order to understand the structure activity relationship. In silico docking studies of some derivatives within the active site of hCA I and II were also carried out in order to rationalize the inhibitory properties of these compounds and understand their inhibition mechanism.

Structure-activity relationships for the interaction of 5,10-dihydroindeno[1,2-b]indole derivatives with human and bovine carbonic anhydrase isoforms I, II, III, IV and VI.

IRONic electrophilic indoles! The C3-regioselective hydroarylation of N-acetyl indoles with aromatic nucleophiles mediated by FeCl(3) features a rare example of the electrophilic reactivity of the indole core in a Friedel-Crafts reaction. This indole umpolung allows us straightforward access to the tetracyclic benzofuroindoline motif found in the natural product diazonamide A, which is a potent antitumor agent.

FeCl3-mediated Friedel-Crafts hydroarylation with electrophilic N-acetyl indoles for the synthesis of benzofuroindolines.

The last two steps of l-tryptophan (Trp) biosynthesis are catalyzed by Trp synthase, a heterotetramer composed of TrpA and TrpB. TrpB catalyzes the condensation of indole, synthesized by TrpA, and serine to Trp. In the hyperthermophilic archaeon Thermococcus kodakarensis, trpA and trpB (trpB1) are located adjacently in the trpCDEGFB1A operon. Interestingly, several organisms possess a second trpB gene (trpB2) encoding TrpB2, located outside of the trp operon in T. kodakarensis. Until now, the physiological function of trpB2 has not been examined genetically. In the present study, we report the biochemical and physiological analyses of TrpB2 from T. kodakarensis. Kinetic analysis indicated that TrpB2 catalyzed the TrpB reaction but did not interact with TrpA as in the case of TrpB1. When growth phenotypes were examined for gene disruption strains, the double-deletion mutant (ΔtrpB1ΔtrpB2) displayed Trp auxotrophy, whereas individual single mutants (ΔtrpB1 and ΔtrpB2 strains) did not. It has been proposed previously that, in Thermotoga maritima, TrpB2 provides an alternate route to generate Trp from serine and free indole (indole salvage). To accurately examine the capacity of TrpB1 and TrpB2 in Trp synthesis via indole salvage, we constructed ΔtrpEB1 and ΔtrpEB2 strains using strain KUW1 (ΔpyrFΔtrpE) as a host, eliminating the route for endogenous indole synthesis. Indole complemented the Trp auxotrophies of ΔtrpEB1 (ΔpyrFΔtrpEΔtrpB1) and ΔtrpEB2 (ΔpyrFΔtrpEΔtrpB2) to similar levels. The results indicate that TrpB1 and TrpB2 both contribute to Trp biosynthesis in T. kodakarensis and can utilize free indole, and that indole salvage does not necessarily rely on TrpB2 to a greater extent.

The tryptophan synthase β-subunit paralogs TrpB1 and TrpB2 in Thermococcus kodakarensis are both involved in tryptophan biosynthesis and indole salvage.

In this study, we investigated the performance of the FilmArray and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in identifying microorganisms from blood culture (BC) bottles prior to positivity. First, we used simulated BacT/Alert FA Plus BC bottles with five each for Escherichia coli and Staphylococcus aureus isolates. The FilmArray identified all 10 isolates before BC positivity with 9/10 at 5 h and 1 at 7.5 h after incubation in the BC system. MALDI-TOF MS failed to identify the isolates prior to positivity. When the bottles were incubated for 2.5 h at room temperature (RT) before we put them into the BC system, the FilmArray identified 6/10 at 2.5 h and the remaining 4 at 5 h. Finally, we tested simulated BC bottles after incubation at RT. Interestingly, 9/10 isolates were identified with the FilmArray after 8 h of incubation at RT. Second, we studied clinical BC bottles in quadruplicate. When three-fourths of the parallel bottles signaled positive, the FilmArray was run on the fourth nonsignaled bottle and was found to be positive in 14/15 such cases. Third, we analyzed the performance of the FilmArray in the identification of microorganisms from clinical BC bottles before incubation in the system. Two milliliters of broth from 400 BC bottles was collected after arrival at the laboratory and stored at -70°C. Sixteen bottles later signaled positive in the system. When the frozen broth from these bottles was analyzed, the FilmArray identified all the microorganisms in 8/16 bottles prior to incubation in the BC system. This study shows that the FilmArray can identify microorganisms from BC bottles prior to positivity and in some cases even prior to incubation in the BC system.

Identification of microorganisms by FilmArray and matrix-assisted laser desorption ionization-time of flight mass spectrometry prior to positivity in the blood culture system.

Molecular docking is widely used to predict novel lead compounds for drug discovery. Success depends on the quality of the docking scoring function, among other factors. An imperfect scoring function can mislead by predicting incorrect ligand geometries or by selecting nonbinding molecules over true ligands. These false-positive hits may be considered "decoys". Although these decoys are frustrating, they potentially provide important tests for a docking algorithm; the more subtle the decoy, the more rigorous the test. Indeed, decoy databases have been used to improve protein structure prediction algorithms and protein-protein docking algorithms. Here, we describe 20 geometric decoys in five enzymes and 166 "hit list" decoys-i.e., molecules predicted to bind by our docking program that were tested and found not to do so-for beta-lactamase and two cavity sites in lysozyme. Especially in the cavity sites, which are very simple, these decoys highlight particular weaknesses in our scoring function. We also consider the performance of five other widely used docking scoring functions against our geometric and hit list decoys. Intriguingly, whereas many of these other scoring functions performed better on the geometric decoys, they typically performed worse on the hit list decoys, often highly ranking molecules that seemed to poorly complement the model sites. Several of these "hits"from the other scoring functions were tested experimentally and found, in fact, to be decoys. Collectively, these decoys provide a tool for the development and improvement of molecular docking scoring functions. Such improvements may, in turn, be rapidly tested experimentally against these and related experimental systems, which are well-behaved in assays and for structure determination.

Decoys for docking.

Sample introduction in microfluidic liquid chromatography often generates wide zones rather than peaks, especially when a large sample volume (relative to column volume) is injected. Formation of wide injection zones can be further amplified when the sample is dissolved in a strong eluent. In some cases sample breakthrough may occur, especially when the injection is performed into short trapping columns. To investigate the band formation and subsequent zone focusing under gradient elution in situations such as these, we developed the Repetitive Injection Method (RIM), based on the temporally resolved introduction of two discrete peaks to a column, mimicking both the leading and trailing edges of a larger, singly injected sample zone. Using titanium microfluidic 0.32 mm I.D. columns, the results of RIM experiments were practically identical to injection of a correspondingly larger single zone volume. It was also experimentally shown that zone width (spacing between two injected peaks) decreases during gradient elution. We utilized RIM experiments to investigate wide sample zones created by strong sample solvent, and subsequent gradient zone focusing for a series of compounds. This experimental work was compared with computationally simulated chromatograms. The success of sample focusing during injection and gradient elution depends not only on an analyte's absolute retention, but also on how rapidly the analyte's retention changes during the mobile phase gradient.

Repetitive injection method: a tool for investigation of injection zone formation and its compression in microfluidic liquid chromatography.

We previously reported a classical quantitative structure-activity relationship (QSAR) equation for permeability coefficients (P(app-pampa)) by parallel artificial membrane permeation assay (PAMPA) of structurally diverse compounds with simple physicochemical parameters, hydrophobicity at a particular pH (logP(oct) and |pK(a)-pH|), hydrogen-accepting ability (SA(HA)), and hydrogen-donating ability (SA(HD)); however, desipramine, imipramine, and testosterone, which have high logP(oct) values, were excluded from the derived QSAR equation because their measured P(app-pampa) values were lower than calculated. In this study, for further investigation of PAMPA permeability of hydrophobic compounds, we experimentally measured the P(app-pampa) of more compounds with high hydrophobicity, including several pesticides, and compared the measured P(app-pampa) values with those calculated from the QSAR equation. As a result, compounds having a calculated logP(app-pampa)>-4.5 showed lower measured logP(app-pampa) than calculated because of the barrier of the unstirred water layer and the membrane retention of hydrophobic compounds. The bilinear QSAR model explained the PAMPA permeability of the whole dataset of compounds, whether hydrophilic or hydrophobic, with the same parameters as the equation in the previous study. In addition, PAMPA permeability coefficients correlated well with Caco-2 cell permeability coefficients. Since Caco-2 cell permeability is effective for the evaluation of human oral absorption of compounds, the proposed bilinear model for PAMPA permeability could be useful for not only effective screening for several drug candidates but also the risk assessment of chemicals and agrochemicals absorbed by humans.

QSAR study on permeability of hydrophobic compounds with artificial membranes.

Growing interest in the use of both the logarithm of the partition coefficient of the neutral species in the alkane/water system (log P(N)(alk)) and the difference between log P(N)(oct) (the logarithm of the partition coefficient of the neutral species in the n-octanol/water system) and log P(N)(alk) (Deltalog P(N)(oct-alk)) in the early stages of drug design has stimulated development of a computational tool based on the Volsurf software to predict virtual (=of each conformer) log P(N)(alk) and virtual log P(N)(oct). From these two pieces of data, it is then possible to calculate Deltalog P(N)(oct-alk) for a given compound as the difference between log P(N)(oct) and log P(N)(alk). Once the pK(a) is known and the legitimacy of neglecting the contribution made by the ionized species has been checked, it is also possible to calculate log D(pH)(alk), which might be an important lipophilicity descriptor in absorption, distribution, metabolism, and excretion (ADME) prediction, from log P(N)(alk).

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