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SAR and QSAR in Environmental Research

M A Azam, S Jupudi, N Saha, R K Paul
The ATP-dependent bacterial MurD enzyme catalyses the formation of the peptide bond between cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine and D-glutamic acid. This is essential for bacterial cell wall peptidoglycan synthesis in both Gram-positive and Gram-negative bacteria. MurD is recognized as an important target for the development of new antibacterial agents. In the present study we prepared the 3D-stucture of the catalytic pocket of the Staphylococcus aureus MurD enzyme by homology modelling...
November 8, 2018: SAR and QSAR in Environmental Research
P M Khan, K Roy
The glass transition temperature is a vital property of polymers with a direct impact on their stability. In the present study, we built quantitative structure-property relationship models for the prediction of the glass transition temperatures of polymers using a data set of 206 diverse polymers. Various 2D molecular descriptors were computed from the single repeating units of polymers. We derived five models from different combinations of six descriptors in each case by employing the double cross-validation technique followed by partial least squares regression...
November 5, 2018: SAR and QSAR in Environmental Research
K Inthajak, P Toochinda, L Lawtrakul
A series of antifolate compounds, i.e. 1-(4-chlorophenyl)-6,6-dimethyl-1,3,5-triazine-2,4-diamine, or cycloguanil analogues, have shown effective inhibiting properties against Plasmodium falciparum dihydrofolate reductase (PfDHFR). In this work, the stereoselectivity of PfDHFR to the R and S enantiomer of cycloguanil analogues was obtained from molecular docking calculations and integrated into QSAR study to obtain a more accurate prediction model. Results indicate that PfDHFR can bind to cycloguanil analogues in the R and S enantiomers...
November 1, 2018: SAR and QSAR in Environmental Research
L Dang, S Zhang
A four-descriptor quantitative structure-property relationship model was constructed to predict 65 intrinsic viscosities [η] of polymer solutions. Four quantum chemical descriptors, the traceless quadrupole moment θ(R) , the hydrogen bond or electrostatic attraction descriptor QH , the partition function QBOT(R) and the frontier orbital descriptor EHOMO , were calculated with density functional theory at the B3LYP/6-31G(d) level and used to develop the model by multivariate linear regression (MLR) analysis...
December 2018: SAR and QSAR in Environmental Research
M Salahinejad, E Zolfonoun
The Quantitative Ion Character-Activity Relationship (QICAR) method was used for correlating metal ionic characteristics with the maximum adsorption capacity (qmax ) of multi-walled carbon for heavy metals. The experimental values of qmax for 25 heavy metal ions, estimated by the Langmuir isotherm model, were used to construct a QICAR model. The genetic algorithm, enhanced replacement method and successive projection algorithm procedures were applied as variable selection algorithms to choose the optimal subsets of descriptors...
December 2018: SAR and QSAR in Environmental Research
R Tumdam, A Kumar, N Subbarao, B S Balaji
Bromodomain-containing protein 4 (BRD4) is a member of the bromodomain and extra-terminal domain (BET) family of proteins. It epigentically regulates the transcription of growth-promoting genes and has become an attractive target for the development of anticancer and anti-inflammatory agents. In the current study, we performed an in silico screening of a small-molecule chemical library against the acetyl-lysine binding site of the first bromodomain (BD1) in BRD4 protein. Potential inhibitors identified through virtual screening were further studied through molecular dynamics simulations, water entrapment analysis and Molecular Mechanics (MM)/Poisson-Boltzmann surface area (PBSA) binding free energy calculations...
December 2018: SAR and QSAR in Environmental Research
S Ahmadi, A Akbari
In this investigation, quantitative structure-property relationship (QSPR) modelling of adsorption coefficients of 69 aromatic compounds on multi-wall carbon nanotubes (MWCNTs) was studied using the Monte Carlo method. QSPR models were calculated with CORAL software, and optimal descriptors were calculated with the simplified molecular input line entry system (SMILES) and hydrogen-suppressed molecular graphs (HSGs). The aromatic compound data set was randomly split into training, invisible training, calibration and validation sets...
November 2018: SAR and QSAR in Environmental Research
A K Halder
Multiple Quantitative Structure-Activity Relationship (QSAR) analysis is widely used in drug discovery for lead identification. Human Immunodeficiency Virus (HIV) protease is one of the key targets for the treatment of Acquired Immunodeficiency Syndrome (AIDS). One of the major challenges for the design of HIV-1 protease inhibitors (HIV PRIs) is to increase the inhibitory activities against the enzyme to a level where the problem associated to drug resistance may be considerably delayed. Herein, chemometric analyses were performed with 346 structurally diverse HIV PRIs with experimental bioactivities against a sub-type B mutant to develop highly predictable QSAR models and also to identify the effective structural determinants for higher affinity against HIV PR...
November 2018: SAR and QSAR in Environmental Research
F Zhang, M Bartels, A Clark, T Erskine, T Auernhammer, B Bhhatarai, D Wilson, S Marty
The accurate prediction of toxicokinetic parameters arising from oral, dermal and inhalation routes of chemical exposure is a key element in chemical safety assessments. In this research, the physiologically based pharmacokinetic (PBPK) GastroPlusTM software was evaluated against a series of chemicals for the prediction of toxicokinetic parameters. Overall, 67% of predicted intrinsic clearance (Clint) values were within 1- to 10-fold of empirical data for 463 compounds, and 87% of the predicted fraction unbounded in plasma (Fup) values were 1- to 3-fold of empirical data for 441 compounds...
November 2018: SAR and QSAR in Environmental Research
R Li, Y Du, J Shen
BTK inhibitors have been proved as an effective target for B-cell malignancies. Ibrutinib is the most advanced irreversible BTK inhibitor for treating mantle cell lymphoma/chronic lymphocytic leukaemia but with existing drug resistance and adverse effects. To design novel effective and safety reversible BTK inhibitors, 115 newly cinnoline analogues were selected to perform molecular docking and 3D-QSAR study because of the main scaffold similarity to Ibrutinib. Both established CoMFA and CoMSIA models obtained high predictive and satisfactory value...
November 2018: SAR and QSAR in Environmental Research
Y Xi, Z Qin, A Yan
Cyclooxygenase-1 (COX-1) is one isoform of COX, and it is a main target of nonsteroidal anti-inflammatory drugs (NSAIDs). It is important to develop efficient and selective COX-1 inhibitors. In this work, 12 classification models for 1530 cyclooxygenase-1 (COX-1) inhibitors were built by support vector machine (SVM), decision tree (DT) and random forest (RF) methods. The best classification model (model 1A) was built by SVM with MACCS fingerprints. The classification accuracies for the training and test sets were 99...
October 2018: SAR and QSAR in Environmental Research
O A Raevsky, V Yu Grigorev, D E Polianczyk, O E Raevskaja, J C Dearden
Assessment of the influence of six physicochemical properties used in the multiparameter optimization (MPO) approach for chemical penetration of the blood-brain barrier was carried out by means of application of logistic regression and multiple linear regression, using a data set of 578 diverse chemicals. It was found that use of an aggregation MPO-score descriptor did not give satisfactory results with central nervous system (CNS)/non-CNS classification. Thus an application of the MPO approach for CNS penetration is ambiguous...
October 2018: SAR and QSAR in Environmental Research
C Braeuning, A Braeuning, H Mielke, A Holzwarth, M Peiser
In vivo skin sensitization assays have to be provided by applicants to the competent authorities in the European Union for the approval of active substances (AS) in pesticides. This study aimed to test the practicability of in silico predictions for AS by freely available (Q)SAR tools to evaluate their use as a time- and cost-effective alternative to animal testing in the context of the 3R concept. Predictions of skin sensitization for 48 selected sensitizing and non-sensitizing AS by the software programs CAESAR, Toxtree, OECD (Q)SAR Toolbox, CASE Ultra, Leadscope and SciQSAR were collected and compared...
October 2018: SAR and QSAR in Environmental Research
A Bak, V Kozik, I Malik, J Jampilek, A Smolinski
The current study examines in silico characterization of the structure-inhibitory potency for a set of phenylcarbamic acid derivatives containing an N-arylpiperazine scaffold, considering the electronic, steric and lipophilic properties. The main objective of the ligand-based modelling was the systematic study of classical comparative molecular field analysis (CoMFA)/comparative molecular surface analysis (CoMSA) performance for the modelling of in vitro efficiency observed for these phenylcarbamates, revealing their inhibitory activities against a virulent Mycobacterium tuberculosis H37 Rv strain...
October 2018: SAR and QSAR in Environmental Research
J Devillers
Repellents disrupt the behaviour of blood-seeking mosquitoes protecting humans against their bites which can transmit serious diseases. Since the mid-1950s, N,N-diethyl-m-toluamide (DEET) is considered as the standard mosquito repellent worldwide. However, DEET presents numerous shortcomings. Faced with the heightening risk of mosquito expansion caused by global climate changes and increasing international exchanges, there is an urgent need for a better repellent than DEET and the very few other commercialised repelling molecules such as picaridin and IR3535...
September 2018: SAR and QSAR in Environmental Research
K Venko, V Drgan, M Novič
Nowadays, environmental and biological endpoints can be predicted with in silico approaches if sufficient experimental data of good quality are available. Since the experimental evaluation of acute contact toxicity towards honeybees (Apis mellifera) is a complex and expensive assay, the computational models that follow OECD principles for this endpoint prediction represent important alternatives for safety prioritisation of chemicals, especially pesticides. We developed and validated counter-propagation artificial neural network (CPANN) models for in silico evaluation of toxicity of pesticides towards honeybees by using new in-house software...
September 2018: SAR and QSAR in Environmental Research
E Nagihan Kahraman, M Türker Saçan
Two data sets on the cytotoxicity of diverse chemicals to topminnow (Poeciliopsis lucida) hepatoma cell line (PLHC-1) were modelled with quantitative structure-toxicity relationship (QSTR). The data sets are based on 3-amino-7-dimethylamino-2-methylphenazine hydrochloride (NR) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assays representing lysosomal damage and metabolic impairment, respectively. The descriptors were calculated with DRAGON 6 and SPARTAN 10 software packages. Descriptor selection was made by 'all subset' and genetic algorithm-based features implemented in QSARINS software...
September 2018: SAR and QSAR in Environmental Research
A Furuhama, T I Hayashi, H Yamamoto
Herein, we propose models for predicting fish early-life stage (ELS) toxicity from acute Daphnia magna toxicity and various molecular descriptors. Specifically, eight models were developed with fathead minnow (Pimephales promelas) data and were validated against Japanese medaka (Oryzias latipes) data because the quantity of available Japanese medaka data is much smaller than the quantity of fathead minnow data. The training data set for the models consisted of ELS fathead minnow toxicity data for 77 chemicals; data for 67 of the 77 chemicals originated from the OPP Pesticide Ecotoxicity Database of the US Environmental Protection Agency...
September 2018: SAR and QSAR in Environmental Research
T Tibaut, T Tomašič, V Hodnik, M Anderluh, S Pintar, M Novič, D Turk
A structure-based approach is applied for the development of inhibitors of bacterial N-acetyglucosaminidase (autolysin). Autolysins are enzymes involved in the degradation of peptidoglycan and therefore participate in bacterial cell growth and different lysis phenomena. Several studies indicate that by the inhibition of autolysins, and consequently of bacterial cell division, antibacterial activity can be obtained, thus paving the road to a novel group of therapeutics against human pathogens. As crystal structures of the autolysin E (AtlE)-ligand complexes were obtained in our laboratories, fragment-based virtual screening was the method of choice for the initial studies...
September 2018: SAR and QSAR in Environmental Research
A Rácz, D Bajusz, K Héberger
Prediction performance often depends on the cross- and test validation protocols applied. Several combinations of different cross-validation variants and model-building techniques were used to reveal their complexity. Two case studies (acute toxicity data) were examined, applying five-fold cross-validation (with random, contiguous and Venetian blind forms) and leave-one-out cross-validation (CV). External test sets showed the effects and differences between the validation protocols. The models were generated with multiple linear regression (MLR), principal component regression (PCR), partial least squares (PLS) regression, artificial neural networks (ANN) and support vector machines (SVM)...
September 2018: SAR and QSAR in Environmental Research
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