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 4,687 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

This study presents the first QSAR model for Galectin-3 glycomimetic inhibitors based on docked structures to the carbohydrate recognition domain (CRD). Quantitative numerical methods such as PLS (Partial Least Squares) and ANN (Artificial Neural Networks) have been used and compared on QSAR models to establish correlations between molecular properties and binding affinity values (Kd). Training and validation of QSAR predictive models was performed on a master dataset consisting of 136 compounds. The molecular structures and binding affinities (Kd) (136 compounds) were obtained from the literature. To address the issue of dimensionality reduction, molecular descriptors were selected with PLS contingency approach, ANN, PCA (Principal Component Analysis) and GA (Genetic Algorithms) for the best predictive Galectin-3 binding affinity (Kd). Final sets comprising 56, 31 and 35 descriptors were obtained with PLS, PCA and ANN, respectively. The objective of this prototype QSAR model is to serve as a first guideline for the design of novel and potent Gal-3 selective inhibitors with emphasis on modification at both C-3' and at O-3 positions.
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PMID:A first QSAR model for galectin-3 glycomimetic inhibitors based on 3D docked structures. 1701 87

Three different electrodes were tested for use as nonspecific amperometric sensors for blind analysis on real matrices, namely different fruit juices from different fruits or different brands. The first two electrodes were traditional Pt and Au electrodes, while the third one was modified with poly(3,4-ethylenedioxythiophene) conducting polymer. The sensors were tested separately, tested coupled to each other, and also tested together. The responses of the electrode system(s) were first screened via PCA and then their discriminant capabilities were quantified in terms of the sensitivities and specificities of their corresponding PLS-DA multivariate classification models. Particular attention was paid to analyzing the evolution of the response over subsequent potential sweeps. The modified electrode demonstrated the most discriminating ability, and it was the only system capable of satisfactorily performing the most complex task attempted during the analysis: discriminating between juices from the same fruit but from different brands. Moreover, the electrode "cleaning" procedure required between two subsequent potential sweeps was much simpler for the modified electrode than for the others. This electrode system was therefore shown to be a good candidate for use as an informative element in an electronic tongue applied to the analysis of other food matrices.
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PMID:Development of an electronic tongue based on a PEDOT-modified voltammetric sensor. 1723 99

While for 1H NMR techniques there already exist common analytical and reporting standards, this does not apply to LC-MS metabolic profiling approaches. These standards are the more recommended when applying metabonomics to human biofluids, particularly urine samples, due to the high degree of biological variation compared to animals. A control study was performed, and urine samples of 30 healthy male and female human subjects were collected at intervals of 8 h twice a day for three consecutive days. Using selective multiple reaction monitoring in combination with a column-switching tool for the analysis of the mercapturate pattern, samples were screened for time and gender differences, the most common confounders. Data preprocessing parameters, alignment, scaling to internal standards, and normalization techniques were optimized by PCA, PLS-DA, and OPLS models. Great care was taken in the validation process of both analytical and chemometric protocols. Additionally, a problem of LC-MS, the combination of "different-batch" data to "one-batch" data could be solved by a batchwise scaling procedure. Based on these results, the use of metabolic profiling via mercapturates will be feasible for the detection of disease or toxicity markers in the future since mercapturates are important biomarkers of reactive metabolites known to be involved in many toxic processes.
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PMID:Tools in metabonomics: an integrated validation approach for LC-MS metabolic profiling of mercapturic acids in human urine. 1731 79

Arylpiperazine compounds are promising 5-HT(1A) receptor ligands that can contribute for accelerating the onset of therapeutic effect of selective serotonin reuptake inhibitors. In the present work, the chemometric methods HCA, PCA, KNN, SIMCA and PLS were employed in order to obtain SAR and QSAR models relating the structures of arylpiperazine compounds to their 5-HT(1A) receptor affinities. A training set of 52 compounds was used to construct the models and the best ones were obtained with nine topological descriptors. The classification and regression models were externally validated by means of predictions for a test set of 14 compounds and have presented good quality, as verified by the correctness of classifications, in the case of pattern recognition studies, and by the high correlation coefficients (q(2)=0.76, r(2)=0.83) and small prediction errors for the PLS regression. Since the results are in good agreement with previous SAR studies, we can suggest that these findings can help in the search for 5-HT(1A) receptor ligands that are able to improve antidepressant treatment.
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PMID:A chemometric study of the 5-HT(1A) receptor affinities presented by arylpiperazine compounds. 1756 49

In this paper a method for the automatic DNA spots classification and extraction of profiles associated in DNA polyacrylamide gel electrophoresis is presented and it integrates the use of image processing techniques and chemometrics tools. A software which implements this method was developed; for feature extraction a combination of a PCA analysis and a C4.5 decision tree were used. To obtain good results in the profile extraction only DNA spots are useful; therefore, it was necessary to solve a two-class classification problem among DNA spots and no-DNA spots. In order to perform the classification process with high velocity, effectiveness and robustness, comparative classification studies among support vector machine (SVM), K-NN and PLS-DA classifiers were made. The best results obtained with the SVM classifier demonstrated the advantages attributed to it in the literature as a two-class classifier. A Sequential Cluster Leader Algorithm and another one developed for the restoration of pattern missing spots were needed to conclude the profiles extraction step. The experimental results show that this method has a very effective computational behavior and effectiveness, and provide a very useful tool to decrease the time and increase the quality of the specialist responses.
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PMID:Application of chemometric tools for automatic classification and profile extraction of DNA samples in forensic tasks. 1760 82

A library of chalcones with different basic groups were synthesized and evaluated for antiproliferative activities against the human breast cancer (MCF 7) and colon cancer (HCT 116) cell lines. Structure-activity relationships were analyzed by projection methods (PCA/PLS) and multiple linear regression. Polar volume, hydrogen bonding features, HOMO energies, and charge on the beta carbon were found to be important factors. A basic group on either ring A or B of the chalcone led to a favourable increase in polar volume, but when present on ring B, it increased HOMO energies and decreased the positive charge on the beta carbon, both of which led to lower activity. Several examples showed that final activity of the chalcone was influenced by compensatory interactions among these parameters. In general, a single basic group on ring A was associated with good activity. A notable exception was compound 1-123 which had basic groups on both rings A and B but still maintained a good activity profile with IC(50)<10 microM and selectivity ratios >2.5. There was some evidence to show that structural differences in chalcones influenced not only activity but mechanism of action. Compounds 6-130 and 7-140 which had basic groups on ring A interfered with cell cycle progression, but the dibasic chalcone 1-123 had no effect.
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PMID:Antiproliferative activity of chalcones with basic functionalities. 1780 45

This study demonstrates the capabilities of NIR imaging as an effective tool for characterization of pharmaceutical powder blends. The powder system used in this small-scale powder blending study consists of acetaminophen (APAP, the model API), microcrystalline cellulose (MCC) and lactose monohydrate. Mixtures of these components were blended for different times for a total of ten time points (ten blending trials). Images collected from multiple locations of the blends were used to generate a qualitative description of the components' blending dynamics and a quantitative determination of both the blending end point and the distribution variability of the components. Multivariate analyses, including pure-component PCA and discriminate PLS, were used to treat the imaging data. A good correlation was observed between imaging results and a UV-Vis monitoring method for determining blend homogeneity. Score images indicated general trends of the distribution of blending constituents for all ten blending trials. The API distribution pattern throughout blending was detected and the API domain size for different blending trials was compared. Blending insights obtained from this study may be transferable to large scale powder blending. Blending process understanding obtained from this study has the potential to facilitate the optimization of blending process control in the future.
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PMID:Characterization of pharmaceutical powder blends by NIR chemical imaging. 1794 13

High-resolution Magic Angle Spinning (Hr-MAS) (1)H-NMR spectroscopy was used to analyze intact testicular tissues ex vivo and to investigate the toxicological effects of ethylene glycol monomethyl ether (EGME), a well-known spermatocytes toxicant, on male reproductive organs by NMR-based metabonomic analysis. Especially, we reported the first Hr-MAS (1)H-NMR spectra of epididymis. Sexually matured male rats were treated with 50 and 2,000 mg/kg EGME, and body weight, reproductive organs weight, histopathology and plasma biochemistry were examined at 6 and 24 hr after administration. Two multivariate statistical methods, namely, unsupervised PCA and supervised PLS-DA, indicated that the balance of endogenous metabolites was perturbed in both reproductive organs and biofluids. In the testes, lactate, creatine and glutathione were mainly affected by EGME treatment. In urine and plasma, altered excretions of the TCA cycle intermediates (2-oxoglutarate, citrate and succinate) and the ketone-bodies (acetoacetate and beta-hydroxybutyrate) were also observed. The finding in current integrated metabonomic analysis of both intact tissues and biofluids suggested that EGME-induced testicular toxicity was attributed to perturbation of the energy supply processes, suppression of the TCA cycle, or oxidative stress. Furthermore, Hr-MAS (1)H-NMR proved useful to investigate the molecular snapshot of biological tissues and the mechanism of toxicity.
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PMID:Integrated NMR-based metabonomic investigation of early metabolic effects of ethylene glycol monomethyl ether (EGME) on male reproductive organs in rats. 1819 83

Benefits of capillary electrophoresis to provide a comprehensive snapshot of multiple metabolites in biological samples have been exploited. Afterwards, multivariate statistical methods can be employed in order to mine additional information from the data. Urine fingerprints of control and diabetic rats have shown the clear effects of an antioxidant treatment on diabetic animals, which were not seen in controls, in a rapid, simple and cost-effective way without identifying a single marker. The procedure involves the measurement of samples with a relatively inexpensive tool such as CE-UV, without any previous treatment other than filtration and the application of chemometric tools [PCA (principal components analysis) and PLS-DA (partial least squares discriminant analysis)]. Data pre-treatment of electrophoretic profiles (alignment, normalization and baseline correction) has shown to be key for further chemometric treatment. Once developed, the methodology can easily be applied for a rapid in vivo screening of extracts with potential in vitro activity. Classification was supported by that produced after PCA and PLS-DA of target variables obtained with selectively designed, time and reagent consuming methods.
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PMID:New perspective of diabetes response to an antioxidant treatment through metabolic fingerprinting of urine by capillary electrophoresis. 1831 89

Unbalanced diets generate oxidative stress commonly associated with the development of diabetes, atherosclerosis, obesity and cancer. Dietary flavonoids have antioxidant properties and may limit this stress and reduce the risk of these diseases. We used a metabolomic approach to study the influence of catechin, a common flavonoid naturally occurring in various fruits, wine or chocolate, on the metabolic changes induced by hyperlipidemic diets. Male Wistar rats ( n = 8/group) were fed during 6 weeks normolipidemic (5% w/w) or hyperlipidemic (15 and 25%) diets with or without catechin supplementation (0.2% w/w). Urines were collected at days 17 and 38 and analyzed by reverse-phase liquid chromatography-mass spectrometry (LC-QTOF). Hyperlipidic diets led to a significant increase of oxidative stress in liver and aorta, upon which catechin had no effect. Multivariate analyses (PCA and PLS-DA) of the urine fingerprints allowed discrimination of the different diets. Variables were then classified according to their dependence on lipid and catechin intake (ANOVA). Nine variables were identified as catechin metabolites of tissular or microbial origin. Around 1000 variables were significantly affected by the lipid content of the diet, and 76 were fully reversed by catechin supplementation. Four variables showing an increase in urinary excretion in rats fed the high-fat diets were identified as deoxycytidine, nicotinic acid, dihydroxyquinoline and pipecolinic acid. After catechin supplementation, the excretion of nicotinic acid was fully restored to the level found in the rats fed the low-fat diet. The physiological significance of these metabolic changes is discussed.
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PMID:A liquid chromatography-quadrupole time-of-flight (LC-QTOF)-based metabolomic approach reveals new metabolic effects of catechin in rats fed high-fat diets. 1848 65


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