A simple and efficient method for predicting protein-protein interaction sites.

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).

Solid-phase extraction of ochratoxin A from wine based on a binding hexapeptide prepared by combinatorial synthesis.

In this paper we describe the preparation of a hexapeptide library by combinatorial synthesis and the identification of a peptide with sequence Ser-Asn-Leu-His-Pro-Lys, which showed good affinity (K(eq)=3.4 x 10(4) M(-1)) towards the mycotoxin ochratoxin A (OTA). An immunoaffinity-like stationary phase supporting such a hexapeptide was used to develop a solid-phase extraction method for the quantification of OTA in wine samples at concentration levels down to 0.10 microg l(-1). Several different wine samples fortified with OTA at 2 and 4 microg l(-1) levels showed recovery of 94.7% and 98.4% at 2.0 and 4.0 microg l(-1), respectively, without any effect on the extraction efficiency of the matrix. The efficacy of this approach was successfully tested by comparison with an immunoaffinity extraction performed on commercial cartridges.

Molecularly imprinted solid-phase extraction method for the high-performance liquid chromatographic analysis of fungicide pyrimethanil in wine.

A method for molecularly imprinted solid-phase extraction (MISPE) of the fungicide pyrimethanil from wine samples has been investigated. The molecular imprinted polymer was obtained by iniferter-mediated grafting on porous chloromethylated polystyrene beads, using methacrylic acid as the functional monomer and ethylene glycol dimethacrylate as the cross-linker. The imprinted beads were evaluated for use as a solid-phase extraction sorbent, in order to develop the extraction protocol in aqueous standards and red wine samples. The optimised extraction protocol resulted in a reliable MISPE method suitable for HPLC analysis (stationary phase: Cromolith Performance C18 column, 100 mm x 4.6 mm; mobile phase: acetonitrile-water (3:2, v/v), flow-rate: 1.00 ml/min; detection 270 nm). It was selective for pyrimethanil and the related pyrimidinic fungicides cyprodinil and mepanipyrim, while the non-pyrimidinic fungicides benalaxyl, chlozolinate, furalaxyl, iprodione, metalaxyl, nuarimol, procymidone and vinclozolin were not extracted. Recoveries performed on a wine matrix spiked with pyrimethanil at three different concentration levels were reproducible and were in good agreement with the recoveries performed on buffer, coming out between 80 and 90% (85+/-7.0% at 0.50 microg/ml, 79+/-1.6% at 2.0 microg/ml and 87+/-5.6% at 20 microg/ml). Preconcentration and quantitative extraction of pyrimethanil from wine samples was shown to be feasible down to 0.1 microg/ml.

An oral selective M3 cholinergic receptor antagonist in COPD.

Cholinergic antagonists have been used since the early 1900s as bronchodilators for chronic obstructive pulmonary disease (COPD). The present study investigated whether an oral muscarinic M3-selective anticholinergic agent (OrM3) would provide an improved therapeutic advantage compared with an inhaled anticholinergic agent in patients with COPD. A 6-week, multicentre, randomised, placebo- and active-controlled, parallel-group study was performed at 56 sites in the USA. In total, 412 male and female patients (aged 35-86 yrs) with a clinical history consistent with COPD were randomised to receive OrM3 0.5, 2, 3 or 4 mg orally once daily, ipratropium bromide 36 mug by inhalation four times daily or placebo. OrM3 demonstrated a significant dose-related improvement in serial forced expiratory volume in one second and a trend for dose-related improvement in patient-reported symptoms compared with placebo. However, at a dose that provided efficacy less than that of ipratropium, the incidence of dose-related, mechanism-based side-effects for OrM3 exceeded those observed for ipratropium. In patients with chronic obstructive pulmonary disease, the oral M3-selective agent did not offer a therapeutic advantage over inhaled ipratropium. These results do not support the hypothesis that high selectivity for muscarinic M3 receptors over airway neuronal M2 receptors will represent a more effective therapy than current inhaled anticholinergics in obstructive airway disease.

Effect of montelukast on lung function in asthma patients with allergic rhinitis: analysis from the COMPACT trial.

BACKGROUND: The Clinical Outcomes with Montelukast as a Partner Agent to Corticosteroid Therapy (COMPACT) trial demonstrated that montelukast added to budesonide (MNT + BD) was as efficacious as double the dose of budesonide (dBD) in improving morning peak expiratory flow (AM PEF) in adult asthmatics. Recent studies have demonstrated that montelukast is also effective in treating daytime and nighttime allergic rhinitis (AR) symptoms in asthmatic patients. This analysis was designed to examine whether asthmatic patients with comorbid AR respond differently than patients without comorbid AR in terms of asthma control (lung function). METHODS: There were 216 asthmatic patients in the MNT+BD group and 184 patients in the dBD group with AR. Treatment differences in the change from baseline in AM PEF were compared. Least square (LS) mean and 95% confidence interval (CI) were derived from an anova model adjusting for baseline and study site. RESULTS: There was a 9.2% increase in AM PEF from baseline in the MNT+BD group compared with a 6% increase in the dBD group. The LS mean difference [(MNT+BD)-dBD] was 14.2 l/min (P=0.028). Other secondary endpoints were similar between groups. CONCLUSION: In the subgroup of asthmatic patients with AR, a combined treatment approach that included montelukast and budesonide provided significantly greater efficacy in reducing airflow obstruction compared with doubling the dose of budesonide. These results support recommendations by the Allergic Rhinitis and its Impact on Asthma initiative that suggest a unified approach aimed at treating the airway inflammation common to both diseases is beneficial for the large proportion of asthmatics who also suffer from AR.

Antibody-like peptides as a novel purification tool for drugs design.

New pharmaceutical approaches, such as biotechnology industry, genomic and proteomic studies, require the development of new analytical and preparative tools that should allow the resolution and the characterisation of complex sets of molecule mixtures in a high-throughput mode with the isolation of a single substance from complex matrices in a high degree of purity, low costs and wide availability. In this review we discuss the design of a tailor-made peptide by focusing our attention on the bioinformatic techniques and combinatorial approaches. Then synthesis, purification and characterisation of peptides with recognition properties are discussed by considering different approaches and their fitness to drug design. Moreover, the development of affinity devices and the discussion of their characteristics to optimise the purification phase are reported. Applications of peptide ligands that bind pharmaceutical compounds (i.e. therapeutic proteins, monoclonal antibodies, hormones) are described and analytical tools mentioned and evaluated. Future perspectives, in particular alternative applications of peptide ligands and their substitution with peptidomimetic compounds, are described.

Cognitive development in low risk preterm infants at 3-4 years of life.

BACKGROUND: Major neurological handicaps and neuropsychological disturbances are more common in ex-preterm children than their counterparts born at term. OBJECTIVE: To establish in a prospective study whether a characteristic neuropsychological profile exists in ex-preterm children who do not exhibit neurodevelopmental deficits on routine clinical examination. METHODS: Thirty intellectually normal children born preterm (30-34 weeks gestation) without major neurological disabilities and a control group of term children matched for age, sex, and parental educational and occupational status were assessed at 3-4 years of age to obtain a complete neuropsychological profile. Intellectual ability, language comprehension and expression, perceptual and visual motor function, working memory, and attention and behavioural problems were investigated. RESULTS: Even in the absence of major neurological signs, children born preterm achieved lower mean scores than controls on the Stanford-Binet intelligence scale (110.8 v 121, p<0.001), visual perception test (33.8 v 42.7, p<0.001), visual motor integration test (42.6 v 47.4, p = 0.049), memory for location test (8.4 v 9.5, p = 0.007), sustained attention test (41.6 v 51.5, p = 0.009), and the picture vocabulary test (33.3 v 44.7, p = 0.021). CONCLUSIONS: Neuropsychological abnormalities can be detected early in childhood in apparently normal ex-preterm children and are consistent with a growing body of evidence that prematurity may be associated with long term neuropsychological morbidity in childhood and adolescence.

Multivariate analysis of the selectivity for a pentachlorophenol-imprinted polymer.

A pentachlorophenol (PCP)-imprinted polymer (MIP) was obtained by thermal polymerization of a mixture of template, 4-vinylpyridine and ethylene glycol dimethacrylate with molar ratio 1 +3 + 27, using as porogenic solvent methanol-water ( 3 + 1(v/v)). The polymer was packed in an HPLC column and selectivity towards 52 PCP-related phenols (22-chloro-, 21-alkyl-, 4-aryl-, 3-methoxy- and 6-polyphenols) was measured using acetonitrile-acetic acid (99 + 1(v/v)) as mobile phase. The same was made for a reference polymer obtained without pentachlorophenol (NIP). The molecular recognition properties of the imprinted polymer were expressed in terms of selectivity index (SI), calculated for each phenol as k(NIP)/k(MIP). Sixteen molecular descriptors were calculated for each molecule: qO, the partial charge of the phenolic oxygen atom; qH, the partial charge of the phenolic hydrogen atom; Deltaq, the absolute value of the difference qO - qH; HOMO, the highest occupied molecular orbital; LUMO, the lowest unoccupied molecular orbital; Deltaorb, absolute value of the difference HOMO - LUMO; micro(2), the square of total dipole moment; MW, the molecular weight; SAS, the solvent-accessible molecular surface area; hSAS, the hydrophobic solvent-accessible molecular surface area; Svdw, the van der Waals molecular surface area; hSvdw, the hydrophobic part of Svdw; MOv, the molecular ovality; RG, the radius of gyration; logP, the logarithm of n-octanol-water partition coefficient; pK, the phenolic dissociation constant. Correlations between selectivity index and these descriptors were searched utilizing multivariate principal component analysis (PCA). The multivariate model obtained by regression on the principal components correlate collectively several of the calculated descriptors with the polymer selectivity. The magnitude of the model's parameters shows that selectivity is strongly influenced by molecular descriptors having structural character, such as MW, hSvdw and logP, while the effect of molecular descriptors having electronic character, such as qO and pK, is much less marked.

Increase in urinary leukotriene LTE4 levels in acute asthma: correlation with airflow limitation.

BACKGROUND: Leukotrienes play a key role in the pathophysiology of chronic asthma. Activation of leukotriene pathways is accompanied by rises in detectable urinary levels of leukotriene E4 (LTE4). The relationship between urinary LTE4 levels and factors associated with acute asthma has not been determined. METHODS: Adults aged 15-54 years presenting with moderate to severe acute asthma were evaluated at emergency departments in 16 US sites. Forced expiratory volume in 1 second (FEV1) was measured during the first 60 minutes after arrival and at specified times until discharge or admission. Urine samples for measurement of LTE4 levels were obtained either on arrival at the study site and/or before discharge. Patients were seen 2 weeks later for follow up, at which time repeat FEV1 measurements and urine samples for LTE4 were obtained. RESULTS: One hundred and eighty four patients were evaluated; LTE4 results from both the acute and follow up periods were available for analysis in 146. Urinary LTE4 levels were increased during asthma exacerbations compared with levels obtained 2 weeks later (geometric means 111.7 and 75.6 pg/mg creatinine, respectively, mean percentage change -32.3; 95% confidence interval (CI) for the mean percentage change -39.6 to -24.3, p<0.001). The correlation between improvement in FEV1 and decline in LTE4 over the 2 week interval was significant (p<0.001, r=0.43). CONCLUSIONS: Activation of leukotriene pathways in acute asthma is correlated with the degree of airflow obstruction, and resolution of the asthma exacerbation is associated with a reduction in leukotriene levels.

Binding properties of 2,4,5-trichlorophenoxyacetic acid-imprinted polymers prepared with different molar ratios between template and functional monomer.

Several molecularly-imprinted polymers binding the herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) were prepared with a molar ratio between the functional monomer and the template molecule in the pre-polymerisation mixture set between 1+2 and 20+1. The functional monomer used was 4-vinylpyridine (4-VP), the cross-linker was ethylene dimethacrylate, and the porogenic solvent was a mixture of methanol-water 3+1 (v/v). The polymers obtained were grinded, sieved and packed in 100 mm x3.9 mm HPLC columns. The effects of the mobile phase composition were evaluated by eluting the columns with acetonitrile-water mixtures. The results obtained indicate that column capacity, selectivity factor and the imprinting effect are controlled by ion-pair and hydrophobic interactions between the analyte and the stationary phase. In the full range of ratios considered, column capacity, selectivity factor and imprinting effect are inversely proportional to the molar ratio between the template molecule and the functional monomer.

Expression of heme oxygenase in the oxygen-sensing regions of the rostral ventrolateral medulla.

Recently, unique regions in the rostral ventrolateral medulla (RVLM) have been found to be oxygen sensitive. However, the mechanism of sensing oxygen in these RVLM regions is unknown. Because heme oxygenase (HO) has been shown to be involved in the hypoxic responses of the carotid body and pulmonary artery, the aim of this study was to determine whether HO is present in the RVLM and whether expression of HO is altered by chronic hypoxia. Adult rats were exposed to hypoxia (10% O(2)) or normoxia (21% O(2)) for 10 days, and the mRNA for HO-1 and HO-2 was examined in the RVLM by using RT-PCR. Expression of HO-2 mRNA was seen in the RVLM of both control and hypoxic samples, whereas expression of HO-1 mRNA was only seen in the RVLM of hypoxic samples. HO-2 was immunocytochemically localized in brain sections (40 microm) to the C1 region and pre-Bötzinger complex of the RVLM. Together, these results indicate that HO-2 is present in the RVLM under control conditions and that HO-1 is induced in the RVLM during chronic hypoxia, consistent with a potential role for HO in the oxygen-sensing function of these cardiorespiratory RVLM regions.

Functionalized biopolymers as soluble macromolecular chelating agents.

Two different conjugates of bovine serum albumin (BSA) with lysine and a derivative of imidazole have been synthesized to obtain watersoluble macromolecules with binding properties against bivalent transition metal ions. Syntheses have been carried out using the 60 aminogroups or the 99 carboxylic groups on BSA for the coupling reactions, with such molar ratios able to produce highly substituted BSA. The skill of each conjugate to bind metal ions in aqueous medium was studied through the use of titration curves with some metal ions, characterized by a good affinity for the free ligand. Both the conjugates allow us to recover a high number of metal ions per protein molecule, close to the number of ligand molecules on the BSA surface in the case of the lysine conjugate, whereas in the case of the imidazole conjugate M3L complexes are performed.

The complexation of mercury (II) and organomercurial compounds by 8-hydroxyquinoline-bovine serum albumin conjugates.

The complexing properties of conjugates between 8-hydroxyquinoline and bovine serum albumin (Ox-BSA) towards inorganic and organic mercury were studied. Two Ox-BSA conjugates (different substitution ratio) were prepared and their complexing properties were studied. Through the use of titration curves with mercury (II), methylmercury and ethylmercury an evaluation of the complex stoichiometry and stability was obtained, showing that Ox-BSA has good affinity for all investigated mercuric compounds and that the stability increases in the order: Hg (II) < CH3Hg+ < C2H5Hg+, whatever conjugate is considered. Complexes show a stoichiometry of 1:1 between mercury and 8-hydroxyquinoline residues, except with the high substituted conjugate and Hg2+ ion. The skill of the high substituted conjugate to bind inorganic and organic mercury in the presence of NaCl was also studied. Organic mercuric complexes do not show significant modification due to NaCl. Nevertheless, considering inorganic mercury, the number of retained metal ions per protein molecule increases if the NaCl concentration becomes higher than 0.1 M, probably because at high NaCl concentrations 1:1 complexes between mercury and 8-hydroxyquinoline are preferred to 1:2 complexes.

Molecularly imprinted solid-phase extraction sorbent for the clean-up of chlorinated phenoxyacids from aqueous samples.

A molecularly imprinted polymer (MIP) was synthesized using the herbicide 2,4,5-trichlorophenoxyacetic acid as a template, 4-vinylpyridine as an interacting monomer, ethylendimethacrylate as a cross-linker and a methanol-water mixture as a porogen. The binding properties and the selectivity of the polymer towards the template were investigated by frontal and zonal liquid chromatography. The polymer was used as a solid-phase extraction material for the clean-up of the template molecule and some related herbicides (2,4-dichlorophenoxyacetic acid, fenoprop, dichlorprop) from river water samples at a concentration level of ng/ml with quantitative recoveries comparable with those obtained with a traditional C18 reversed-phase column when analyzed by capillary electrophoresis. The results obtained show that the MIP-based approach to the solid-phase extraction is comparable with the more traditional solid-phase extraction with C18 reversed-phase columns in terms of recovery, but it is superior in terms of sample clean-up.

Role of proteolysis and apoptosis in regression of pulmonary vascular remodeling.

Remodeled pulmonary arteries return to normal structural conditions after the increase in pulmonary artery flow resistance is reversed. We studied whether proteolysis of extracellular matrix proteins and apoptosis occur during reversal of remodeling produced by chronic hypoxia in the rat. Main pulmonary arteries were removed at different times during a 10-day period of exposure to 10% O2 and 14 days after return to air. Content and rates of degradation of collagen and elastin as well as immunoreactive collagenase in tissue and isolated mast cells were measured. Immunoblots for collagenase and tissue inhibitor of metalloproteinases (TIMP) were performed. Apoptosis was assessed by cleavage of DNA and TUNEL assay. Excess collagen and elastin present at 10 days of hypoxia decreased to near normal levels after 3-5 days of air. Transient increases in collagenolytic and elastolytic enzyme activities accompanied the rapid decrease in matrix proteins. Mast cells containing collagenase accumulated in remodeled pulmonary arteries, and the active form of collagenase appeared at the time of peak proteolytic activity. TIMP increased during remodeling. Apoptosis was maximal 3 days after return to air. Our results suggest that activation of enzymes, which degrade matrix proteins, and apoptosis play a role in resolution of vascular remodeling.

A general method to perform a noncompetitive immunoassay for small molecules.

A new general method to perform a noncompetitive immunoassay for low-molecular-mass analytes (less than 6000 Da) is described and checked using cortisol as a model system. The method is based on the use of a "polydentate ligand" (cortisol-poly(L-lysine) conjugate) able to block the antibody sites unoccupied by the analyte, followed by the replacement of an antibody-bound analyte by an enzyme-labeled analyte (cortisol-horseradish peroxidase), and permits the direct measurement of the analyte bound sites. The observed signal shows a near-linear correlation with the analyte concentration. The characteristics of interactions between the analyte and polydentate ligand with the specific antibody were studied to perform a preliminary evaluation of the noncompetitive immunoassay for cortisol. The noncompetitive assay was compared with a competitive immunoassay obtained under the same conditions and using the same reagents. The results of the experiments showed a lower detection limit for the noncompetitive model (0.15 ng mL-1 rather than 0.72 ng mL-1), emphasizing that the model is successful. Moreover, as the polydentate ligand is prepared from the same hapten used for the immunogen synthesis, this type of noncompetitive immunoassay appears generally applicable to all small molecules for which antibodies have been obtained.

Flow cytometric determination of cell proliferation in hypertensive blood vessels.

BACKGROUND: Measurement of vascular cell proliferation in animal models of hypertension is currently accomplished by demonstrating [(3)H]-thymidine ([(3)H]-dT) incorporation into DNA using autoradiography. This method, however, is labor intensive, requires radioactivity, and is limited by the inherent difficulty in discriminating labeled and unlabeled cells. To address these limitations, a flow cytometric-based method is described utilizing incorporation of 5-bromo-2'-deoxyuridine (BrdU) into DNA of nuclei isolated from blood vessels. METHODS: Pulmonary hypertension was induced in rats by exposure to 10% O(2) (hypoxia) for varying periods of time. Pulmonary arteries and aorta from rats injected with BrdU prior to sacrifice were isolated, fixed with 10% formalin, and digested with Protease XIV. The intact nuclei liberated by this treatment were successively treated with HCl/Triton X-100 and sodium borate. Processed nuclei were probed with a BrdU-specific fluorescein-conjugated antibody, and the percentage of BrdU staining cells was determined using flow cytometry. RESULTS: An approximately 20-fold increase in BrdU-positive cells at 3 days of hypoxia in pulmonary arteries (relative to control) with no change in aorta was observed. These results were similar to previous studies using [(3)H]-dT labeling. CONCLUSIONS: Flow cytometric determination of cell proliferation in blood vessels is a simple, objective technique that may facilitate measurement of cell proliferation in animal models of vascular disease.

Mosaic trisomy 17 in amniocytes: phenotypic outcome, tissue distribution, and uniparental disomy studies.

Mosaicism for trisomy 17 in amniocyte cultures is a rare finding, whilst postnatal cases are exceptional. In order to gain insight into the possible effects of the distribution of the trisomic line and of uniparental disomy (UPD) on embryofoetal development, we have performed follow-up clinical, cytogenetic and molecular investigations into three newly detected prenatal cases of trisomy 17 mosaicism identified in cultured amniotic fluid. In the first case, the pregnancy ended normally with the birth of a healthy girl, and analysis of newborn lymphocytes and of multiple extra-embryonic tissues was indicative of confined placental mosaicism. The second case was also associated with a normal pregnancy outcome and postnatal development, and only euploid cells were found in peripheral blood after birth. However, maternal isodisomy 17 consequent to a meiosis II error and loss of a chromosome 17 homologue was detected in peripheral lymphocytes postnatally. In the third case, pathological examination after termination of pregnancy showed growth retardation and minor dysmorphisms, and the trisomic line was detected in foetal skin fibroblasts. In addition, biparental derivation of chromosome 17 was demonstrated in the euploid lineage. These results, together with previously reported data, indicate that true amniotic trisomy 17 mosaicism is more commonly of extra-embryonic origin and associated with normal foetal development. Phenotypic consequences may arise when the trisomic line is present in foetal tissues. Case 2 also represents the first observation of maternal UPD involving chromosome 17; the absence of phenotypic anomalies in the child suggests that chromosome 17 is not likely to be subject to imprinting in maternal gametes.

Remodeling of rat neonatal pulmonary artery: role of matrix metalloproteinases.

We studied whether rapid thinning of large pulmonary arteries of neonatal rats is associated with breakdown of collagen. Pulmonary artery extracts from fetal to 21 days of age were assayed for collagen content and matrix metalloproteinases. Within 3 days postpartum, no changes in collagen content, collagenolytic activity, or levels of stromelysin-l or gelatinase A were observed. After day 3, collagen content and total proteolytic activity increased with little change in matrix metalloproteinase expression. Thus, collagen was not degraded, and the late increases in collagen and total proteolytic activity were probably growth related. Unlike adult rats in which collagen is broken down after reversal of hypoxic pulmonary artery remodeling, collagen is not broken down in neonatal pulmonary arteries during adaptation to extrauterine life.