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SAR and QSAR in Environmental Research

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https://www.readbyqxmd.com/read/28161994/conformation-dependent-qsar-approach-for-the-prediction-of-inhibitory-activity-of-bromodomain-modulators
#1
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...
February 6, 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
#2
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...
January 25, 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
#3
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 20, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28094550/pharmacophore-modelling-atom-based-3d-qsar-generation-and-virtual-screening-of-molecules-projected-for-mpges-1-inhibitory-activity
#4
S Misra, M Saini, H Ojha, D Sharma, K Sharma
COX-2 inhibitors exhibit anticancer effects in various cancer models but due to the adverse side effects associated with these inhibitors, targeting molecules downstream of COX-2 (such as mPGES-1) has been suggested. Even after calls for mPGES-1 inhibitor design, to date there are only a few published inhibitors targeting the enzyme and displaying anticancer activity. In the present study, we have deployed both ligand and structure-based drug design approaches to hunt novel drug-like candidates as mPGES-1 inhibitors...
January 17, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28056566/large-scale-classification-of-p-glycoprotein-inhibitors-using-smiles-based-descriptors
#5
V Prachayasittikul, A Worachartcheewan, A P Toropova, A A Toropov, N Schaduangrat, V Prachayasittikul, C Nantasenamat
P-glycoprotein (Pgp) inhibition has been considered as an effective strategy towards combating multidrug-resistant cancers. Owing to the substrate promiscuity of Pgp, the classification of its interacting ligands is not an easy task and is an ongoing issue of debate. Chemical structures can be represented by the simplified molecular input line entry system (SMILES) in the form of linear string of symbols. In this study, the SMILES notations of 2254 Pgp inhibitors including 1341 active, and 913 inactive compounds were used for the construction of a SMILE-based classification model using CORrelation And Logic (CORAL) software...
January 6, 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
#6
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/27748622/molecular-mechanism-of-the-protective-effect-of-monomer-polyvinylpyrrolidone-on-antioxidants-experimental-and-computational-studies
#7
W Liu, J Wang, M Li, W Tang, J Han
We previously developed a lutein-polyvinylpyrrolidone (PVP) complex with improved aqueous saturation solubility and stability, though the conjugation mechanism is still unclear. In this paper, experiments with astaxanthin-PVP complex and curcumin-PVP complex were carried out, which indicated that PVP could improve the solubility and stability of astaxanthin and curcumin. We aimed to construct a computational model capable of understanding the protective effect in complexes formed between PVP and antioxidants, through which the binding mode of PVP and antioxidants was investigated with molecular modelling in order to obtain the interactions, binding energy, binding site and surface area between PVP and antioxidants...
December 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27707004/n-tuple-topological-geometric-cutoffs-for-3d-n-linear-algebraic-molecular-codifications-variability-linear-independence-and-qsar-analysis
#8
C R García-Jacas, Y Marrero-Ponce, S J Barigye, T Hernández-Ortega, L Cabrera-Leyva, A Fernández-Castillo
Novel N-tuple topological/geometric cutoffs to consider specific inter-atomic relations in the QuBiLS-MIDAS framework are introduced in this manuscript. These molecular cutoffs permit the taking into account of relations between more than two atoms by using (dis-)similarity multi-metrics and the concepts related with topological and Euclidean-geometric distances. To this end, the kth two-, three- and four-tuple topological and geometric neighbourhood quotient (NQ) total (or local-fragment) spatial-(dis)similarity matrices are defined, to represent 3D information corresponding to the relations between two, three and four atoms of the molecular structures that satisfy certain cutoff criteria...
December 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27667445/3d-qsar-analysis-of-a-series-of-s-dabo-derivatives-as-anti-hiv-agents-by-comfa-and-comsia
#9
H R Xu, L Fu, P Zhan, X Y Liu
In this study, we retrieved a series of 59 dihydroalkylthio-benzyloxopyrimidine (S-DABO) derivatives, which is a class of highly potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) reported from published articles, and analysed them with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Statistically significant three-dimensional quantitative structure-activity relationship (3D-QSAR) models by CoMFA and CoMSIA were derived from a training set of 46 compounds on the basis of the rigid body alignment...
December 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27658742/qspr-studies-for-predicting-polarity-parameter-of-organic-compounds-in-methanol-using-support-vector-machine-and-enhanced-replacement-method
#10
H Golmohammadi, Z Dashtbozorgi
In the present work, enhanced replacement method (ERM) and support vector machine (SVM) were used for quantitative structure-property relationship (QSPR) studies of polarity parameter (p) of various organic compounds in methanol in reversed phase liquid chromatography based on molecular descriptors calculated from the optimized structures. Diverse kinds of molecular descriptors were calculated to encode the molecular structures of compounds, such as geometric, thermodynamic, electrostatic and quantum mechanical descriptors...
December 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27885862/an-automated-curation-procedure-for-addressing-chemical-errors-and-inconsistencies-in-public-datasets-used-in-qsar-modelling
#11
K Mansouri, C M Grulke, A M Richard, R S Judson, A J Williams
The increasing availability of large collections of chemical structures and associated experimental data provides an opportunity to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experimental data. Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publicly available PHYSPROP physicochemical properties and environmental fate datasets...
November 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27885861/additional-synthesis-on-thiophene-containing-trisubstituted-methanes-trsms-as-inhibitors-of-m-tuberculosis-and-3d-qsar-studies
#12
P Singh, T Saha, P Mishra, M K Parai, S Ireddy, S Lavanya Kumar M, S Krishna, S K Kumar, V Chaturvedi, S Sinha, M I Siddiqi, G Panda
We earlier reported thiophene-containing trisubstituted methanes (TRSMs) as novel cores carrying anti-tubercular activity, and identified S006-830 as the phenotypic lead with potent bactericidal activity against single- and multi-drug resistant clinical isolates of Mycobacterium tuberculosis (M. tb). In this work, we carried out additional synthesis of several TRSMs. The reaction scheme essentially followed the Grignard reaction and Friedel-Crafts alkylation, followed by insertion of a dialkylaminoethyl chain...
November 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27827546/applicability-domain-towards-a-more-formal-definition
#13
T Hanser, C Barber, J F Marchaland, S Werner
In recent years the applicability domain (AD) of a prediction system has become an important concern in (Q)SAR modelling, especially in the context of human safety assessment. Today AD is an active research topic, and many methods have been designed to estimate the adequacy of a model and the confidence in its outcome for a given prediction task. Unfortunately, the wide spectrum of techniques developed for this purpose is based on various definitions of the concept of AD, often taking into account different types of information...
November 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27762146/combined-qsar-based-virtual-screening-and-fluorescence-binding-assay-to-identify-natural-product-mediators-of-interferon-regulatory-factor-7-irf-7-in-pulmonary-infection
#14
Y Liu, L Huang, H Ye, X Lv
Interferon regulatory factor-7 (IRF-7) is involved in pulmonary infection and pneumonia. Here, a synthetic strategy that combined quantitative structure-activity relationship (QSAR)-based virtual screening and in vitro binding assay was described to identify new and potent mediator ligands of IRF-7 from natural products. In the procedure, a QSAR scoring function was developed and validated using Gaussian process (GP) regression and a structure-based set of protein-ligand affinity data. By integrating hotspot pocket prediction, pharmacokinetics profile analysis and molecular docking calculations, the scoring function was successfully applied to virtual screening against a large library of structurally diverse, drug-like natural products...
November 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27767343/acute-to-chronic-estimation-of-daphnia-magna-toxicity-within-the-qsaar-framework
#15
A Furuhama, T I Hayashi, N Tatarazako
We constructed models for acute to chronic estimation of the Daphnia magna reproductive toxicities of chemical substances from their Daphnia magna acute immobilization toxicities. The models combined the acute toxicities with structural and physicochemical descriptors. We used multiregression analysis and selected the descriptors for the models by means of a genetic algorithm. Of the best 100 models (as indicated by the lack of fit score), 90% included the following descriptors: acute toxicity (i.e. an activity parameter), distribution coefficient (log D) and structural indicator variables that indicate the presence of -NH2 attached to aromatic carbon and the presence of a chlorine atom...
October 21, 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27762155/improving-confidence-in-q-sar-predictions-under-canada-s-chemicals-management-plan-a-chemical-space-approach
#16
S A Kulkarni, E Benfenati, T S Barton-Maclaren
One of the key challenges of Canada's Chemicals Management Plan (CMP) is assessing chemicals with limited/no empirical hazard data for their risk to human health. In some instances, these chemicals have not been tested broadly for their toxicological potency; as such, limited information exists on their potential to induce human health effects following exposure. Although (quantitative) structure activity relationship ((Q)SAR) models are able to generate predictions to address data gaps for certain toxicological endpoints, the confidence in predictions also needs to be addressed...
October 20, 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27748631/quantitative-structure-permeability-relationships-at-various-ph-values-for-neutral-and-amphoteric-drugs-and-drug-like-compounds
#17
Mare Oja, Uko Maran
Human intestinal absorption is a key property for orally administered drugs and is dependent on pH. This study focuses on neutral and amphoteric compounds and their membrane permeabilities across the range of pH values found in the human intestine. The membrane permeability values for 15 neutral and 60 amphoteric compounds at pH 3, 5, 7.4 and 9 were measured using the parallel artificial membrane permeability assay (PAMPA). For each data series the quantitative structure-permeability relationships were developed and analysed...
October 17, 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27710037/classification-of-biodegradable-materials-using-qsar-modelling-with-uncertainty-estimation
#18
W F C Rocha, D A Sheen
The ability to determine the biodegradability of chemicals without resorting to expensive tests is ecologically and economically desirable. Models based on quantitative structure-activity relations (QSAR) provide some promise in this direction. However, QSAR models in the literature rarely provide uncertainty estimates in more detail than aggregated statistics such as the sensitivity and specificity of the model's predictions. Almost never is there a means of assessing the uncertainty in an individual prediction...
October 6, 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27775436/ecotoxicity-interspecies-qaar-models-from-daphnia-toxicity-of-pharmaceuticals-and-personal-care-products
#19
A Sangion, P Gramatica
Pharmaceutical and Personal Care Products (PPCPs) became a class of contaminants of emerging concern because are ubiquitously detected in surface water and soil, where they can affect wildlife. Ecotoxicological data are only available for a few PPCPs, thus modelling approaches are essential tools to maximize the information contained in the existing data. In silico methods may be helpful in filling data gaps for the toxicity of PPCPs towards various ecological indicator organisms. The good correlation between toxicity toward Daphnia magna and those on two fish species (Pimephales promelas and Oncorhynchus mykiss), improved by the addition of one theoretical molecular descriptor, allowed us to develop predictive models to investigate the relationship between toxicities in different species...
October 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27667641/machine-learning-rule-and-pharmacophore-based-classification-on-the-inhibition-of-p-glycoprotein-and-nora
#20
T-D Ngo, T-D Tran, M-T Le, K-M Thai
The efflux pumps P-glycoprotein (P-gp) in humans and NorA in Staphylococcus aureus are of great interest for medicinal chemists because of their important roles in multidrug resistance (MDR). The high polyspecificity as well as the unavailability of high-resolution X-ray crystal structures of these transmembrane proteins lead us to combining ligand-based approaches, which in the case of this study were machine learning, perceptual mapping and pharmacophore modelling. For P-gp inhibitory activity, individual models were developed using different machine learning algorithms and subsequently combined into an ensemble model which showed a good discrimination between inhibitors and noninhibitors (acctrain-diverse = 84%; accinternal-test = 92% and accexternal-test = 100%)...
September 2016: SAR and QSAR in Environmental Research
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