Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors` ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Gaining ligand selectivity in thyroid hormone receptors via entropy

Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TR beta) vs. TR alpha reduce cholesterol and fat without effects on heart rate; thus, it is important to understand TR beta-selective binding. Binding of 3 selective ligands (GC-1, KB141, and GC-24) is characterized at the atomic level; preferential binding depends on a nonconserved residue (Asn-331 beta) in the TR beta ligand-binding cavity (LBC), and GC-24 gains extra selectivity from insertion of a bulky side group into an extension of the LBC that only opens up with this ligand. Here we report that the natural TH 3,5,3`-triodothyroacetic acid (Triac) exhibits a previously unrecognized mechanism of TR beta selectivity. TR x-ray structures reveal better fit of ligand with the TR alpha LBC. The TR beta LBC, however, expands relative to TR alpha in the presence of Triac (549 angstrom(3) vs. 461 angstrom(3)), and molecular dynamics simulations reveal that water occupies the extra space. Increased solvation compensates for weaker interactions of ligand with TR beta and permits greater flexibility of the Triac carboxylate group in TR beta than in TR alpha. We propose that this effect results in lower entropic restraint and decreases free energy of interactions between Triac and TR beta, explaining subtype-selective binding. Similar effects could potentially be exploited in nuclear receptor drug design.

Structural and chemical basis for anticancer activity of a series of 'beta'-tubulin ligands: molecular modeling and 3D QSAR studies

An important approach to cancer therapy is the design of small molecule modulators that interfere with microtubule dynamics through their specific binding to the ²-subunit of tubulin. In the present work, comparative molecular field analysis (CoMFA) studies were conducted on a series of discodermolide analogs with antimitotic properties. Significant correlation coefficients were obtained (CoMFA(i), q² =0.68, r²=0.94; CoMFA(ii), q² = 0.63, r²= 0.91), indicating the good internal and external consistency of the models generated using two independent structural alignment strategies. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the 3D contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of discodermolide analogs, and should be useful for the design of new specific ²-tubulin modulators with potent anticancer activity.

Antileishmanial Activity of the Hydroalcoholic Extract of Miconia langsdorffii, Isolated Compounds, and Semi-Synthetic Derivatives

The in vitro activity of the crude hydroalcoholic extract of the aerial parts of Miconia langsdorffii Cogn. was evaluated against the promastigote forms of L. amazonensis, the causative agent of cutaneous leishmaniasis in humans. The bioassay-guided fractionation of this extract led to identification of the triterpenes ursolic acid and oleanolic acid as the major compounds in the fraction that displayed the highest activity. Several ursolic acid semi-synthetic derivatives were prepared, to find out whether more active compounds could be obtained. Among these ursolic acid-derived substances, the C-28 methyl ester derivative exhibited the best antileishmanial activity.

Anti-Plasmodium Activity of Angiotensin II and Related Synthetic Peptides

Plasmodium species are the causative agents of malaria, the most devastating insect-borne parasite of human populations. Finding and developing new drugs for malaria treatment and prevention is the goal of much research. Angiotensins I and II (ang I and ang II) and six synthetic related peptides designated Vaniceres 1-6 (VC1-VC6) were assayed in vivo and in vitro for their effects on the development of the avian parasite, Plasmodium gallinaceum. Ang II and VC5 injected into the thoraces of the insects reduced mean intensities of infection in the mosquito salivary glands by 88% and 76%, respectively. Although the mechanism(s) of action is not completely understood, we have demonstrated that these peptides disrupt selectively the P. gallinaceum cell membrane. Additionally, incubation in vitro of sporozoites with VC5 reduced the infectivity of the parasites to their vertebrate host. VC5 has no observable agonist effects on vertebrates, and this makes it a promising drug for malaria prevention and chemotherapy.

omega-Transaminases as efficient biocatalysts to obtain novel chiral selenium-amine ligands for Pd-catalysis

omega-Transaminases have been evaluated as biocatalysts in the reductive amination of organoselenium acetophenones to the corresponding amines, and in the kinetic resolution of racemic organoselenium amines. Kinetic resolution proved to be more efficient than the asymmetric reductive amination. By using these methodologies we were able to obtain both amine enantiomers in high enantiomeric excess (up to 99%). Derivatives of the obtained optically pure o-selenium 1-phenylethyl amine were evaluated as ligands in the palladium-catalyzed asymmetric alkylation, giving the alkylated product in up to 99% ee.

Nickel sorption capacity of ground xylem of Quercus ilex trees and effects of selected ligands present in the xylem sap

In this work the influence of four different ligands present in the xylem sap of Quercus ilex (histidine, citric, oxalic and aspartic acids) on Ni(II) adsorption by xylem was investigated. Grinded xylem was trapped in acrylic columns and solutions of Ni(II), in the absence and presence of the four ligands prepared in KNO(3) 0-1 mol L(-1) at pH 5.5, were percolated through the column. Aliquots of solutions were recovered in the column end for Ni determination by graphite furnace atomic absorption spectrometry (GFAAS). The experimental. data to describe Ni sorption by xylem in both the presence and absence of ligands was better explained by the Freundlich isotherm model. The decreasing affinity order of ligands for Ni was: oxalic acid > citric acid > histidine > aspartic acid. On the other hand, the Ni(II) adsorption by xylem increased following the inverse sequence of ligands. Potentiometric titrations of acidic groups were carried out to elucidate the sorption site groups available in Q. ilex xylem. The potentiometric titration has shown three sorption sites: pK(a) 2.6 (57.7% of the sorption sites), related to monobasic aliphatic carboxylic acids or nitrogen aromatic bases, pK(a) 8.1 (9.6%) and pK(a) 9.9 (32.7%), related to phenolic groups. (C) 2008 Elsevier GmbH. All rights reserved.

Effect of impeller type and mechanical agitation on the mass transfer and power consumption aspects of ASBR operation treating synthetic wastewater

The effect of flow type and rotor speed was investigated in a round-bottom reactor with 5 L useful volume containing 2.0 L of granular biomass. The reactor treated 2.0 L of synthetic wastewater with a concentration of 800 mgCOD/L in 8-h cycles at 30 degrees C. Five impellers, commonly used in biological processes, have been employed to this end, namely: a turbine and a paddle impeller with six-vertical-flat-blades, a turbine and a paddle impeller with six-45 degrees-inclined-flat-blades and a three-blade-helix impeller. Results showed that altering impeller type and rotor speed did not significantly affect system stability and performance. Average organic matter removal efficiency was about 84% for filtered samples, total volatile acids concentration was below 20 mgHAc/L and bicarbonate alkalinity a little less than 400 mgCaCO(3)/L for most of the investigated conditions. However, analysis of the first-order kinetic model constants showed that alteration in rotor speed resulted in an increase in the values of the kinetic constants (for instance, from 0.57 h(-1) at 50 rpm to 0.84 h(-1) at 75 rpm when the paddle impeller with six-45 degrees-inclined-flat-blades was used) and that axial flow in mechanically stirred reactors is preferable over radial-flow when the vertical-flat-blade impeller is compared to the inclined-flat-blade impeller (for instance at 75 rpm, from 0.52 h(-1) with the six-flat-blade-paddle impeller to 0.84 h(-1) with the six-45 degrees-inclined-flat-blade-paddle impeller), demonstrating that there is a rotor speed and an impeller type that maximize solid-liquid mass transfer in the reaction medium. Furthermore, power consumption studies in this reduced reactor volume showed that no high power transfer is required to improve mass transfer (less than 0.6 kW/10(3) m(3)). (C) 2008 Elsevier Ltd. All rights reserved.

Influence of organic shock loads in an ASBBR treating synthetic wastewater with different concentration levels

Safe application of the anaerobic sequencing biofilm batch reactor (ASBBR) still depends on deeper insight into its behavior when faced with common operational problems in wastewater treatments such as tolerance to abrupt variations in influent concentration, so called shock loads. To this end the current work shows the effect of organic shock loads on the performance of an ASBBR, with a useful volume of 5 L, containing 0.5-cm polyurethane cubes and operating at 30 degrees C with mechanical stirring of 500 rpm. In the assays 2 L of two types of synthetic wastewater were treated in 8-h cycles. Synthetic wastewater I was based on sucrose-amide-cellulose with concentration of 500 mg COD/L and synthetic wastewater II was based on volatile acids with concentration ranging from 500 to 2000 mg COD/L. Organic shock loads of 2-4 times the operation concentration were applied during one and two cycles. System efficiency was monitored before and after application of the perturbation. When operating with concentrations from 500 to 1000 mg COD/L and shock loads of 2-4 times the influent concentration during one or two cycles the system was able to regain stability after one cycle and the values of organic matter, total and intermediate volatile acids, bicarbonate alkalinity and pH were similar to those prior to the perturbations. At a concentration of 2000 mg COD/L the reactor appeared to be robust, regaining removal efficiencies similar to those prior to perturbation at shock loads twice the operation concentration lasting one cycle and stability was recovered after two cycles. However, for shock loads twice the operation concentration during two cycles and shock loads four times the operation concentration during one or two cycles filtered sample removal efficiency decreased to levels different from those prior to perturbation, on an average of 90-80%, approximately, yet the system managed to attain stability within two cycles after shock application. Therefore, this investigation envisions the potential of full scale application of this type of bioreactor which showed robustness to organic shock loads, despite discontinuous operation and the short times available for treating total wastewater volume. (c) 2007 Elsevier Ltd. All rights reserved.

Fluidized ASBR treating synthetic wastewater: Effect of recirculation velocity

An investigation has been performed on the effect of liquid phase recirculation velocity and increasing influent concentration on the stability and efficiency of an anaerobic sequencing batch reactor (ASBR) containing granular biomass. The reactor treated 1.3 L synthetic wastewater at 30 degrees C in 6 h cycles. Initially the effect of recirculation velocity was investigated employing velocities of 5, 7 and 10 m/h and influent concentration of 500 mg COD/L. At these velocities, filtered sample organic matter removal efficiencies were 83, 85 and 84%, respectively. A first order kinetic model could also be fitted to the experimental organic matter concentration profiles. The kinetic parameter values of this model were 1.35, 2.36 and 1.00 h(-1) at the recirculation velocities of 5, 7 and 10 m/h, respectively. The recirculation velocity of 7 m/h was found to be the best operating strategy and this value was maintained while the influent concentration was altered in order to verify system efficiency and stability at increasing organic load. Influent concentration of 1000 mg COD/L resulted in filtered sample organic matter removal efficiency of 80%, and a first order kinetic parameter value of 1.14 h(-1), whereas the concentration of 1500 mg COD/L resulted in an efficiency of 82% and a kinetic parameter value of 1.31 h(-1). (C) 2007 Elsevier B.V. All rights reserved.

Chemical characterization and anticorrosion properties of corrosion products formed on pure copper in synthetic rainwater of Rio de Janeiro and Sao Paulo

This work aims to characterize corrosion products formed on copper samples exposed to synthetic rainwater of Rio Janeiro and Sao Paulo. XRD and XPS were employed to determine their composition, while electrochemical techniques were used to evaluate their protective properties. XRD and XPS indicated the thickening of the corrosion layer with time. Electrochemical results showed that the protectiveness of the corrosion layer depends on the solution composition. Based on our findings a corrosion mechanism for copper in simulated rainwater is proposed where the role of NH(4)(+) ions in the cuprite layer partial regeneration is taken into account. (C) 2009 Elsevier Ltd. All rights reserved.

Liquid-Liquid Equilibrium of Aqueous Two-Phase Systems Containing Some Synthetic Polyelectrolytes and Polyethylene Glycol

Experimental results are presented for the liquid-liquid equilibrium of aqueous two-phase systems containing a synthetic polyelectrolyte (polysodium acrylate, polysodium methacrylate, and polysodium ethylene sulfonate) and polyethylene glycol at (298.2 and 323.2) K. A total of 40 phase diagrams were obtained, comprising data both of the binodal curve (obtained through cloud-point measurements) and of equilibrium compositions. The influences of temperature, the nature of the polyelectrolyte monomer unit, and the chain length of both types of polymers are analyzed and discussed.

Thermodynamics of aqueous solutions of polyelectrolytes: Experimental results for the activity of water in aqueous solutions of (a single synthetic polyelectrolyte and sodium chloride)

Experimental results for the activity of water in aqueous solutions of 10 single, synthetic polyelectrolytes (polysodium acrylate, polysodium methacrylate, polyammonium acrylate, polysodium ethylene sulfonate, and polysodium styrene sulfonate) and sodium chloride at 298.2 K are presented. The experimental work was performed by applying the isopiestic method with sodium chloride as a reference substance. As expected, the activity of water decreases when the concentration of a polyelectrolyte and/or sodium chloride increases. At constant concentration of a polyelectrolyte and sodium chloride, the activity of water depends on the monomer unit and the molecular mass of the polyelectrolyte. The new data are to be used in future work to develop and test models for the Gibbs excess energy of aqueous solutions of polyelectrolytes.

Thermodynamics of aqueous solutions of polyelectrolytes: Experimental results for the activity of water in aqueous solutions of some single synthetic polyelectrolytes

Experimental results for the activity of water in aqueous solutions of 10 single polyelectrolytes (two polysodium acrylates, two polysodium methacrylates, three polyammonium acrylates, two polysodium ethylene sulfonates, and one polysodium styrene sulfonate) at (298.2 and 323.2) K are reported. The isopiestic method was employed in these experiments with aqueous solutions of sodium chloride as references. The polyelectrolytes were characterized by three averaged molecular masses determined by gel permeation chromatography. Furthermore, the density and the refractive index increments of the aqueous polyelectrolyte solutions are reported. Although a similar pattern for the activity of water was observed for all systems (i.e., the osmotic coefficient increases with rising polyelectrolyte concentration), the experimental results show that this property depends on the monomer type as well as on the size of the polymer chain. The temperature (varied from (298.2 to 323.2) K) has only a small influence on the activity of water.

The sorption of toxic elements onto natural zeolite, synthetic goethite and modified powdered block carbon

Inorganic elements analyses of Carapicuiba lake reveal that As, Cr, Pb and Mn are above the recommended drinking water standards. The mean total concentrations of toxic elements in surface water decrease in the order Mn > Cr > Pb > As. At elevated concentrations, toxic elements like Cr can accumulate in soils and enter the food chain, leading to serious health hazards and threatening the long-term sustainability of the local ecosystem. Absorbing materials has often been used to improve water quality. In this investigation three types of material were studied: the natural zeolite (mordenite); synthetic goethite and the powdered block carbon modified. The adsorption of Pb(2+) and Mn(2+) onto natural zeolite as a function of their concentrations was studied at 24 degrees C by varying the metal concentration from 100 to 400 mg L(-1) while keeping all other parameters constant. The low-cost zeolites removed Pb from water without any pretreatment at pH values <6. The maximum adsorption attained was as follows: Pb(2+) 78.7% and Mn(2+) 19.6%. The modified powdered block carbon effectively removed As(V) and Cr(VI) while goethite removed more chromate than arsenate in the pH range 5-6. Results of this study will be used to evaluate the application these materials for the treatment of the Carapicuiba lake`s water.