Read by QxMD icon Read


Sahila Mohammed Marunnan, Babitha Pallikkara Pulikka, V K Gopalakrishnan, Srinivas Bandaru, Mukesh Yadav, Anuraj Nayarisseri, Victor Arokia Doss
Deficits in GABAnergic system is implicated in the pathophysiology of schizophrenia. Available antipsychotics that target GABA receptor form a desirable therapeutic strategy in the treatment regimen of schizophrenia but, unfortunately, suffers serious setback due to their prolonged side effects. The present investigation focuses on developing QSAR models from the biological activity of herbal compounds and their derivatives that promise to be alternative candidates to GABA uptake inhibitors. Three sets of compounds were undertaken in the study to develop the QSAR models...
December 5, 2016: Current Neuropharmacology
Meimei Chen, Fafu Yang, Jie Kang, Xuemei Yang, Xinmei Lai, Yuxing Gao
In this study, in silico approaches, including multiple QSAR modeling, structural similarity analysis, and molecular docking, were applied to develop QSAR classification models as a fast screening tool for identifying highly-potent ABCA1 up-regulators targeting LXRβ based on a series of new flavonoids. Initially, four modeling approaches, including linear discriminant analysis, support vector machine, radial basis function neural network, and classification and regression trees, were applied to construct different QSAR classification models...
November 29, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Lukas Linden, Kai-Uwe Goss, Satoshi Endo
Binding of organic chemicals to α-cyclodextrin (αCD) is a typical example for host-guest complexation that is influenced by the 3D-structure of both the binding site (host) and the solute (guest). Prediction of the binding constant is challenging and requires a successful representation of the binding site-solute interactions in the 3D-space. In this study, we tested if a 3D quantitative structure activity relationship (3D-QSAR) model with quantum mechanically based local sigma profiles (LSPs) derived from the COSMOsar3D method is capable of predicting αCD binding constants from the most recent literature and how the model performs in comparison to a standard comparative molecular field analysis and to a reference 2D-QSAR...
November 30, 2016: Chemosphere
Chaeuk Im
Aurora A kinase is involved in the inactivation of apoptosis leading to ovarian, breast, colon, and pancreatic cancers. Inhibitors of Aurora A kinase promote aberrant mitosis resulting in arrest at a pseudo G1 state to induce mitotic catastrophe, ultimately leading to apoptosis. In this study, ligand-based and docking-based three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses of imidazole and thiazolidine derivatives as potential Aurora A kinase inhibitors were performed. The results provided highly reliable and predictive 3D-QSAR comparative molecular similarity index analysis (CoMSIA) models with a cross-validated q(2) value of 0...
December 1, 2016: Archives of Pharmacal Research
Jing Tu, Jiao Jiao Li, Zhi Jie Shan, Hong Lin Zhai
The non-nucleoside drugs have been developed to treat HBV infection owing to their increased efficacy and lesser side effects, in which heteroaryldihydropyrimidines (HAPs) have been identified as effective inhibitors of HBV capsid. In this paper, the binding mechanism of HAPs targeting on HBV capsid protein was explored through three-dimensional quantitative structure-activity relationship, molecular dynamics and binding free energy decompositions. The obtained models of comparative molecular field analysis and comparative molecular similarity indices analysis enable the sufficient interpretation of structure-activity relationship of HAPs-HBV...
November 28, 2016: Antiviral Research
Vytautas Raskevicius, Visvaldas Kairys
BACKGROUND: Design of isoform-specific inhibitors is a major challenge in the new therapeutic agents development. METHODS: The article describes the development of a robust selectivity for CA XII QSAR and 3D-QSAR models of 40 benzenesulfonamide derivatives bearing pyrimidine moieties using PHASE module of Schrödinger for 3D-QSAR or E-DRAGON and R software for 2D-QSAR. Two QSAR protocols were explored: traditional (affinity) and selectivity (affinity ratio) based...
November 29, 2016: Current Computer-aided Drug Design
Christiaan Jardínez, Alberto Vela, Julián Cruz-Borbolla, Rodrigo J Alvarez-Mendez, José G Alvarado-Rodríguez
The relationship between the chemical structure and biological activity (log IC50) of 40 derivatives of 1,4-dihydropyridines (DHPs) was studied using density functional theory (DFT) and multiple linear regression analysis methods. With the aim of improving the quantitative structure-activity relationship (QSAR) model, the reduced density gradient s( r) of the optimized equilibrium geometries was used as a descriptor to include weak non-covalent interactions. The QSAR model highlights the correlation between the log IC50 with highest molecular orbital energy (E HOMO), molecular volume (V), partition coefficient (log P), non-covalent interactions NCI(H4-G) and the dual descriptor [Δf(r)]...
December 2016: Journal of Molecular Modeling
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
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
Cong-Jun Liu, Tao Zhang, Shu-Ling Yu, Xing-Jie Dai, Ya Wu, Jing-Chao Tao
Two series of novel acylthiosemicarbazide and oxadiazole fused-isosteviol derivatives were synthesized based on the 19-carboxyl modification. The target compounds were evaluated for their cytotoxicities against 3 cancer cell lines (HCT-116, HGC-27 and JEKO-1) using an MTT assay. Lead compounds from the acylthiosemicarbazides (4) showed IC50 values in the lower μmolar range. For example, compounds (4i, 4l, 4m, 4r and 4s) exhibited significant inhibitory activities against the 3 cell lines with IC50 values of 0...
November 23, 2016: Chemical Biology & Drug Design
Frank Hämmerling, Christopher Ladd Effio, Sebastian Andris, Jörg Kittelmann, Jürgen Hubbuch
Precipitation of proteins is considered to be an effective purification method for proteins and has proven its potential to replace costly chromatography processes. Besides salts and polyelectrolytes, polymers, such as polyethylene glycol (PEG), are commonly used for precipitation applications under mild conditions. Process development, however, for protein precipitation steps still is based mainly on heuristic approaches and high-throughput experimentation due to a lack of understanding of the underlying mechanisms...
November 19, 2016: Journal of Biotechnology
Abraham Yosipof, Klimentiy Shimanovich, Hanoch Senderowitz
Material informatics is engaged with the application of informatic principles to materials science in order to assist in the discovery and development of new materials. Central to the field is the application of data mining techniques and in particular machine learning approaches, often referred to as Quantitative Structure Activity Relationship (QSAR) modeling, to derive predictive models for a variety of materials-related "activities". Such models can accelerate the development of new materials with favorable properties and provide insight into the factors governing these properties...
December 2016: Molecular Informatics
Dongmei Yang, Hui Wang, Haijian Yuan, Shujun Li
Cinnamaldehyde, of the genius Cinnamomum, is a major constituent of the bark of the cinnamon tree and possesses broad-spectrum antimicrobial activity. In this study, we used best multiple linear regression (BMLR) to develop quantitative structure activity relationship (QSAR) models for cinnamaldehyde derivatives against wood-decaying fungi Trametes versicolor and Gloeophyllun trabeum. Based on the two optimal QSAR models, we then designed and synthesized two novel cinnamaldehyde compounds. The QSAR models exhibited good correlation coefficients: R²Tv = 0...
November 17, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Olubukayo-Opeyemi Oyetayo, Oscar Méndez-Lucio, Andreas Bender, Hans Kiefer
Solvents used for therapeutic proteins in downstream processing and in formulations often contain stabilizing additives that inhibit denaturation and aggregation. Such additives are mostly selected based on their positive effect on thermal stability of the protein, and are often derived from naturally occuring osmolytes. To better understand the structural basis underlying the effect of additives, we selected a diverse library of compounds comprising 79 compounds of the polyol, amino acid and methylamine chemical classes and determined the effect of each compound on thermal stability of a monoclonal antibody as a function of compound concentration...
November 16, 2016: European Journal of Pharmaceutical Sciences
Lukasz Bzdzion, Hanna Krezel, Karol Wrzeszcz, Irmina Grzegorek, Katarzyna Nowinska, Grzegorz Chodaczek, Wieslaw Swietnicki
Enteropathogenic E. coli (EPEC) is a human pathogen using type III secretion system for delivery of proteins directly into the human host. The system contains a single ATPase, EscN, which is essential for uncoupling of proteins from their complexes with chaperones before the delivery. The structure of EscN ATPase (PDB code: 2obm) was used to screen computationally for small molecule inhibitors blocking its active site. Two lead candidates were examined but only one, Compound 54, was selected for further optimization...
November 18, 2016: Acta Biochimica Polonica
Abdo A Elfiky, Samah M Mahdy, Wael M Elshemey
A number of human coronaviruses (HCoVs) were reported in the last and present centuries. Some outbreaks of which (e.g. SARS and MERS CoVs) caused the mortality of hundreds of people worldwide. The problem of finding a potent drug against HCoV strains lies in the inability of finding a drug that stops the viral replication through inhibiting its important proteins. In spite of its limited efficacy and potential side effects, Ribavirin is extensively used as a first choice against HCoVs. Therefore, scientists reverted towards the investigation of different drugs that can more specifically target proteins...
November 19, 2016: Journal of Medical Virology
Alla P Toropova, Andrey A Toropov, Maria Raskova, Ivan Raska
By optimization of so-called correlation weights of attributes of simplified molecular input-line entry system (SMILES) quantitative structure - activity relationships (QSAR) for toxicity towards Pimephales promelas are established. A new SMILES attribute has been utilized in this work. This attribute is a molecular descriptor, which reflects (i) presence of different kinds of bonds (double, triple, and stereo chemical bonds); (ii) presence of nitrogen, oxygen, sulphur, and phosphorus atoms; and (iii) presence of fluorine, chlorine, bromine, and iodine atoms...
December 2016: Environmental Toxicology and Pharmacology
Nareman D H Khaleel, Waleed M M Mahmoud, Oliver Olsson, Klaus Kümmerer
Trimipramine (TMP) is an antidepressant drug used for the treatment of a variety of depressive states and other psychiatric disorders. It has been already detected in the aquatic environment. Currently, no further knowledge is available on fate and effects of TMP in the aquatic environment. Therefore, we studied the biodegradability of TMP and of its photolysis transformation products (PTPs) generated by irradiation with polychromatic UV light in aqueous solution. Different conditions including initial drug concentration, pH, and temperature were applied during TMP photolysis...
January 1, 2017: Water Research
Sk Abdul Amin, Nilanjan Adhikari, Sonam Bhargava, Tarun Jha, Shovanlal Gayen
BACKGROUND: Thiazole-2-ethylamine is recently reported to be an interesting scaffold having antitrypansomal activity for the treatment of sleeping sickness. METHODS: Statistically significant, robust and validated regression-based QSAR models are constructed for a series of antitrypansomal thiazol-2-ethylamines. Moreover, classification-based QSAR analyses (linear discriminate analysis and Bayesian classification modelling) are also performed to identify the important structural features controlling antitrypanosomal activity...
November 17, 2016: Current Drug Discovery Technologies
Fucheng Song, Anling Zhang, Hui Liang, Lianhua Cui, Wenlian Li, Hongzong Si, Yunbo Duan, Honglin Zhai
A new analysis strategy was used to classify the carcinogenicity of aromatic amines. The physical-chemical parameters are closely related to the carcinogenicity of compounds. Quantitative structure activity relationship (QSAR) is a method of predicting the carcinogenicity of aromatic amine, which can reveal the relationship between carcinogenicity and physical-chemical parameters. This study accessed gene expression programming by APS software, the multilayer perceptrons by Weka software to predict the carcinogenicity of aromatic amines, respectively...
November 15, 2016: International Journal of Environmental Research and Public Health
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"