QSAR as a random event: criteria of predictive potential for a chance model

The CORAL software (http://www.insilico.eu/coral) was suggested as a tool to build up quantitative structure–property/activity relationships (QSPRs/QSARs). This software is based on conception “a QSPR/QSAR model should be interpreted as a random event.” This is reflection of fact: different distributions into the training set (substances involved in modeling process) and the validation set (substances, which are not known at the moment of the modeling process) give models with significant dispersion in the statistical quality of the QSPR/QSAR. Results of experiments with the software and possible ways of further improvement of this software are discussed. The most attractive new ways to estimate predictive potential of the CORAL model seem to be the following ones: (i) index of ideality of correlation and (ii) correlation contradiction index. These can be also proposed as criteria of predictive potential for arbitrary QSPR/QSAR.

     

Hasse diagram technique as a tool for water quality assessment

The management of the quality large water catchments is a complex problem which requires intelligent data analysis on various levels – analytical, spatial, and temporal. Recently, a successful approach is developed combining advanced multivariate data treatment approaches like self-organizing maps of Kohonen (SOM) and Hasse diagram technique (HDT). In the first step of the environmetric analysis the monitoring data were subject to pre-processing using SOMs to reduce the number of objects and/or water quality parameters. In the next step HDT for partial ranking (both in spatial and temporal aspect) was applied according to the pre-selected set of the water quality parameters. The use of the water quality norms issued by the Bulgarian environmental authorities revealed important details in assessing the Maritsa River water quality. Thus, the relations between different water quality patterns and sampling stations could be used by water management authorities during the period of observation.     

The bulk viscosity of a fluid: the inverse power potential

The bulk viscosity coefficient of a moderately dense gas has been evaluated numerically for an inverse power potential. The calculation, to order density squared, is based on the microscopic theory of Snider et al. The results are compared to those from the corresponding expression of the modified Enskog theory. Agreement between the sets of values is within 1%.     

Determining the validity of a QSAR model--a classification approach

The determination of the validity of a QSAR model when applied to new compounds is an important concern in the field of QSAR and QSPR modeling. Various scoring techniques can be applied to specific types of models. We present a technique with which we can state whether a new compound will be well predicted by a previously built QSAR model. In this study we focus on linear regression models only, though the technique is general and could also be applied to other types of quantitative models. Our technique is based on a classification method that divides regression residuals from a previously generated model into a good class and bad class and then builds a classifier based on this division. The trained classifier is then used to determine the class of the residual for a new compound. We investigated the performance of a variety of classifiers, both linear and nonlinear. The technique was tested on two data sets from the literature and a hand built data set. The data sets selected covered both physical and biological properties and also presented the methodology with quantitative regression models of varying quality. The results indicate that this technique can determine whether a new compound will be well or poorly predicted with weighted success rates ranging from 73% to 94% for the best classifier.     

Antioxidant therapy as a potential approach to severe influenza-associated complications

With the appearance of the novel influenza A (H1N1) virus 2009 strain we have experienced a new influenza pandemic and many patients have died from severe complications associated with this pandemic despite receiving intensive care. This suggests that a definitive medical treatment for severe influenza-associated complications has not yet been established. Many studies have shown that superoxide anion produced by macrophages infiltrated into the virus-infected organs is implicated in the development of severe influenza-associated complications. Selected antioxidants, such as pyrrolidine dithiocabamate, N-acetyl-L-cysteine, glutathione, nordihydroguaiaretic acid, thujaplicin, resveratrol, (+)-vitisin A, ambroxol, ascorbic acid, 5,7,4-trihydroxy-8-methoxyflavone, catechins, quercetin 3-rhamnoside, iso- quercetin and oligonol, inhibit the proliferation of influenza virus and scavenge superoxide anion. The combination of antioxidants with antiviral drugs synergistically reduces the lethal effects of influenza virus infections. These results suggest that an agent with antiviral and antioxidant activities could be a drug of choice for the treatment of patients with severe influenza-associated complications. This review article updates knowledge of antioxidant therapy as a potential approach to severe influenza-associated complications.     

Polyelectrolyte-modified inverse microemulsions and their use as templates for the formation of magnetite nanoparticles

This paper is focused on the characterization of polyelectrolyte-modified inverse microemulsions and their use as templates for the synthesis of magnetite nanoparticles. It is shown that the cationic polyelectrolyte poly(diallyldimethylammonium chloride) (PDADMAC) of low molar mass can be incorporated into the individual inverse microemulsion droplets (L2 phase) consisting of heptanol, water, and an amphoteric surfactant with a sulfobetaine head group. Up to a polymer concentration of 20% by weight in the aqueous phase and for different molecular weights of the polymer, an isotropic phase still exists. At a PDADMAC concentration of 10% the area of the isotropic L2 phase is shifted in direction to the water corner. In the percolated area of the L2 phase, i.e., at higher water content, a temperature-dependent change in the conductivity can by observed, and bulk water can be detected by means of differential scanning calorimetry measurements. The unusual temperature-dependent behavior of the polymer-modified system, i.e., the conductivity decrease with increasing temperature, can be explained by temperature-sensitive polyelectrolyte-surfactant interactions, influencing the droplet-droplet interactions. These PDADMAC-modified microemulsions can be successfully used as a template for the formation of ultrafine magnetite particles, in contrast to the nonmodified microemulsion, where the process is misdirected due to the "disturbing" effect of the surfactants. However, in the presence of PDADMAC the surfactant head groups were masked, and therefore magnetite can be synthesized. During the process of magnetite formation the PDADMAC controls the particle growing and stabilizes spherical magnetite particles with a diameter of 17 nm, which can be redispersed without a change in size.     

QMQSAR: utilization of a semiempirical probe potential in a field-based QSAR method

A semiempirical quantum mechanical approach is described for the creation of molecular field-based QSAR models from a set of aligned ligand structures. Each ligand is characterized by a set of probe interaction energy (PIE) values computed at various grid points located near the surface of the ligand. Single-point PM3 calculations afford these PIE values, which represents a pool of independent variables from which multilinear regression models of activity are built. The best n-variable fit is determined by constructing an initial regression using standard forward stepwise selection, followed by refinement using a simulated annealing technique. The resulting fit provides an easily interpreted 3D physical model of ligand binding affinity. Validation against three literature datasets demonstrates the ability of the semiempirical potential to model critical binding interactions in diverse systems.     

Theoretical studies of Pt-Ti nanoparticles for potential use as PEMFC electrocatalysts

A theoretical investigation is presented of alloying platinum with titanium to form binary Pt-Ti nanoalloys as an alternative to the expensive pure platinum catalysts commonly used for Proton Exchange Membrane Fuel Cell cathode electrocatalysts. Density Functional Theory calculations are performed to investigate compositional effects on structural properties as well as Oxygen Reduction Reaction kinetics and poisoning effects. High symmetry A(32)-B(6) clusters are studied to investigate structural properties. From these structures binding energies of hydroxyl and carbon monoxide are studied on a range of sites on the surface of the clusters. Promising results are obtained suggesting that the bimetallic Pt-Ti nanoalloys may exhibit enhanced properties compared to pure platinum catalysts.     

On further application of r as a metric for validation of QSAR models

Validation is a crucial aspect for quantitative structure–activity relationship (QSAR) model development. External validation is considered, in general, as the most conclusive proof of predictive capacity of a QSAR model. In the absence of truly external data set, external validation is usually performed on test set compounds, which are members of the original data set but not used in model development exercise. In the case of small data sets, QSAR researchers experience problem in model development due to the fact that the developed models may be less reliable on account of the small number of training set compounds and such models may also show poor external predictability because the models may not have captured all necessary features required for the particular structure–activity relationships. The present paper attempts to show that ‘true r_(LOO)’ statistic calculated based on the model derived from the undivided data set with application of variable selection strategy at each cycle of leave‐one‐out (LOO) validation may reflect external validation characteristics of the developed model thus obviating the requirement of splitting of the data set into training and test sets. This approach may be helpful in the case of small data sets as it uses all available data for model development and validation thus making the resulting model more reliable. Copyright © 2009 John Wiley & Sons, Ltd.     

The potential of tetrandrine as a protective agent for ischemic stroke

Stroke is one of the leading causes of mortality, with a high incidence of severe morbidity in survivors. The treatment to minimize tissue injury after stroke is still unsatisfactory and it is mandatory to develop effective treatment strategies for stroke. The pathophysiology of ischemic stroke is complex and involves many processes including energy failure, loss of ion homeostasis, increased intracellular calcium level, platelet aggregation, production of reactive oxygen species, disruption of blood brain barrier, and inflammation and leukocyte infiltration, etc. Tetrandrine, a bisbenzylisoquinoline alkaloid, has many pharmacologic effects including anti-inflammatory and cytoprotective effects. In addition, tetrandrine has been found to protect the liver, heart, small bowel and brain from ischemia/reperfusion injury. It is a calcium channel blocker, and can inhibit lipid peroxidation, reduce generation of reactive oxygen species, suppress the production of cytokines and inflammatory mediators, inhibit neutrophil recruitment and platelet aggregation, which are all devastating factors during ischemia/reperfusion injury of the brain. Because tetrandrine can counteract these important pathophysiological processes of ischemic stroke, it has the potential to be a protective agent for ischemic stroke.     

Exploration of nitroimidazoles as radiosensitizers: application of multilayered feature selection approach in QSAR modeling

Structural Chemistry - Radiosensitizers are aimed to augment tumor cell killing by radiation while having much less effect on normal tissues. Nitroimidazoles and related analogues are efficient...     

The potential of wattle tannin extracts for fine use

As a contribution to the fine use of wattle tannin, four fractions, purified tannin (Tp), ether extracts (Te), ethyl acetate extracts (Ta) and water fraction (Tw), were obtained by the methods of precipitation and liquid-liquid extraction of commercial wattle tannin. The number average molecular weights (M(n)) of Tp, Te, Ta and Tw were determined as 2660, 440, 980 and 2050 Da, respectively. The biological activities including protein precipitation, enzyme inhibition and antibacterial potency of each fraction were studied and compared. The results indicated that the molecular weight of each fraction is directly associated with its biological activities. The fraction of Tw showed the strongest capacity to precipitate protein and Ta showed the strongest capacity to inhibit enzyme activities, while Ta and Te showed better antibacterial potency.