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SAR and QSAR in Environmental Research

A V Rudik, A V Dmitriev, V M Bezhentsev, A A Lagunin, D A Filimonov, V V Poroikov
Biotransformation is a process of the chemical modifications which may lead to the reactive metabolites, in particular the epoxides. Epoxide reactive metabolites may cause the toxic effects. The prediction of such metabolites is important for drug development and ecotoxicology studies. Epoxides are formed by some oxidation reactions, usually catalysed by cytochromes P450, and represent a large class of three-membered cyclic ethers. Identification of molecules, which may be epoxidized, and indication of the specific location of epoxide functional group (which is called SOE - site of epoxidation) are important for prediction of epoxide metabolites...
November 20, 2017: SAR and QSAR in Environmental Research
Y Wang, F Yan, Q Jia, Y Dai, Q Wang
The development of new and safe anti-human immunodeficiency virus (anti-HIV) drugs has been an urgent task for medical research recently. Herein, based on the norm-index descriptors proposed in this work and previous works, a couple of models were developed for investigating the quantitative structure-activity/toxicity relationship (QSAR/QSTR) of dual-target anti-HIV integrase (IN) and reverse transcriptase (RT) inhibitors. The validation results proved that the developed models were stable and reliable, both in statistical quality and predictive capacity...
November 20, 2017: SAR and QSAR in Environmental Research
M Vračko, V Drgan
Methods for clustering and measures of similarity of chemical structures have become an important supporting tool in chemoinformatics. They represent the basis for categorization of chemicals and read-across, where a molecular property is estimated from 'similar molecules'. This study proposes a clustering scheme within the given dataset with respect to a reference dataset. The scheme was applied on two datasets ToxCast_AR_Agonist and ToxCast_AR_Antagonists with 1654 and 1522 compounds, respectively. The compounds are tested to androgen receptor activity (AR) in 11 high throughput screening assays...
November 20, 2017: SAR and QSAR in Environmental Research
M F Andrada, E G Vega-Hissi, M R Estrada, J C Garro Martinez
This study performed an analysis of the influence of the training and test set rational selection on the quality and predictively of the quantitative structure-activity relationship (QSAR) model. The study was carried out on three different datasets of Influenza Neuraminidase (H1N1) inhibitors. The three datasets were divided into training and test sets using three rational selection methods: based on k-means, Kennard-Stone algorithm and Activity and the results were compared with Random selection. Then, a total of 31,490 mathematical models were developed and those models that presented a determination coefficient higher than: r(2)train > 0...
November 14, 2017: SAR and QSAR in Environmental Research
S S Bhunia, A K Saxena
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25...
November 14, 2017: SAR and QSAR in Environmental Research
D K Behera, P M Behera, L Acharya, A Dixit
Lipid metabolism plays a significant role in influenza virus replication and subsequent infection. The regulatory mechanism governing lipid metabolism and viral replication is not properly understood to date, but both Phospholipase D (PLD1 and PLD2) activities are stimulated in viral infection. In vitro studies indicate that chemical inhibition of PLD1 delays viral entry and reduction of viral loads. The current study reports a three-dimensional pharmacophore model based on 35 known PLD1 inhibitors. A sub-set of 25 compounds was selected as the training set and the remaining 10 compounds were kept in the test set...
November 8, 2017: SAR and QSAR in Environmental Research
S Bhargava, N Adhikari, S A Amin, K Das, S Gayen, T Jha
Application of HIV-1 protease inhibitors (as an anti-HIV regimen) may serve as an attractive strategy for anti-HIV drug development. Several investigations suggest that there is a crucial need to develop a novel protease inhibitor with higher potency and reduced toxicity. Monte Carlo optimized QSAR study was performed on 200 hydroxyethylamine derivatives with antiprotease activity. Twenty-one QSAR models with good statistical qualities were developed from three different splits with various combinations of SMILES and GRAPH based descriptors...
October 26, 2017: SAR and QSAR in Environmental Research
J F Aranda, D E Bacelo, M S Leguizamón Aparicio, M A Ocsachoque, E A Castro, P R Duchowicz
The ANTARES dataset is a large collection of known and verified experimental bioconcentration factor data, involving 851 highly heterogeneous compounds from which 159 are pesticides. The BCF ANTARES data were used to derive a conformation-independent QSPR model. A large set of 27,017 molecular descriptors was explored, with the main intention of capturing the most relevant structural characteristics affecting the studied property. The structural descriptors were derived with different freeware tools, such as PaDEL, Epi Suite, CORAL, Mold(2), RECON, and QuBiLs-MAS, and so it was interesting to find out the way that the different descriptor tools complemented each other in order to improve the statistical quality of the established QSPR...
October 2, 2017: 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
J A Castillo-Garit, G M Casañola-Martin, S J Barigye, H Pham-The, F Torrens, A Torreblanca
The phenols are structurally heterogeneous pollutants and they present a variety of modes of toxic action (MOA), including polar narcotics, weak acid respiratory uncouplers, pro-electrophiles, and soft electrophiles. Because it is often difficult to determine correctly the mechanism of action of a compound, quantitative structure-activity relationship (QSAR) methods, which have proved their interest in toxicity prediction, can be used. In this work, several QSAR models for the prediction of MOA of 221 phenols to the ciliated protozoan Tetrahymena pyriformis, using Chemistry Development Kit descriptors, are reported...
September 2017: SAR and QSAR in Environmental Research
A Furuhama, T I Hayashi, H Yamamoto, N Tatarazako
We evaluated the predictivity and applicability of previously proposed models for the reproductive toxicity of chemicals to Daphnia magna [SAR QSAR Environ. Res. 27:10, 833-850] by using external data from the United States Environmental Protection Agency database ECOTOX. These models were based on quantitative structure-activity-activity relationships (QSAARs) and a quantitative activity-activity relationship (QAAR): the models can be categorized as acute-to-chronic models with (QSAAR) and without (QAAR) structural and physicochemical (e...
September 2017: SAR and QSAR in Environmental Research
M Manal, K Manish, D Sanal, A Selvaraj, V Devadasan, M J N Chandrasekar
Abnormal HDAC function triggers irregular gene transcription that hampers the essential cellular activities leading to tumour activation and progression. HDAC inhibition has, therefore, been reported as a potential target for cancer treatment. In the present study, a sequential computational framework was carried out to discover newer lead compounds, namely HDAC8 inhibitors for cancer therapy. Pharmacophoric hypotheses were generated based on hydroxamic acid derivatives reported earlier for HDAC inhibition...
September 2017: SAR and QSAR in Environmental Research
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No abstract text is available yet for this article.
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
A M Al-Fakih, Z Y Algamal, M H Lee, M Aziz
A robust screening approach and a sparse quantitative structure-retention relationship (QSRR) model for predicting retention indices (RIs) of 169 constituents of essential oils is proposed. The proposed approach is represented in two steps. First, dimension reduction was performed using the proposed modified robust sure independence screening (MR-SIS) method. Second, prediction of RIs was made using the proposed robust sparse QSRR with smoothly clipped absolute deviation (SCAD) penalty (RSQSRR). The RSQSRR model was internally and externally validated based on [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], Y-randomization test, [Formula: see text], [Formula: see text], and the applicability domain...
August 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
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