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SAR and QSAR in Environmental Research

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https://www.readbyqxmd.com/read/28610432/qsar-model-for-prediction-of-the-therapeutic-potency-of-n-benzylpiperidine-derivatives-as-ache-inhibitors
#1
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
https://www.readbyqxmd.com/read/28604113/qsar-models-for-predicting-the-toxicity-of-piperidine-derivatives-against-aedes-aegypti
#2
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
https://www.readbyqxmd.com/read/28573881/in-silico-estimation-of-basic-activity-relevant-parameters-for-a-set-of-drug-absorption-promoters
#3
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
https://www.readbyqxmd.com/read/28490186/two-dimensional-quantitative-structure-activity-relationship-study-of-1-4-naphthoquinone-derivatives-tested-against-hl-60-human-promyelocytic-leukaemia-cells
#4
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
https://www.readbyqxmd.com/read/28480742/read-across-of-ready-biodegradability-based-on-the-substrate-specificity-of-n-alkyl-polypropylene-polyamine-degrading-microorganisms
#5
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
https://www.readbyqxmd.com/read/28423913/application-of-iata-a-case-study-in-evaluating-the-global-and-local-performance-of-a-bayesian-network-model-for-skin-sensitization
#6
J M Fitzpatrick, G Patlewicz
The information characterizing key events in an Adverse Outcome Pathway (AOP) can be generated from in silico, in chemico, in vitro and in vivo approaches. Integration of this information and interpretation for decision making are known as integrated approaches to testing and assessment (IATA). One such IATA was published by Jaworska et al., which describes a Bayesian network model known as ITS-2. The current work evaluated the performance of ITS-2 using a stratified cross-validation approach. We also characterized the impact of replacing the most significant component of the network, output from the expert system TIMES-SS, with structural alert information from the OECD Toolbox and Toxtree...
April 20, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28399673/pharmacophore-generation-atom-based-3d-qsar-and-molecular-dynamics-simulation-analyses-of-pyridine-3-carboxamide-6-yl-urea-analogues-as-potential-gyrase-b-inhibitors
#7
M A Azam, J Thathan
DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR...
April 12, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28590848/exploring-the-qsar-s-predictive-truthfulness-of-the-novel-n-tuple-discrete-derivative-indices-on-benchmark-datasets
#8
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
https://www.readbyqxmd.com/read/28562086/exploring-the-structural-requirements-in-multiple-chemical-scaffolds-for-the-selective-inhibition-of-plasmodium-falciparum-calcium-dependent-protein-kinase-1-pfcdpk-1-by-3d-pharmacophore-modelling-and-docking-studies
#9
R B Aher, K Roy
Current research on antimalarial protein kinases has provided an opportunity to design kinase-based antimalarial drugs. We have developed a common feature-based pharmacophore model from a set of multiple chemical scaffolds including derivatives of 3,6-imidazopyridazines, pyrazolo[2,3-d]pyrimidines and imidazo[1,5-a]pyrazines, in order to incorporate the maximum structural diversity information in the model for the Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) target. The best pharmacophore model (Hypo-1) with the essential features of two hydrogen bond donors (HBD), one hydrophobic aromatic (HYAr) and one ring aromatic (RA) showed the classification accuracies of 86...
May 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28539063/a-qsar-classification-model-for-neuraminidase-inhibitors-of-influenza-a-viruses-h1n1-based-on-weighted-penalized-support-vector-machine
#10
Z Y Algamal, M K Qasim, H T M Ali
Descriptor selection is a procedure widely used in chemometrics. The aim is to select the best subset of descriptors relevant to the quantitative structure-activity relationship (QSAR) study being considered. In this paper, a new descriptor selection method for the QSAR classification model is proposed by adding a new weight inside L1-norm. The experimental results from classifying the neuraminidase inhibitors of influenza A viruses (H1N1) demonstrate that the proposed method in the QSAR classification model performs effectively and competitively compared with other existing penalized methods in terms of classification performance and the number of selected descriptors...
May 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28524703/computer-aided-prediction-and-cytotoxicity-evaluation-of-dithiocarbamates-of-9-10-anthracenedione-as-new-anticancer-agents
#11
M Stasevych, V Zvarych, V Lunin, N G Deniz, Z Gokmen, O Akgun, E Ulukaya, V Poroikov, T Gloriozova, V Novikov
Anticancer activity as an associated action for a series of dithiocarbamates of 9,10-anthracenedione was predicted using the PASS computer program and analysed with PharmaExpert software. The predicted cytotoxic activity of the dithiocarbamate derivatives of 9,10-anthracenedione was evaluated in vitro on cancer cells of the human lung (A549), prostate (PC3), colon (HT29) and human breast (MCF7) using the sulforhodamine B (SRB) cell viability assay. Among these compounds, 9,10-dioxo-9,10-dihydroanthracen-1-yl pyrrolidin-1-carbodithioate and 9,10-dioxo-9,10-dihydroanthracen-2-yl pyrrolidin-1-carbodithioate were identified as the most potent anticancer agents with cytotoxic activity against the MCF-7 human breast cell line with GI50 values of 1...
May 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28521600/quantitative-structure-activity-relationship-study-of-amide-mosquito-repellents
#12
P Wang, X Xu, S Liao, J Song, G Fan, S Chen, Z Wang
A quantitative structure-activity relationship (QSAR) study on 43 amide repellents was carried out by the heuristic method in order to reveal the correlations between molecular parameters of these amides and their repellency against Aedes aegypti. Sketches and optimizations of molecular structures were achieved by the Gaussian software package. Generation and screening of molecular parameters were accomplished using CODESSA 2.7.10 software. The leave-one-out method was applied for the model validation. The results showed that a four-descriptor QSAR model with r(2) of 0...
April 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28332439/use-of-biopartitioning-micellar-chromatography-and-rp-hplc-for-the-determination-of-blood-brain-barrier-penetration-of-%C3%AE-adrenergic-imidazoline-receptor-ligands-and-qspr-analysis
#13
J Vucicevic, M Popovic, K Nikolic, S Filipic, D Obradovic, D Agbaba
For this study, 31 compounds, including 16 imidazoline/α-adrenergic receptor (IRs/α-ARs) ligands and 15 central nervous system (CNS) drugs, were characterized in terms of the retention factors (k) obtained using biopartitioning micellar and classical reversed phase chromatography (log kBMC and log kwRP, respectively). Based on the retention factor (log kwRP) and slope of the linear curve (S) the isocratic parameter (φ0) was calculated. Obtained retention factors were correlated with experimental log BB values for the group of examined compounds...
March 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28332438/quantitative-structure-activity-relationship-analysis-and-virtual-screening-studies-for-identifying-hdac2-inhibitors-from-known-hdac-bioactive-chemical-libraries
#14
H Pham-The, G Casañola-Martin, K Diéguez-Santana, N Nguyen-Hai, N T Ngoc, L Vu-Duc, H Le-Thi-Thu
Histone deacetylases (HDAC) are emerging as promising targets in cancer, neuronal diseases and immune disorders. Computational modelling approaches have been widely applied for the virtual screening and rational design of novel HDAC inhibitors. In this study, different machine learning (ML) techniques were applied for the development of models that accurately discriminate HDAC2 inhibitors form non-inhibitors. The obtained models showed encouraging results, with the global accuracy in the external set ranging from 0...
March 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28322591/insight-into-the-structural-requirements-of-pyrimidine-based-phosphodiesterase-10a-pde10a-inhibitors-by-multiple-validated-3d-qsar-approaches
#15
A K Halder, S A Amin, T Jha, S Gayen
Schizophrenia is a complex disorder of thinking and behaviour (0.3-0.7% of the population is affected). The over-expression of phosphodiesterase 10A (PDE10A) enzyme may be a potential target for schizophrenia and Huntington's disease. Because 3D QSAR analysis is one of the most frequently used modelling techniques, in the present study, five different 3D QSAR tools, namely CoMFA, CoMSIA, kNN-MFA, Open3DQSAR and topomer CoMFA methods, were used on a dataset of pyrimidine-based PDE10A inhibitors. All developed models were validated internally and externally...
March 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28290719/molecular-dynamics-and-pharmacophore-modelling-studies-of-different-subtype-alk-and-egfr-t790m-inhibitors-in-nsclc
#16
P K Singh, O Silakari
Extensively validated 3D pharmacophore models for ALK (anaplastic lymphoma kinase) and EGFR (T790M) (epithelial growth factor receptor with acquired secondary mutation) were developed. The pharmacophore model for ALK (r(2) = 0.96, q(2) = 0.692) suggested that two hydrogen bond acceptors and three hydrophobic groups arranged in 3-D space are essential for the binding affinity of ALK inhibitors. Similarly, the pharmacophore model for EGFR (T790M) (r(2) = 0.92, q(2) = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M)...
March 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28271914/monte-carlo-method-based-qsar-modelling-of-natural-lipase-inhibitors-using-hybrid-optimal-descriptors
#17
A Kumar, S Chauhan
Obesity is one of the most provoking health burdens in the developed countries. One of the strategies to prevent obesity is the inhibition of pancreatic lipase enzyme. The aim of this study was to build QSAR models for natural lipase inhibitors by using the Monte Carlo method. The molecular structures were represented by the simplified molecular input line entry system (SMILES) notation and molecular graphs. Three sets - training, calibration and test set of three splits - were examined and validated. Statistical quality of all the described models was very good...
March 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28235392/a-quantum-chemical-based-toxicity-study-of-estimated-reduction-potential-and-hydrophobicity-in-series-of-nitroaromatic-compounds
#18
A Gooch, N Sizochenko, L Sviatenko, L Gorb, J Leszczynski
Nitroaromatic compounds and the products of their degradation are toxic to bacteria, cells and animals. Various studies have been carried out to better understand the mechanism of toxicity of aromatic nitrocompounds and their relationship to humans and the environment. Recent data relate cytotoxicity of nitroaromatic compounds to their single- or two-electron enzymatic reduction. However, mechanisms of animal toxicity could be more complex. This work investigates the estimated reduction and oxidation potentials of 34 nitroaromatic compounds using quantum chemical approaches...
February 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28235391/sar-and-qsar-study-on-the-bioactivities-of-human-epidermal-growth-factor-receptor-2-her2-inhibitors
#19
D Qu, A Yan, J S Zhang
In this paper, structure-activity relationship (SAR, classification) and quantitative structure-activity relationship (QSAR) models have been established to predict the bioactivity of human epidermal growth factor receptor-2 (HER2) inhibitors. For the SAR study, we established six SAR (or classification) models to distinguish highly and weakly active HER2 inhibitors. The dataset contained 868 HER2 inhibitors, which was split into a training set including 580 inhibitors and a test set including 288 inhibitors by a Kohonen's self-organizing map (SOM), or a random method...
February 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28235390/qsar-analysis-for-6-arylpyrazine-2-carboxamides-as-trypanosoma-brucei-inhibitors
#20
V H Masand, N N E El-Sayed, D T Mahajan, V Rastija
Human African trypanosomiasis (HAT) is prevalent in African countries, covering 37 countries, mostly sub-Saharan. A limited number of drugs are available to cure this neglected disease. In the present work, quantitative structure-activity (toxicity) relationships (QSA(T)R) analysis has been performed for a dataset of 54 6-arylpyrazine-2-carboxamides as Trypanosoma brucei inhibitors to identify the important structural features required for future optimization of lead candidates. The QSA(T)R models satisfy OECD guidelines and have high statistical robustness...
February 2017: SAR and QSAR in Environmental Research
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