New designs for inhibitors of the NF-κB: DNA binding

We present a series of new inhibitors of the association between nuclear factor kappa B (NF-B) and the corresponding B site in DNA. They were designed using the lead compound 15-deoxy-^12,14 -prostaglandin J₂ (PGJ2), which is a natural product with demonstrated inhibitory efficiency for this system. First, the binding mode of PGJ2 to NF-B was unraveled by GOLD docking calculation. Subsequently, substitutions were made to PGJ2 to optimize its association with NF-B. Care was taken not to strongly increase the reactivity of the new compounds, and to keep the overall shape, size and hydrophilicity of the lead compound, which should render them a similar bioavailability. Molecular mechanics calculations were performed to decide on the suitability of the substitutions, and to evaluate the energies of association with NF-B. Density functional theory calculations were performed also to study the overall reactivity of the substituted drugs towards NF-B. Important general conclusions were obtained, concerning the improvement of these natural inhibitors; namely, a set of rational methodologies were deduced to improve the association between the PGJ2 derivatives and NF-B, and their efficiency demonstrated by generating a set of substituted complexes, some of them with a very much increased affinity for NF-B, opening new doors to enlarge the therapeutic capabilities of this class of drugs.     

Characterization of Saccharomyces Sp. through determination of amino acid profiles by capillary gas chromatography

The Saccharomyces strains uvarum, montuliensis, bayanus, capensis and florentinus were grown in liquid media prepared from a 1% aqueous glucose solution to which 0.05% of ammonium sulfate or urea were added as the only nitrogen supply. The amino acids exuded during incubation were isolated by cation exchange and derivatized as the corresponding N,O-heptafluorobutyryl isopropyl esters. Separation was achieved on a highly deactivated glass capillary column coated with OV-101. A characteristic amino acid profile was obtained for each of the species studied, allowing the construction of a chemotaxonomic tree, on the basis of present or absent acids.     

Conformational Study of Naringenin in the Isolated and Solvated States by Semiempirical and Ab Initio Methods

Naringenin is a natural widespread flavanone occurring in different foodstuffs that presents several important biological activities. Although its properties are well documented, its mechanisms of action are still controversial. The present article reports a conformational analysis of naringenin, using the semiempirical AM1 and ab initio methods, at the Hartree–Fock level of theory. The 3-21G, 3-21G*, 6-31G, and 6-31G** basis sets were used. The electron correlation effects were included through the Møller–Plesset second-order perturbation theory. The solvation of naringenin has been investigated through the standard SCRF, the supermolecule (SM), and the combined SM/SCRF models. The results have shown that there are two degenerate forms of naringenin, differing mainly by the orientation of a hydroxyl group (C4—OH). The energy barrier for the interconversion between them is ca. 6 kcal.mol^–1, suggesting some conjugation between the -system of the aromatic B ring and the hydroxyl group (C4—OH).     

Liquid secondary ion mass spectrometry of porphyrin dimers: reduction reactions and structural characterisation

New synthesised porphyrin dimers, with an amide or ester linkage between the two porphyrin units, were studied using liquid secondary ion mass spectrometry (LSIMS). The formation of reduced species was observed for all the compounds and it was found that the extent of reduction is dependent on the matrix used and on the structure of the porphyrin dimer. The main fragmentation pathways lead to monomer fragments resulting from cleavage of the amide or ester linkage between the two porphyrin units. The consistency of the fragmentations for all the dimers studied leads to the proposal of a common designation for the fragment ions. LSIMS, in addition to molecular weight determination, can provide important structural information for this type of compound.     

Detection of soil pollution by hydrocarbons using headspace-mass spectrometry and identification of compounds by headspace-fast gas chromatography-mass spectrometry

The direct coupling of a headspace sampler with a mass spectrometer is proposed as a screening tool for the rapid detection of soil pollution by hydrocarbons from petroleum and derivatives. The samples are subjected to the headspace generation process, with no prior treatment, and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of the sample analysed. Suitable treatment of the signal by chemometric techniques allows unequivocal characterisation of the different types of sample. The use of fast gas chromatography with a mass spectrometer detector coupled to the headspace sampler allows identification of the major hydrocarbons present in the mineral and organic polluted samples, interpretation of the results obtained, and demonstrates the analytical potential of headspace-mass spectrometry coupling.     

Atmospheric selenium in an industrialized area of Portugal

Summary Selenium is determined by instrumental neutron activation analysis (INAA), based on measurement of the long-lived ⁷⁵Se nuclide. In the urban and industrialized areas of Portugal selenium contents have been found of the order of of 0.5-1 ng/m³ in PM10 and PM2.5, according to the data collected since 1994. From November 12, 2001 and for not more than 3 months, the Se contents in PM10 and PM2.5 increased by a factor of 1000 in the northern area of Lisbon. More than other nutrients, selenium illustrates the dichotomy between essentiality and toxicity. There is no legislation on Se for ambient air and on indoor ambient point threshold limit values (US and Germany legislation), were 100 times higher than the abnormal values found that winter. The increase was also visible for mercury although not to such an extent. Attempts were made to understand the trend, going into a study of the emission sources located in the area using both INAA and PIXE. It was concluded that the observation occurred due to abnormal meteorological wind direction, which pushed the pollutants towards the populated area, when usually they flow into the Tagus estuary.     

Spectrophotometric study of the equilibria in aqueous copper(II) azide solutions

The reaction between copper (II) and azide has been studied spectrophotometrically at four wavelengths, at 25 degrees , and ionic strength 4.00M (sodium perchlorate). The formation constants beta(2) and beta(3) found are 2.90 +/- 0.08 x 10(4) and 3.02 +/- 0.07 x 10(6) respectively. The results obtained from potentiometric measurements with a solid-state electrode disagree with those calculated from the spectrophotometric data. Causes of the discrepancy are discussed.     

Atomistic Modeling of Silica Based Sol-Gel Processes

Density Functional Theory is used to study water, methanol, ethanol, TMOS, and TEOS molecules and the most important silica clusters participating in sol-gel processes. Calculated bond lengths, bond angles and electric dipole moments compare well with experimental data. The energy of these molecules is reported and used to discuss the energetics of the hydrolysis and condensation reactions. Molecular Dynamics is employed to simulate liquid water, methanol, ethanol, TMOS, TEOS and experimental sol-gel solutions. Calculated densities and enthalpies of vaporisation compare well with experimental data. Preliminary results are presented for MD simulations of sol-gel solutions.     

Hydrolytic protein cleavage mediated by unusual mononuclear copper(II) complexes: X-ray structures and solution studies

The crystal structures and redox and UV-vis/EPR spectroscopic properties of two new mononuclear copper(II) complexes, [Cu(HL1)Cl2] (1) and [Cu(L1)Cl] (2), prepared through the reaction between copper(II) chloride and the ligand 2-[(bis(pyridylmethyl)amino)methyl]-4-methyl-6-formylphenol (HL1) under distinct base conditions, are reported along with solution studies. Also, we demonstrate that these CuII complexes are able to cleave unactivated peptide bonds from bovine serum albumin (BSA) and the thermostable enzyme Taq DNA polymerase at micromolar concentration, under mild pH and temperature conditions. The cleavage activity seems to be specific with defined proteolytic fragments appearing after protein treatment. The location of the specific cleavage sites was tentatively assigned to solvent-accessible portions of the protein. These are two of the most active Cu(II) complexes described to date, since their cleavage activity is detected in minutes and evidence is here presented for a hydrolytic mechanism mediating protein cleavage by these complexes.     

Stability of anthocyanins extracted from grape skins

Summary The extractability and stability of anthocyanins from the skins ofVitis vinifera were determined at different pH values. Anthocyanins were extracted using acetone, partitioned with chloroform and pre-purified by solid-phase extraction (SPE). They were analysed by RP-HPLC, and the kinetic parameters of decomposition were calculated. The total monomeric anthocyanin content was determined by spectrophotometry. Anthocianins were well separated by RP-HPLC. The efficiency of extraction depended strongly on the pH of the extracting agent and on the character of the pigment to be extracted. The amount of anthocyanins decreased with increasing duration of storage, more so at elevated temperatures. Presented at Balaton Symposium '01 on High-Performance Separation Methods Siófok, Hungary, September 2–4, 2001.