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SAR and QSAR in Environmental Research

A L Brock, M Kästner, S Trapp
In biodegradation studies with isotope-labelled pesticides, fractions of non-extractable residues (NER) remain, but their nature and composition is rarely known, leading to uncertainty about their risk. Microbial growth leads to incorporation of carbon into the microbial mass, resulting in biogenic NER. Formation of microbial mass can be estimated from the microbial growth yield, but experimental data is rare. Instead, we suggest using prediction methods for the theoretical yield based on thermodynamics. Recently, we presented the Microbial Turnover to Biomass (MTB) method that needs a minimum of input data...
September 12, 2017: SAR and QSAR in Environmental Research
O A Raevsky, V Y Grigorev, D E Polianczyk, O E Raevskaja, J C Dearden
Aqueous solubility at pH = 7.4 is a very important property for medicinal chemists because this is the pH value of physiological media. The present work describes the application of three different methods (support vector machine (SVM), random forest (RF) and multiple linear regression (MLR)) and three local quantitative structure-property relationship (QSPR) models (regression corrected by nearest neighbours (RCNN), arithmetic mean property (AMP) and local regression property (LoReP)) to construct stable QSPRs with clear mechanistic interpretation...
September 11, 2017: SAR and QSAR in Environmental Research
A S Korotkov, M Gravit
The applicability of 3D map modelling for melting point prediction was studied. The melting points in the ammonium polyphosphate-pentaerythritol-melamine chemical system of intumescent flame-retardant coatings over a wide range of concentrations were collected. The ternary diagram (triangle) of the melting points was plotted and an approximated 3D map was built for the range 205-345°C. The present work contains the thermal data for the observed ternary system and provides a new graphic system for making predictions for intumescent flame-retardant coatings...
September 8, 2017: SAR and QSAR in Environmental Research
W Larisch, K-U Goss
Calculation of the concentration-time profile in four consecutive, well-mixed compartments that are connected by diffusional transport is a frequently occurring problem for chemists and engineers. Mathematically this is equivalent to many other problems such as the concentration profiles of a parent compound and its three consecutive reaction products resulting from reversible first-order kinetics. Here we present an analytical solution to this problem implemented in a Microsoft Excel spreadsheet (available for download) and we discuss various examples of how this simple-to-use tool can be applied to very different scenarios from various fields of science...
September 1, 2017: SAR and QSAR in Environmental Research
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August 17, 2017: SAR and QSAR in Environmental Research
D T Manallack
Drug-likeness has long been studied in the pursuit of finding new medicines. Similarly, in the agrochemical field there is value in exploring the properties of the chemicals involved. Patterns that emerge can potentially influence future discovery campaigns to improve the probability of commercial success. In this study we investigate the acid/base properties and physicochemical characteristics of three classes of compounds: fungicides, herbicides and insecticides. In comparison with FDA-approved drugs, it was noted that the pesticides were generally smaller, possessed a neutral charge state and were more lipophilic...
August 11, 2017: SAR and QSAR in Environmental Research
K Khan, K Roy
In this study, externally validated quantitative structure-toxicity relationship (QSTR) models were developed for toxicity of cosmetic ingredients on three different ecotoxicologically relevant organisms, namely Pseudokirchneriella subcapitata, Daphnia magna and Pimephales promelas following the OECD guidelines. The final models were developed by partial least squares (PLS) regression technique, which is more robust than multiple linear regression. The obtained model for P. subcapitata shows that molecular size and complexity have significant impacts on the toxicity of cosmetics...
August 7, 2017: SAR and QSAR in Environmental Research
J C Dearden, M Hewitt, G M Bresnen, C N Gregg
Animal models are known not to predict human responses well, in general. However, we have been able to demonstrate that, for a series of non-steroidal anti-inflammatory drugs that are or were in clinical use, the incorporation of two simple physicochemical properties results in excellent correlations between human and rodent potencies for anti-inflammatory, analgesic and anti-pyretic activities. This has the potential to allow the use of historical data to improve drug development.
July 25, 2017: SAR and QSAR in Environmental Research
C R García-Jacas, Y Marrero-Ponce, T Hernández-Ortega, K Martinez-Mayorga, L Cabrera-Leyva, J C Ledesma-Romero, I Aguilera-Fernández, A R Rodríguez-León
A novel mathematical procedure to codify chiral features of organic molecules in the QuBiLS-MIDAS framework is introduced. This procedure constitutes a generalization to that commonly used to date, where the values 1 and -1 (correction factor) are employed to weight the molecular vectors when each atom is labelled as R (rectus) or S (sinister) according to the Cahn-Ingold-Prelog rules. Therefore, values in the range [Formula: see text] with steps equal to 0.25 may be accounted for. The atoms labelled R or S can have negative and positive values assigned (e...
July 14, 2017: SAR and QSAR in Environmental Research
S Önlü, M Türker Saçan
Quantitative structure-activity relationship (QSAR) modelling is a major tool employed in the prediction of various endpoints. However, current QSAR literature is missing a full understanding of the impact of quantum chemical calculation methods on the estimation of molecular descriptors and model performance. Here, we provide a comprehensive analysis of the quantitative effects of different geometry optimization methods (semi-empirical, ab initio Hartee-Fock and density functional theory) on the molecular descriptors...
July 14, 2017: SAR and QSAR in Environmental Research
T M Martin, C R Lilavois, M G Barron
Previous modelling of the median lethal dose (oral rat LD50) has indicated that local class-based models yield better correlations than global models. We evaluated the hypothesis that dividing the dataset by pesticidal mechanisms would improve prediction accuracy. A linear discriminant analysis (LDA) based-approach was utilized to assign indicators such as the pesticide target species, mode of action, or target species - mode of action combination. LDA models were able to predict these indicators with about 87% accuracy...
July 13, 2017: SAR and QSAR in Environmental Research
D López-Malo, J I Bueso-Bordils, M J Duart, P A Alemán-López, R V Martín-Algarra, G M Antón-Fos, L Lahuerta-Zamora, J Martínez-Calatayud
Fluorimetric analysis is still a growing line of research in the determination of a wide range of organic compounds, including pharmaceuticals and pesticides, which makes necessary the development of new strategies aimed at improving the performance of fluorescence determinations as well as the sensitivity and, especially, the selectivity of the newly developed analytical methods. In this paper are presented applications of a useful and growing tool suitable for fostering and improving research in the analytical field...
July 2017: SAR and QSAR in Environmental Research
C Chen, D Wang, H Wang, Z Lin, Z Fang
Quorum sensing inhibitors (QSIs) are promising alternatives to antibiotics, but they are discharged into the environment after their use cycle. This poses joint effects on the organisms in the environment. Therefore, it is of great importance to study the combined toxicities of QSIs and antibiotics. In this study, we investigated the single and combined toxicities of four potential QSIs and 11 sulfonamides (SAs) on Escherichia coli. The results revealed that the single toxicities of SAs were greater than those of QSIs, and the toxicities were found positively related to the binding energies (Ebind) with their target proteins, for both antibiotics and QSIs...
July 2017: SAR and QSAR in Environmental Research
S Bitam, M Hamadache, S Hanini
A new family of AChE inhibitors, N-benzylpiperidines, showed exceptional efficacy in vitro and in vivo, minimal side effects and high selectivity for acetylcholinesterase (AChE). Three regression methods were chosen in this work to develop robust predictive models, namely multiple linear regression (MLR), genetic function approximation (GFA) and multilayer perceptron network (MLP). Ten descriptors were selected for a dataset of 99 molecules, using a genetic algorithm. The best results were obtained for MLP with a 10-6-1 artificial neural network model trained with the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm...
June 14, 2017: SAR and QSAR in Environmental Research
J P Doucet, E Papa, A Doucet-Panaye, J Devillers
QSAR models are proposed for predicting the toxicity of 33 piperidine derivatives against Aedes aegypti. From 2D topological descriptors, calculated with the PaDEL software, ordinary least squares multilinear regression (OLS-MLR) treatment from the QSARINS software and machine learning and related approaches including linear and radial support vector machine (SVM), projection pursuit regression (PPR), radial basis function neural network (RBFNN), general regression neural network (GRNN) and k-nearest neighbours (k-NN), led to four-variable models...
June 12, 2017: SAR and QSAR in Environmental Research
A Bak, V Kozik, A Smolinski, J Jampilek
Finding a balance between a desired drug's potency and its physicochemical properties that are important for its molecule pharmacokinetic or pharmacodynamics profile is still a challenging issue in rational drug discovery. Quantitative assessment of the lipophilic characteristics of potential drug molecules is indispensable for efficient development of Absorption, Distribution, Metabolism, Excretion, Toxicity-tailored structure-activity models; therefore reliable procedures for deriving log P from molecular structure are desirable...
June 2, 2017: SAR and QSAR in Environmental Research
N H Dimitrova, I A Dermen, N D Todorova, K G Vasilev, S D Dimitrov, O G Mekenyan, Y Ikenaga, T Aoyagi, Y Zaitsu, C Hamaguchi
In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL...
June 2017: SAR and QSAR in Environmental Research
M C A Costa, M M C Ferreira
A series of 50 derivatives of 1,4-naphthoquinone tested against human HL-60 leukaemic cells showed activity at a wide range of concentrations. A multivariate quantitative structure-activity relationship (QSAR) study of 45 compounds was performed through principal component analysis (PCA) and partial least squares (PLS) regression. A good PLS regression model was obtained with two factors describing 60.1% of the total variance, and the selected descriptors were partial atomic charge at carbons 1 and 10 (C1 and C10) and total dipole moment (DIP)...
May 11, 2017: SAR and QSAR in Environmental Research
R Geerts, C G van Ginkel, C M Plugge
The biodegradation of N-alkyl polypropylene polyamines (NAPPs) was studied using pure and mixed cultures to enable read-across of ready biodegradability test results. Two Pseudomonas spp. were isolated from activated sludge with N-oleyl alkyl propylene diamine and N-coco alkyl dipropylene triamine, respectively. Both strains utilized all NAPPs tested as the sole source of carbon, nitrogen and energy for growth. Mineralization of NAPPs was independent of the alkyl chain length and the size of the polyamine moiety...
May 8, 2017: SAR and QSAR in Environmental Research
O Martínez-Santiago, Y Marrero-Ponce, R Vivas-Reyes, O M Rivera-Borroto, E Hurtado, M A Treto-Suarez, Y Ramos, F Vergara-Murillo, M E Orozco-Ugarriza, Y Martínez-López
Graph derivative indices (GDIs) have recently been defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (finite difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural information based on the concept of the derivative of a molecular graph with respect to a given event (S) over duplex, triplex and quadruplex relations of atoms (vertices)...
May 2017: SAR and QSAR in Environmental Research
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