journal
MENU ▼
Read by QxMD icon Read
search

SAR and QSAR in Environmental Research

journal
https://www.readbyqxmd.com/read/27827546/applicability-domain-towards-a-more-formal-definition
#1
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 9, 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
#2
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
#3
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/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
#4
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...
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
#5
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
#6
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/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/27775436/ecotoxicity-interspecies-qaar-models-from-daphnia-toxicity-of-pharmaceuticals-and-personal-care-products
#13
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
#14
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
https://www.readbyqxmd.com/read/27653817/predicting-the-aquatic-toxicity-mode-of-action-using-logistic-regression-and-linear-discriminant-analysis
#15
Y Y Ren, L C Zhou, L Yang, P Y Liu, B W Zhao, H X Liu
The paper highlights the use of the logistic regression (LR) method in the construction of acceptable statistically significant, robust and predictive models for the classification of chemicals according to their aquatic toxic modes of action. Essentials accounting for a reliable model were all considered carefully. The model predictors were selected by stepwise forward discriminant analysis (LDA) from a combined pool of experimental data and chemical structure-based descriptors calculated by the CODESSA and DRAGON software packages...
September 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27628959/high-dimensional-qsar-modelling-using-penalized-linear-regression-model-with-l1-2-norm
#16
Z Y Algamal, M H Lee, A M Al-Fakih, M Aziz
In high-dimensional quantitative structure-activity relationship (QSAR) modelling, penalization methods have been a popular choice to simultaneously address molecular descriptor selection and QSAR model estimation. In this study, a penalized linear regression model with L1/2-norm is proposed. Furthermore, the local linear approximation algorithm is utilized to avoid the non-convexity of the proposed method. The potential applicability of the proposed method is tested on several benchmark data sets. Compared with other commonly used penalized methods, the proposed method can not only obtain the best predictive ability, but also provide an easily interpretable QSAR model...
September 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27586365/estimating-the-melting-point-entropy-of-fusion-and-enthalpy-of-fusion-of-organic-compounds-via-sparc
#17
T S Whiteside, S H Hilal, A Brenner, L A Carreira
The entropy of fusion, enthalpy of fusion, and melting point of organic compounds can be estimated through three models developed using the SPARC (SPARC Performs Automated Reasoning in Chemistry) platform. The entropy of fusion is modelled through a combination of interaction terms and physical descriptors. The enthalpy of fusion is modelled as a function of the entropy of fusion, boiling point, and flexibility of the molecule. The melting point model is the enthalpy of fusion divided by the entropy of fusion...
August 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27586364/a-quantitative-structure-activity-relationship-to-predict-efficacy-of-granular-activated-carbon-adsorption-to-control-emerging-contaminants
#18
A R Kennicutt, L Morkowchuk, M Krein, C M Breneman, J E Kilduff
A quantitative structure-activity relationship was developed to predict the efficacy of carbon adsorption as a control technology for endocrine-disrupting compounds, pharmaceuticals, and components of personal care products, as a tool for water quality professionals to protect public health. Here, we expand previous work to investigate a broad spectrum of molecular descriptors including subdivided surface areas, adjacency and distance matrix descriptors, electrostatic partial charges, potential energy descriptors, conformation-dependent charge descriptors, and Transferable Atom Equivalent (TAE) descriptors that characterize the regional electronic properties of molecules...
August 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27586363/structure-based-model-profiles-affinity-constant-of-drugs-with-hpept1-for-rapid-virtual-screening-of-hpept1-s-substrate
#19
L Sun, S Meng
The human proton-coupled peptide transporter (hPEPT1) with broad substrates is an important route for improving the pharmacokinetic performance of drugs. Thus, it is essential to predict the affinity constant between drug molecule and hPEPT1 for rapid virtual screening of hPEPT1's substrate during lead optimization, candidate selection and hPEPT1 prodrug design. Here, a structure-based in silico model for 114 compounds was constructed based on eight structural parameters. This model was built by the multiple linear regression method and satisfied all the prerequisites of the regression models...
August 2016: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/27477321/assessment-of-the-classification-abilities-of-the-cns-multi-parametric-optimization-approach-by-the-method-of-logistic-regression
#20
O A Raevsky, D E Polianczyk, A Mukhametov, V Y Grigorev
Assessment of "CNS drugs/CNS candidates" classification abilities of the multi-parametric optimization (CNS MPO) approach was performed by logistic regression. It was found that the five out of the six separately used physical-chemical properties (topological polar surface area, number of hydrogen-bonded donor atoms, basicity, lipophilicity of compound in neutral form and at pH = 7.4) provided accuracy of recognition below 60%. Only the descriptor of molecular weight (MW) could correctly classify two-thirds of the studied compounds...
August 2016: SAR and QSAR in Environmental Research
journal
journal
32085
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"