Competitive inhibition of lipolytic enzymes. V. A monolayer study using enantiomeric acylamino analogues of phospholipids as potent competitive inhibitors of porcine pancreatic phospholipase A2

For the first time, we have shown that a stereospecific interaction occurs between porcine pancreatic phospholipase A₂ and a monomolecular film of amidophospholipid used as inhibitor. Direct binding experiments, using radiolabelled phospholipase A₂, showed that 13 times more enzyme was bound to phospholipid films of the l series by comparison with films of the d series. These results were confirmed by indirect binding studies using re-spreading experiments. Kinetic studies of the porcine pancreatic PLA₂, using enantiomeric acyl-amino phospholipid analogues, have shown that: (1) inhibitors of the l series are more potent than inhibitors of the d series, (2) inhibitors having a negative charge are more potent than zwitterionic inhibitors, (3) inhibitory power values are greater when evaluated in micellar system than in a the monolayer system, (4) the inhibitory power increases continuously with surface pressure.     

Competitive inhibition of lipolytic enzymes. V. A monolayer study using enantiomeric acylamino analogues of phospholipids as potent competitive inhibitors of porcine pancreatic phospholipase A2.

For the first time, we have shown that a stereospecific interaction occurs between porcine pancreatic phospholipase A2 and a monomolecular film of amidophospholipid used as inhibitor. Direct binding experiments, using radiolabelled phospholipase A2, showed that 13 times more enzyme was bound to phospholipid films of the L series by comparison with films of the D series. These results were confirmed by indirect binding studies using re-spreading experiments. Kinetic studies of the porcine pancreatic PLA2, using enantiomeric acyl-amino phospholipid analogues, have shown that: (1) inhibitors of the L series are more potent than inhibitors of the D series, (2) inhibitors having a negative charge are more potent than zwitterionic inhibitors, (3) inhibitory power values are greater when evaluated in micellar system than in a the monolayer system, (4) the inhibitory power increases continuously with surface pressure.     

A Simple Approach for the Computation of Multiple Periodicities in Biological Time Series

We have described a simple approach for the analysis and isolation of multiple periodicities from a biological time series. For the estimation of the periodicities, we used simulated data and data from ongoing experiments in our laboratory. Two time series were simulated, one which consisted of only white noise and the other consisted white noise along with periodicities of 6, 11, 17 and 23 h, to demonstrate that our method can successfully isolate multiple patterns in a time series. Our method of analysis is objective, simple, flexible and adaptive since it distinctly delineates the individual contribution from an overlap of multiple periodicities. The key features of our method are: (i) identification of a reliable phase reference point, (ii) scanning the time series using a moving window in increments, (iii) use of Siegel's modification of Fisher's method to detect significant periodicit(y)ies in the time series. The use of window sizes of increasing length to examine the time series elegantly reduces noise while identifying periodicities that are otherwise not apparent. Finally, the periodogram can be smoothed in order to normalize the contribution by attendant frequency components within the waveform. A minimum critical value for relative contribution of various frequencies was calculated to delineate the periodicities that contributed significantly to the time series. We executed this method of time series analysis using MS Excel and C.     

A Simple Approach for the Computation of Multiple Periodicities in Biological Time Series

We have described a simple approach for the analysis and isolation of multiple periodicities from a biological time series. For the estimation of the periodicities, we used simulated data and data from ongoing experiments in our laboratory. Two time series were simulated, one which consisted of only white noise and the other consisted white noise along with periodicities of 6, 11, 17 and 23 h, to demonstrate that our method can successfully isolate multiple patterns in a time series. Our method of analysis is objective, simple, flexible and adaptive since it distinctly delineates the individual contribution from an overlap of multiple periodicities. The key features of our method are: (i) identification of a reliable phase reference point, (ii) scanning the time series using a moving window in increments, (iii) use of Siegel's modification of Fisher's method to detect significant periodicit(y)ies in the time series. The use of window sizes of increasing length to examine the time series elegantly reduces noise while identifying periodicities that are otherwise not apparent. Finally, the periodogram can be smoothed in order to normalize the contribution by attendant frequency components within the waveform. A minimum critical value for relative contribution of various frequencies was calculated to delineate the periodicities that contributed significantly to the time series. We executed this method of time series analysis using MS Excel and C.     

The Tubifex tubifex assay for the determination of acute toxicity

An express (3-minute) test for acute toxicity determination by using the oligochaete annelid, Tubifex tubifex, is described. The EC50(Tubifex tubifex) [EC50(Tt)] for movement inhibition was calculated by using a concentration-response dependence. The reproducibility of the test was checked over several years and by several workers. Its applicability is limited to compounds which are soluble in water. The calculated EC50(Tt) indices correlate with LC50 values determined by using the fish, Pimephales promelas (96-hour assay), and with ICG50 values determined by using the ciliate, Tetrahymena pyriformis (48-hour assay) with high statistical significance (r = 0.822, n = 35, and r = 0.927, n = 80, respectively). The correlation between the EC50(Tt) indices and rat oral LD50 values (48-hour assay) was r = 0.519 (n = 67). The correlation within organic compounds was closer (r = 0.635, n = 60) than with the heterogeneous series of chemicals. A similar trend was noticed for the correlation with mouse oral LD50 values (r = 0.479, n = 56) with the heterogeneous series of chemicals, as compared that with the series without inorganic salts (r = 0.605, n = 42), and similarly with mouse intraperitoneal LD50 values, where r = 0.543 (n = 50) with the heterogeneous series of chemicals and r = 0.893 (n = 33) with the series of organic chemicals.     

Toward the development of highly homozygous diploid potato lines using the self-compatibility controlling Sli gene.

Cultivated diploid potatoes (2n = 2x = 24) are self-incompatible, but can be altered to become self-compatible using the Sli gene. Previously, a diploid clone 97H32-6 was selfed up to S3 using the Sli gene. To explore the usefulness of the Sli gene for the production of highly homozygous diploid potatoes, 2 S4 families from the above 97H32-6 derived S3 lines (inbred series A) and 3 S5 families by continuous selfings from a different F1 (= S0) plant (inbred series B) were developed. The level of heterozygosity and the location of heterozygous loci on the genetic map were investigated using RFLP and AFLP markers. The average heterozygosity levels of the originally heterozygous loci decreased from 100% in S0 to 10.7% in S4 and 8.6% in S5 (inbred series A and B, respectively). The average rate of reduction in heterozygosity per generation (38.4% and 38.5% for inbred series A and B, respectively) was lower than the theoretically expected rate (50%). However, none of the loci or chromosome sections was exclusively heterozygous in the advanced self-progeny. Thus, highly homozygous and seed-propagated diploid potatoes could be obtained by repeated selfing using the Sli gene.     

Binding specificity of the two major DNA-binding proteins in human serum.

The two major DNA-binding proteins of human serum (DNA-binding protein 1 and DNA-binding protein 2) were shown to bind preferentially to single-stranded polynucleotides rich in guanine residues. Equilibrium competition experiments using a nitrocellulose filter assay system containing labeled human lymphocyte DNA and various competing natural and synthetic polynucleotides indicated that both proteins recognized sequences of bases containing a keto group in either position 6 (purines) or 4 (pyrimidines) and that these keto groups must be readily accessible for effective binding to occur. Guanine was shown to be the preferred nucleotide through inhibition experiments using a series of synthetic homopolymers and a series of bacterial DNAs of differing G + C content. The relationship between protein affinity and G + C content was shown to be directly proportional. The equilibrium constants for the binding of the human lymphocyte DNA by both proteins were on the order of 10(-6) M, and the length of the nucleotide sequence necessary for effective binding was found to be 12 to 18 bases using a series of oligomers of poly(dG).     

Design and synthesis of substituted nicotinamides as inhibitors of soluble epoxide hydrolase

A series of potent nicotinamide inhibitors of soluble epoxides hydrolase (sEH) is disclosed. This series was designed using structure-based deconstruction and a combination of two HTS hit series, resulting in hybrid analogs that retained the optimal potency from one series, and acceptable in vitro metabolic stability from the other. Structure-guided optimization of these analogs gave rise to nanomolar inhibitors of human sEH that had acceptable plasma exposure to qualify them as probes to determine the in vivo phenotypic consequences of sEH inhibition.     

Discovery of 4-(dimethylamino)quinazolines as potent and selective antagonists for the melanin-concentrating hormone receptor 1

A series of 4-(dimethylamino)quinazoline based antagonists of the melanin-concentrating hormone receptor 1 (MCH-R1) is described. This series was derived from a lead compound, AR129330, identified by HTS of a GPCR-directed library using a functional assay with a constitutively activated (CART) form of the receptor. The preliminary optimization resulted in the identification of compounds 20, 21, and 23.     

Selective COX-2 inhibitors. Part 1: synthesis and biological evaluation of phenylazobenzenesulfonamides

A series of phenylazobenzenesulfonamide derivatives were designed and synthesized for the evaluation as selective cyclooxygenase-2 (COX-2) inhibitors in a cellular assay using human whole blood (HWB) and an enzymatic assay using purified ovine enzymes. Extensive structure-activity relationships (SAR) were studied within this series, and several of selective COX-2 inhibitors have been identified. Among them, compound 8, 4-(4-amino-2-methylsulfanyl-phenylazo)benzenesulfonamide, showed a potent inhibitory activity to the cyclooxygenase enzymes (IC(50)'s for COX-1: 23.28 microM; COX-2: 2.04 microM), being active but less COX-2 selective than celecoxib.     

The influence of climatic variability on the quality of wine

In this paper, the quality of the wine from the Dão (Viseu) region of Portugal is examined and relationships between wine quality and climatic variability are obtained using spectral and correlation analysis to determine the structure of the temporal variations. The spectra of the series of quality of wine values show statistically significant oscillations coherent with those found in the series of teleconnection indices. The series cover a period of 33 years. A significant correlation was obtained between wine quality and minimum air temperature in May, December and total precipitation in April. The teleconnection circulation indices are used to provide some physical insight into the most significant oscillating components of the climatic and the wine quality series. We found significant and positive correlations between the quality of the wine and the Southern Oscillation Index (SOI) of August and negative with the SOI of January and with the North Atlantic Oscillation of April. Wine quality and climatic series can be predicted using statistical models depending on significant oscillations.     

Anti-HIV-1 entry optimization of novel imidazopiperidine-tropane CCR5 antagonists

A novel series of imidazopiperidine-tropane CCR5 antagonists is described. The series was optimized for anti-HIV-1 potency using a set of phenotypic viral entry assays. This strategy resulted in the identification of several very potent (IC(50)<10nM) inhibitors of HIV-1 entry. One compound (40) was further profiled and was found to have attractive selectivity, pharmacokinetic, and antiviral properties.     

Dynamic simulation of an in vitro multi-enzyme system

Parameters often are tuned with metabolite concentration time series data to build a dynamic model of metabolism. However, such tuning may reduce the extrapolation ability (generalization capability) of the model. In this study, we determined detailed kinetic parameters of three purified Escherichia coli glycolytic enzymes using the initial velocity method for individual enzymes; i.e., the parameters were determined independently from metabolite concentration time series data. The metabolite concentration time series calculated by the model using the parameters matched the experimental data obtained in an actual multi-enzyme system consisting of the three purified E. coli glycolytic enzymes. Thus, the results indicate that kinetic parameters can be determined without using an undesirable tuning process.     

Early classification of multivariate temporal observations by extraction of interpretable shapelets

ABSTRACT: BACKGROUND: Early classification of time series is beneficial for biomedical informatics problems suchincluding, but not limited to, disease change detection. Early classification can be oftremendous help by identifying the onset of a disease before it has time to fully take hold. Inaddition, extracting patterns from the original time series helps domain experts to gaininsights into the classification results. This problem has been studied recently using timeseries segments called shapelets. In this paper, we present a method, which we callMultivariate Shapelets Detection (MSD), that allows for early and patient-specificclassification of multivariate time series. The method extracts time series patterns, calledmultivariate shapelets, from all dimensions of the time series that distinctly manifest thetarget class locally. The time series were classified by searching for the earliest closestpatterns. RESULTS: The proposed early classification method for multivariate time series has been evaluated oneight gene expression datasets from viral infection and drug response studies in humans. Inour experiments, the MSD method outperformed the baseline methods, achieving highlyaccurate classification by using as little as 40%-64% of the time series. The obtained resultsprovide evidence that using conventional classification methods on short time series is notas accurate as using the proposed methods specialized for early classification. CONCLUSION: For the early classification task, we proposed a method called Multivariate ShapeletsDetection (MSD), which extracts patterns from all dimensions of the time series. Weshowed that the MSD method can classify the time series early by using as little as40%-64% of the time series' length.     

Dependency of characteristics of heart rate variability on the average value of the R--R-intervals

By the means of spectral analysis, dependency of heart rate variability (HRV) on average R--R-intervals (R--Rav, sec) is explored at controlled (forced) breathing. According to our findings, the dependency of the peak frequency at a spectral density graph for source series of R--R-intervals upon the RRav may be presented by the following formula: fp 1.0 = fr: RRav, where fp 1.0--peak frequency when R--Rav = 1.0 sec, fp--peak frequency at current R--Rav. For correcting (standardization) the frequency domain borders of spectral power (fd) of sources series of the R--Rav-intervals it is possible to use the formula: fd = fd 1.0 R--Rav, where fd 1.0--frequency domain border at R--Rav = 1.0 sec. The correction (standardization) of frequency domain borders of spectral power (fd), frequency peaks (fp 1.0) of sources series of the R--Rav-intervals as compared to current R--Rav allows to compare different series of the R--Rav-intervals without using the transformation to the discrete event series (DES).     

3D-QSAR studies with the aid of molecular docking for a series of non-steroidal FXR agonists

The farnesoid x receptor (FXR) has become a potential drug target for treating cholesterol-related and bile acid-related diseases recently. In this paper, 3-dimensional quantitative structure-activity (structure-affinity and structure-efficacy) relationships are investigated for a series of non-steroidal agonists (fexaramine series) by using the comparative molecular field analysis (CoMFA), where molecular docking method (FlexX) is employed to construct molecular superimposition maps. A proposal to design some new agonists is discussed lastly.     

The discovery of indole-derived long acting beta2-adrenoceptor agonists for the treatment of asthma and COPD

The design and profile of a series of indole containing long acting beta(2)-adrenoceptor agonists is described. Evaluation of these analogues using an in vitro guinea pig trachea tissue model demonstrates that analogues within this series have salmeterol-like duration of action with potential for long duration of action in humans.     

The discovery of long acting beta2-adrenoreceptor agonists

The design and profile of a series of saligenin containing long acting beta(2)-adrenoreceptor agonists is described. Evaluation of these analogues using a guinea-pig tissue model demonstrates that analogues within this series have significantly longer durations of action than salmeterol and have the potential for a once daily profile in human.     

Discovery of estrogen receptor α modulators from natural compounds in Si-Wu-Tang series decoctions using estrogen-responsive MCF-7 breast cancer cells

The binding between the estrogen receptor α (ER-α) and a variety of compounds in traditional Chinese formulae, Si-Wu-Tang (SWT) series decoctions, was studied using a stably-transfected human breast cancer cell line (MVLN). In 38 compounds tested from SWT series decoctions, the estrogen-like activity of 22 compounds was above 60% in 20 μg mL(-1). Furthermore, theoretical affinity of these compounds was certificated using the functional virtual screen of ER-α modulators by FlexX-Pharm. The accuracy of functional virtual screening of ER-α modulators could reach to 77.27%. The results showed that some compounds, such as organic acids and flavones in SWT series decoctions could be used as selective estrogen receptor modulators (SERMs) and could be selected for further development as potential agents for estrogen related diseases.     

Cariporide enables hemodynamically more effective chest compression by leftward shift of its flow-depth relationship

When given during closed-chest resuscitation, cariporide (4-isopropyl-methylsulfonylbenzoyl-guanidine methanesulfonate; a selective inhibitor of the Na(+)/H(+) exchanger isoform-1) enables generation of viable perfusion pressures with less depth of compression. We hypothesized that this effect results from greater blood flows generated for a given depth of compression. Two series of 14 rats each underwent 10 min of untreated ventricular fibrillation followed by 8 min of chest compression before defibrillation was attempted. Compression depth was adjusted to maintain an aortic diastolic pressure (ADP) between 26 and 28 mmHg in the first series and between 36 and 38 mmHg in the second series. Within each series, rats were randomized to receive cariporide (3 mg/kg) or NaCl (0.9%; control) before chest compression was started. Blood flow was measured using 15-mum fluorescent microspheres. Less depth of compression was required to maintain the target ADP when cariporide was present in both series 1 (13.6 +/- 1.2 vs. 16.6 +/- 1.2 mm; P < 0.001) and series 2 (15.3 +/- 1.0 vs. 18.9 +/- 1.5 mm; P < 0.001). Despite less compression depth, the cardiac index in cariporide-treated rats was comparable to control rats in series 1 (11.1 +/- 0.7 vs. 11.3 +/- 1.4 ml.min(-1).kg(-1); P = not significant) but higher in series 2 (15.5 +/- 2.3 vs. 9.9 +/- 1.4 ml.min(-1).kg(-1); P < 0.05). Increases in compression depth (from series 1 to series 2) increased myocardial, cerebral, and adrenal blood flow in cariporide-treated rats. We conclude that cariporide enhances the efficacy of closed-chest resuscitation by leftward shift of the flow-depth relationship.