Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors

Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute ?9.8 kcal/mol to the free energy of binding, with a 10⁸-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is ?11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO^?₂ group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.     

Contrasting behavior in azide pyrolyses: an investigation of the thermal decompositions of methyl azidoformate, ethyl azidoformate and 2-azido-N, N-dimethylacetamide by ultraviolet photoelectron spectroscopy and matrix isolation infrared spectroscopy

The thermal decompositions of methyl azidoformate (N3COOMe), ethyl azidoformate (N3COOEt) and 2-azido-N,N-dimethylacetamide (N3CH2CONMe2) have been studied by matrix isolation infrared spectroscopy and real-time ultraviolet photoelectron spectroscopy. N2 appears as an initial pyrolysis product in all systems, and the principal interest lies in the fate of the accompanying organic fragment. For methyl azidoformate, four accompanying products were observed: HNCO, H2CO, CH2NH and CO2, and these are believed to arise as a result of two competing decomposition routes of a four-membered cyclic intermediate. Ethyl azidoformate pyrolysis yields four corresponding products: HNCO, MeCHO, MeCHNH and CO2, together with the five-membered-ring compound 2-oxazolidone. In contrast, the initial pyrolysis of 2-azido-N,N-dimethyl acetamide, yields the novel imine intermediate Me2NCOCH=NH, which subsequently decomposes into dimethyl formamide (HCONMe2), CO, Me2NH and HCN. This intermediate was detected by matrix isolation IR spectroscopy, and its identity confirmed both by a molecular orbital calculation of its IR spectrum, and by the temperature dependence and distribution of products in the PES and IR studies. Mechanisms are proposed for the formation and decomposition of all the products observed in these three systems, based on the experimental evidence and the results of supporting molecular orbital calculations.     

Durbin-Watson statistic as a morphological estimator of information content

The present work proposes a new approach for the evaluation of the information content in latent variables, and therefore, for the determination of the regression model dimensionality. Several examples are provided, using simulated, real-world, and reference datasets. The results showed that the application of the Durbin-Watson (DW) criterion could be used for the determination of the number of latent variables. Moreover, the method is straightforward in its implementation and could help in the understanding of model behaviour, particularly in complex datasets. A comparison is made with cross-validation techniques for the case of reference datasets, showing the potential of the Durbin-Watson criterion in the characterisation of the regression model. The advantages and disadvantages of this procedure (compared to cross-validation) are discussed. The properties of the information content of the regression vectors (loadings p, w and b vectors) are shown as well as how to use them for the current purpose.     

Applicability of Microaerobic Technology to Enhance BTEX Removal from Contaminated Waters

As the addition of low concentrations of oxygen can favor the initial degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) compounds, this work verified the applicability of the microaerobic technology to enhance BTEX removal in an anaerobic bioreactor supplemented with high and low co-substrate (ethanol) concentrations. Additionally, structural alterations on the bioreactor microbiota were assessed throughout the experiment. The bioreactor was fed with a synthetic BTEX-contaminated water (~ 3 mg L^?1 of each compound) and operated at a hydraulic retention time of 48 h. The addition of low concentrations of oxygen (1.0 mL min^?1 of atmospheric air at 27 °C and 1 atm) assured high removal efficiencies (> 80%) for all compounds under microaerobic conditions. In fact, the applicability of this technology showed to be viable to enhance BTEX removal from contaminated waters, especially concerning benzene (with a 30% removal increase), which is a very recalcitrant compound under anaerobic conditions. However, high concentrations of ethanol adversely affected BTEX removal, especially benzene, under anaerobic and microaerobic conditions. Finally, although bacterial community richness decreased at low concentrations of ethanol, in general, the bioreactor microbiota could deal with the different operational conditions and preserved its functionality during the whole experiment.     

Replacing Synthetic with Microbial Surfactants as Collectors in the Treatment of Aqueous Effluent Produced by Acid Mine Drainage,Using the Dissolved Air Flotation Technique

Dissolved air flotation (DAF) is a well-established separation process employing micro bubbles as a carrier phase. The application of this technique in the treatment of acid mine drainage, using three yeast biosurfactants as alternative collectors, is hereby analyzed. Batch studies were carried out in a 50-cm high acrylic column with an external diameter of 2.5 cm. High percentages (above 94%) of heavy metals Fe(III) and Mn(II) were removed by the biosurfactants isolated from Candida lipolytica and Candida sphaerica and the values were found to be similar to those obtained with the use of the synthetic sodium oleate surfactant. The DAF operation with both surfactant and biosurfactants, achieved acceptable turbidity values, in accordance with Brazilian standard limits. The best ones were obtained by the biosurfactant from C. lipolytica, which reached 4.8 NTU. The results obtained with a laboratory synthetic effluent were also satisfactory. The biosurfactants removed almost the same percentages of iron, while the removal percentages of manganese were slightly higher compared with those obtained in the acid mine drainage effluent. They showed that the use of low-cost biosurfactants as collectors in the DAF process is a promising technology for the mining industries.     

Radiolabeling of low molecular weight d-galactose-based glycodendrimer with technetium-99m and biodistribution studies

Glycodendrimers are neoglycoconjugates that can be considered as bioisosters of glycoproteins, since they can mimic the multivalent interactions of lectin-carbohydrate. The ability of glycodendrimers to present multivalent interactions with lectins as compared to a monovalent ligand is referred to as “cluster effect”. It is expected that, because of the cluster effect, glycodendrimers would result in a better association with lectins than mono-carbohydrate anchored systems. Radioisotopes are useful to evaluate biodistribution of molecules. This study is important to obtain information about molecule–receptor interactions. Indeed, such study can provide an exquisite tool to evaluate the affinity of certain molecules to specific areas in the body, leading to the development of new radiopharmaceuticals and/or drug delivery systems. Herein, we describe a d-galactose coated low molecular weight PAMAM G0 dendrimer that was successfully radiolabeled with technetium-99m. Biodistribution studies and scintigraphic images were performed in healthy mice. It was observed high liver uptake which was significantly reduced in blocking studies, indicating hepatic specificity. Therefore, low molecular weight glycodendrimer can be considered as useful platform for selective targeting of drugs to the liver and to assess hepatic function.     

A Robust Algorithm for Roots Selection and Saturation Pressure Calculation for Cubic Equations of State

Journal of Solution Chemistry - In this work, a robust and rigorous procedure for roots calculation and selection for a Cubic Equation of State is presented. Roundoff errors are detected and...     

Selected Thoughts on Hydrophobicity in Drug Design

The fundamental aim of drug design in research and development is to invent molecules with selective affinity towards desired disease-associated targets. At the atomic loci of binding surfaces, systematic structural variations can define affinities between drug candidates and biomolecules, and thereby guide the optimization of safety, efficacy and pharmacologic properties. Hydrophobic interaction between biomolecules and drugs is integral to binding affinity and specificity. Examples of antiviral drug discovery are discussed.