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SAR and QSAR in Environmental Research

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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
#1
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 25, 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
#2
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 19, 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
#3
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
#4
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
#5
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
#6
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/28521600/quantitative-structure-activity-relationship-study-of-amide-mosquito-repellents
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28235389/structure-based-modelling-scoring-screening-and-in-vitro-kinase-assay-of-anesthetic-pkc-inhibitors-against-a-natural-medicine-library
#16
B X Shi, F R Chen, X Sun
Protein kinase C (PKC) is an intracellular effector of the inositol phosphate-mediated signal transduction pathway. Evidence is emerging that certain general anaesthetics can influence the activity of PKC by interacting with the regulatory domain of the enzyme, and targeting PKC kinase domain is considered as a strategy to modulate the anaesthetic effects. Here, an integrated method was used to perform virtual screening against a large library of natural compounds for the discovery of new and potent PKC modulators...
February 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28121178/classification-of-sphingosine-kinase-inhibitors-using-counter-propagation-artificial-neural-networks-a-systematic-route-for-designing-selective-sphk-inhibitors
#17
M S Neiband, A Mani-Varnosfaderani, A Benvidi
Accurate and robust classification models for describing and predicting the activity of 330 chemicals that are sphingosine kinase 1 (SphK1) and/or sphingosine kinase 2 (SphK2) inhibitors were derived. The classification models developed in this work assist in finding selective subspaces in chemical space occupied by particular groups of SphK inhibitors. A combination of a genetic algorithm (GA) and a counter propagation artificial neural network (CPANN) was utilized to select the most efficient subsets of the molecular descriptors...
February 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28176549/a-new-adaptive-l1-norm-for-optimal-descriptor-selection-of-high-dimensional-qsar-classification-model-for-anti-hepatitis-c-virus-activity-of-thiourea-derivatives
#18
Z Y Algamal, M H Lee
A high-dimensional quantitative structure-activity relationship (QSAR) classification model typically contains a large number of irrelevant and redundant descriptors. In this paper, a new design of descriptor selection for the QSAR classification model estimation method is proposed by adding a new weight inside L1-norm. The experimental results of classifying the anti-hepatitis C virus activity of thiourea derivatives demonstrate that the proposed descriptor selection method in the QSAR classification model performs effectively and competitively compared with other existing penalized methods in terms of classification performance on both the training and the testing datasets...
January 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28161994/conformation-dependent-qsar-approach-for-the-prediction-of-inhibitory-activity-of-bromodomain-modulators
#19
C R García-Jacas, K Martinez-Mayorga, Y Marrero-Ponce, J L Medina-Franco
Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large compound collections from their structural information. In this manuscript, QSAR models to predict the inhibitory activity of a diverse and heterogeneous set of 88 organic molecules against the bromodomains BRD2, BRD3 and BRD4 are presented...
January 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28105856/evaluation-of-in-silico-tools-to-predict-the-skin-sensitization-potential-of-chemicals
#20
G R Verheyen, E Braeken, K Van Deun, S Van Miert
Public domain and commercial in silico tools were compared for their performance in predicting the skin sensitization potential of chemicals. The packages were either statistical based (Vega, CASE Ultra) or rule based (OECD Toolbox, Toxtree, Derek Nexus). In practice, several of these in silico tools are used in gap filling and read-across, but here their use was limited to make predictions based on presence/absence of structural features associated to sensitization. The top 400 ranking substances of the ATSDR 2011 Priority List of Hazardous Substances were selected as a starting point...
January 2017: SAR and QSAR in Environmental Research
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