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.     

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that presenting a structure similar to the transition state of the reaction to be catalyzed--with shorter distances between the carbon atoms to be bonded and more diaxial character. With respect to the reorganization effect, an energy decomposition analysis of the potential energies of the reactive reactant and of the reaction transition state in aqueous solution and in the enzyme shows that the enzyme structure is better adapted to the transition structure. This means not only a more negative electrostatic interaction energy with the transition state but also a low enzyme deformation contribution to the energy barrier. Our calculations reveal that the structure of the enzyme is responsible for stabilizing the transition state structure of the reaction, with concomitant selection of the reactive form of the reactants. This is, the same enzymatic pattern that stabilizes the transition structure also promotes those reactant structures closer to the transition structure (i.e., the reactive reactants). In fact, both reorganization and preorganization effects have to be considered as the two faces of the same coin, having a common origin in the effect of the enzyme structure on the energy surface of the substrate.     

Determination of salicylate in blood serum using an amperometric biosensor based on salicylate hydroxylase immobilized in a polypyrrole-glutaraldehyde matrix

The use of an amperometric biosensor for the salicylate determination in blood serum is described. The biosensor is based on salicylate hydroxylase (EC 1.14.13.1) electropolymerized onto a glassy carbon-working electrode with polypyrrole and glutaraldehyde, to improve the biosensor lifetime. The hexacyanoferrate (II) was also incorporated to work as a redox mediator to minimize possible interferences. The salicylate is enzymatically converted to catechol, which is monitored amperometrically by its electrooxidation at+0.170 V versus SCE (saturated calomel electrode). Salicylate determination was carried out maintaining the ratio between beta-NADH and salicylate at 4:1 (30 degrees C). The amperometric response of the biosensor was linearly proportional to the salicylate concentration between 2.3x10(-6) and 1.4x10(-5) mol l(-1), in 0.1 mol l(-1) phosphate buffer (pH 7.8), containing 0.1 mol l(-1) KCl and 5.0x10(-4) mol l(-1) Na(2)H(2)EDTA, as supporting electrolyte. The recovery studies, in the presence of several interfering compounds, showed recoveries between 96.4 and 104.8%. The useful lifetime of the biosensor in the concentration range evaluated was at least 40 days, in continuous use. Blood serum samples analyzed by this biosensor showed a good correlation compared to the spectrophotometric method (Trinder) used as reference, presenting relative deviations lower than 7.0%.     

Studying lateral diffusion in lipid bilayers by combining a magic angle spinning NMR probe with a microimaging gradient system

An alternative technique for studying the lateral diffusion in lipid membranes using pulsed field gradients in combination with magic angle spinning is presented. It is shown that MAS probes inserted in a microimaging device that produce high field gradients can be used to monitor also slow diffusion processes. As an example, measurements of the lateral diffusion of lipids embedded in the bilayer of a cubic phase are presented.     

Trace elements in a profile of the unsaturated zone of the São Paulo Basin

This study comprises Tertiary sediments (clays, silts, and fine clayey sands) from the unsaturated zone of the Experimental Station in the University of São Paulo, taken from a nine meters depth profile; ten samples were separated in bulk and <53 m fractions. Chemical composition was determined by INAA to ascertain the distribution of trace elements throughout the sediment deposition, and to establish the background parameters, useful for mobilization studies of such elements after industrial waste disposal.     

Analysis of the Association Process Between a Series of Phenol Derivatives with Two Novel Fluorinated Stationary Phase Using the Cl− Anion as Retention Marker

Summary Lithium chloride (LiCl) effect on the retention process of a phenol derivative series was investigated on two types of fluorinated stationary phase (i.e. a silica grafted with fluorinated linear alkyl chain (L-FSP) and a silica grafted with fluorinated aromatic ring stationary phase (A-FSP)). The results showed that the solute retention is enhanced when the A-FSP was used instead of the L-FSP due to additional – interactions. For the two fluorinated stationary phases (FSPs), the phenol-FSP association process can be divided into two LiCl concentration domains demonstrated that it was important to take into account the adsorbtion of Cl^– anion on the FSPs. As well, enthalpy-entropy compensation revealed that the solute retention mechanism was independent of the solute molecular structure and confirmed a change on the solute retention mechanism at a critical LiCl concentration value around 0.02M.     

Spectrophotometric flow injection determination of total phosphorus in beer using on-line UV/thermal induced digestion

A flow injection system for the automatic determination of total phosphorus in beer is described. The developed manifold uses a two-stage photooxidation/thermal digestion procedure together with oxidizing and hydrolyzing reagents to convert all forms of phosphorus compounds to orthophosphate. Polyphosphates are hydrolyzed by acid and heat, and organo-phosphates are digested by UV-catalyzed peroxodisulfate oxidation. The orthophosphate formed is then spectrophotometrically determined by the phosphomolybdenum blue reaction, using stannous chloride as reducing agent. The results obtained for a set of 19 beer samples (with concentrations from 120 to 735 mg P/L) were in good agreement with the reference method, the maximum relative deviation found being 4.7%. Relative standard deviations for ten consecutive determinations were lower than 1.5%, and a detection limit of 1 mg P/L was achieved.     

A novel synthesis of enantiopure octahydropyrrolo[3,4-b]pyrroles by intramolecular [3 + 2] dipolar cycloaddition on chiral perhydro-1,3-benzoxazines

[reaction: see text] Condensation of N-substituted glycines with chiral 3-allyl-2-formyl perhydro-1,3-benzoxazines forms an azomethine ylide that cyclizes to give octahydropyrrolo[3,4-b]pyrrole derivatives. The [3 + 2] dipolar cycloadditions are stereoespecific leading to a single diastereoisomer. The chemical yields are dependent on the reaction temperature and the presence or absence of a base.     

A New ent‐Kaurane Diterpene from Stems of Alibertia macrophylla K. Schum. (Rubiaceae)

Phytochemical investigations of the stems of a specimen of Alibertia macrophylla led to the isolation and characterization of the new diterpene ent‐kaurane‐2β,3α,16α‐triol ( 1 ), along with triterpenes 2 – 8 , iridoids 9 – 12 , and phenolic acids 13 – 15 . The structure of 1 was established based on spectroscopic studies (¹H‐ and ¹³C‐NMR, IR, and HR‐ESI‐MS). This is the first report of the isolation of a diterpene from the Alibertia genus in Rubiaceae.