Physicochemical and Graph Theoretical Descriptors in Developmental Toxicity SAR: A Comparative Study

Abstract

Chemical insults to the developing fetus can lead to growth retardation, malformation, death, and functional deficits. The present study seeks to determine if physicochemical and/or graph theoretical parameters can be used to determine a structure-activity relationship (SAR) for developmental toxicity, and if consistency is observed among the selected features. The biological data utilized consists of a diverse series of compounds evaluated within the Chernoff-Kavlock in vivo mouse assay. Physicochemical parameters calculated correspond to electronic, steric, and transport properties. Graph theoretical parameters calculated include the simple, valence, and kappa indices. Both sets of parameters were independently applied to derive SARs in order to compare the quality of the respective models. Multiple random sampling, without replacement, was utilized to obtain ten training/test partitions. Models were built by linear discriminant analysis, decision trees, and neural networks respectively. Comparisons on identical sets of data were carried out to determine if any of the model building procedures had a significant advantage in terms of predictive performance. Furthermore, comparison of the features selected within and across the model building processes led to the determination of model consistency. Our results indicate that consistent features related to developmental toxicity are observed and that both physicochemical and graph theoretical parameters have equal utility.     

Study of the Molecular Mobility in Polymers with the Thermally Stimulated Recovery Technique—A Review

Thermally stimulated recovery (TSR) is a non‐conventional mechanical spectroscopy technique that allows to analyse in detail the relaxation processes of polymeric systems in the low frequency region. This work reviews the main aspects and potentialities of this technique. The different kinds of TSR experiments that can be performed, global and thermal sampling (TS) experiments, are described and illustrated with several examples. Also, the different methods for the determination of the thermokinetic parameters (activation energy and pre‐exponential factor) of the thermal sampling (TS) procedure are explained and compared. In this context, the compensation phenomenon, which always appears in TSR results when the studies are performed in the glass transition region of a given system, is discussed. Examples of the application of this technique to different polymeric systems during the last 20 years are provided. An emphasis will be made on the analysis of the effect of crystallinity degree and crosslink density on the TSR response. A comparison between the results (characteristic times and activation energies) obtained by different techniques, namely TSR, dynamic mechanical analysis (DMA), and differential scanning calorimetry (DSC), is made.     

Solid phase microextraction fills the gap in tissue sampling protocols

Metabolomics and biomarkers discovery are an integral part of bioanalysis. However, untargeted tissue analysis remains as the bottleneck of such studies due to the invasiveness of sample collection, as well as the laborious and time-consuming sample preparation protocols. In the current study, technology integrating in vivo sampling, sample preparation and global extraction of metabolites – solid phase microextraction was presented and evaluated during liver and lung transplantation in pig model. Sampling approaches, including selection of the probe, transportation, storage conditions and analyte coverage were discussed. The applicability of the method for metabolomics studies was demonstrated during lung transplantation experiments.     

FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Free‐energy differences between states with different conformational ensembles

Multiple conformations separated by high‐energy barriers represent a challenging problem in free‐energy calculations due to the difficulties in achieving adequate sampling. We present an application of thermodynamic integration (TI) in conjunction with the local elevation umbrella sampling (LE/US) method to improve convergence in alchemical free‐energy calculations. TI‐LE/US was applied to the guanosine triphosphate (GTP) to 8‐Br‐GTP perturbation, molecules that present high‐energy barriers between the anti and syn states and that have inverted preferences for those states. The convergence and reliability of TI‐LE/US was assessed by comparing with previous results using the enhanced‐sampling one‐step perturbation (OSP) method. A linear interpolation of the end‐state biasing potentials was sufficient to dramatically improve sampling along the chosen reaction coordinate. Conformational free‐energy differences were also computed for the syn and anti states and compared to experimental and theoretical results. Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8‐substituted GTP analogs. © 2013 Wiley Periodicals, Inc.     

The Use of Various Chromatographic Techniques for the Determination of Phenylurea Herbicides and Their Corresponding Anilines in Environmental Samples,II. Applications

Abstract

In earlier work, various strategies have been developed for the trace-level determination of phenylurea herbicides and the anilines which are their main degradation products. They include catalytic hydrolysis of the phenylureas on silica, liquid chromatographic fractionation of complex mixtures of herbicides and anilines, derivatization of anilines and herbicides with electron-capture-sensitive reagents, and final analysis by means of capillary gas chromatography. In the present paper, the application of these principles to trace-level analysis of surface water, soil and crop samples is demonstrated.     

Determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry using Pd/Mg chemical modifier and slurry sampling

Effectiveness of Pd/Mg chemical modifier for the accurate direct determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry (GF-AAS) using slurry samples was evaluated. A calibration curve prepared by aqueous zinc standard solution with addition of Pd/Mg chemical modifier is used to determine the zinc concentration in the sediment. The accuracy of the proposed method was confirmed using Certified Reference Materials, NMIJ CRM 7303-a (lacustrine sediment) from National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Japan, and MESS-3 (marine sediment) and PACS-2 (marine sediment) from National Research Council, Canada. The analytical results obtained by employing Pd/Mg modifier are in good agreement with the certified values of all the reference sediment materials. Although for NRC MESS-3 an accurate determination of zinc is achieved even without the chemical modifier, the use of Pd/Mg chemical modifier is recommended as it leads to establishment of a reliable and accurate direct analytical method. One quantitative analysis takes less than 15 minutes after we obtain dried sediment samples, which is several tens of times faster than conventional analytical methods using acid digested sample solutions. The detection limits are 0.13?µg?g^?1 (213.9?nm) and 16?µg?g^?1 (307.6?nm), respectively, in sediment samples, when 40?mg of dried powdered samples are suspended in 20?mL of 0.1?mol?L^?1 nitric acid and a 10?µl portion of the slurry sample is measured. The precision of the proposed method is 8–15% (RSD).     

Volatile organic compounds in an urban environment: a comparison among Belgium,Vietnam and Ethiopia

The effects of urban and indoor air pollution on human health are a major environmental concern for all, but not much has been researched in the developing world. Specifically, quantitative data on the occurrence of volatile organic compounds (VOCs) – main contributors to air pollution – in Asia and Africa are scarce compared to the availability of data in the developed world. This paper presents one of the first studies focusing on the analysis and occurrence of VOCs in Vietnam and Ethiopia, which constitutes part of the novelty of this work. A spectrum of 34 VOCs was measured at eight different urban sites in Ghent (Belgium), Hanoi (Vietnam), Jimma and Addis Ababa (Ethiopia) during three sampling campaigns from September 2008 to September 2010. Sampling was done in an active way by means of sorbent tubes filled with Tenax TA. The analysis was done by TD-GC-MS using internal standard calibration. Data were interpreted and compared in terms of (i) individual, subgroup and total VOCs concentration (TVOCs), (ii) indoor-to-outdoor (I/O) concentration ratios, (iii) source identification by diagnostic ratio and/or correlation coefficients, and (iv) ozone formation potential (OFP) at outdoor sites based on up-to-date maximum incremental reactivity (MIR). I/O concentration ratios varied between 0.2 and 30, with big differences noticed with respect to the type of VOC(s) considered and the type of outdoor sampling location. The highest TVOC concentrations were measured in street samples with maximum values of 54?µg/m³ in Ghent, 507?µg/m³ in Hanoi and 318?µg/m³ in Addis Ababa illustrating the large difference in ambient air quality levels. This is also reflected in the arithmetic mean OFP values (µg/m³) of 82, 1308 and 596 in Ghent, Hanoi and Addis Ababa, respectively. Results of this study could be helpful to support formulation of national policy with regard to ambient air quality.