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https://www.readbyqxmd.com/read/28205401/computer-aided-drug-design-to-explore-cyclodextrin-therapeutics-and-biomedical-applications
#1
Azizeh Abdolmaleki, Fatemeh Ghasemi, Jahan B Ghasemi
Cyclodextrin (CD) is a subset of the macrocyclic structural class, which is an important class of small organic agents that are useful functional excipients. They have wide range application possibilities in different fields of sciences such as material preparation, medicine, analytical chemistry, and separation processes. They are used widely in pharmaceutical formulations and drug delivery for increasing the water solubility of low soluble drugs and drug candidates. Due to the ring structure, they behave differently than smaller molecules and may be capable of hitting new classes of targets...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28197603/general-baseline-toxicity-qsar-for-nonpolar-polar-and-ionisable-chemicals-and-their-mixtures-in-the-bioluminescence-inhibition-assay-with-aliivibrio-fischeri
#2
Beate I Escher, Andreas Baumer, Kai Bittermann, Luise Henneberger, Maria König, Christin Kühnert, Nils Klüver
The Microtox assay, a bioluminescence inhibition assay with the marine bacterium Aliivibrio fischeri, is one of the most popular bioassays for assessing the cytotoxicity of organic chemicals, mixtures and environmental samples. Most environmental chemicals act as baseline toxicants in this short-term screening assay, which is typically run with only 30 min of exposure duration. Numerous Quantitative Structure-Activity Relationships (QSARs) exist for the Microtox assay for nonpolar and polar narcosis. However, typical water pollutants, which have highly diverse structures covering a wide range of hydrophobicity and speciation from neutral to anionic and cationic, are often outside the applicability domain of these QSARs...
February 15, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28196626/the-index-of-ideality-of-correlation-a-criterion-of-predictability-of-qsar-models-for-skin-permeability
#3
Alla P Toropova, Andrey A Toropov
New criterion of the predictive potential of quantitative structure-property/activity relationships (QSPRs/QSARs) is suggested. This criterion is calculated with utilization of the correlation coefficient between experimental and calculated values of endpoint for the calibration set, with taking into account the positive and negative dispersions between experimental and calculated values. The utilization of this criterion improves the predictive potential of QSAR models of dermal permeability coefficient, logKp (cm/h)...
February 11, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28187825/characterization-of-acetylcholinesterase-from-elm-left-beetle-xanthogaleruca-luteola-and-qsar-of-temephos-derivatives-against-its-activity
#4
Mahboobeh Sharifi, Mohammad Ghadamyari, Khodayar Gholivand, Ali Asghar Ebrahimi Valmoozi, Reza H Sajedi
Insect acetylcholinesterase (AChE) is the principal target for organophosphate (OP) and carbamate (CB) insecticides. In this research, an AChE from third instar larvae of elm left beetle, Xanthogaleruca luteola was purified by affinity chromatography. The enzyme was purified 75.29-fold with a total yield of 8.51%. As shown on denaturing SDS-PAGE, the molecular mass of purified AChE was 70kDa. The enzyme demonstrated maximum activity at pH7 and 35°C. Furthermore, a series of temephos (Tem) derivatives with the general structure of P(O)XP(O) (1-44) were prepared, synthesized and characterized by (31)P, (13)C, (1)H NMR and FT-IR spectral techniques...
March 2017: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/28185538/synthesis-and-biological-evaluation-of-hybrid-1-5-and-2-5-disubstituted-indoles-as-potentially-new-antitubercular-agents
#5
Ana Soares, Mónica S Estevão, M Manuel B Marques, Vasily Kovalishyn, Diogo A R S Latino, João Aires-de-Sousa, Jorge Ramos, Miguel Viveiros, Filomena Martins
BACKGROUND: Tuberculosis (TB) is the second leading cause of mortality worldwide being a highly contagious and insidious illness caused by Mycobacterium tuberculosis, Mtb. Additionally, the emergence of multidrug-resistant and extensively drug-resistant strains of Mtb, together with significant levels of co-infection with HIV and TB (HIV/TB) makes the search for new antitubercular drugs urgent and challenging. METHODS: This work was based on the hypothesis that an active compound could be obtained if substituents present in some other active compounds were attached on a core of an important structure, in this case the indole scaffold, thus generating a hybrid compound...
February 9, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28182408/design-synthesis-structure-activity-relationship-studies-and-three-dimensional-quantitative-structure-activity-relationship-3d-qsar-modeling-of-a-series-of-o-biphenyl-carbamates-as-dual-modulators-of-dopamine-d3-receptor-and-fatty-acid-amide-hydrolase
#6
Alessio De Simone, Debora Russo, Gian Filippo Ruda, Alessandra Micoli, Mariarosaria Ferraro, Rita Maria Concetta Di Martino, Giuliana Ottonello, Maria Summa, Andrea Armirotti, Tiziano Bandiera, Andrea Cavalli, Giovanni Bottegoni
We recently reported molecules designed according to the multi-target-directed ligand paradigm to exert combined activity at human fatty acid amide hydrolase (FAAH) and dopamine receptor subtype D3 (D3R). Both targets are relevant for tackling several types of addiction (most notably nicotine addiction) and other compulsive behaviors. Here, we report an SAR exploration of a series of biphenyl-N-[4-[4-(2,3-substituted-phenyl)piperazine-1-yl]alkyl]carbamates, a novel class of molecules that had shown promising activities at the FAAH - D3R target combination in preliminary studies...
February 9, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28177949/progress-with-structure-activity-relationship-modelling-of-occupational-chemical-respiratory-sensitizers
#7
Martin J Seed, Raymond M Agius
PURPOSE OF REVIEW: This appraises currently available computer-based ('in silico') models relating the molecular structure of low molecular weight compounds to their respiratory sensitization hazard. The present review places focus on the two main applications of such structure--activity relationship (SAR) models: hypotheses on disease mechanisms and toxicological prediction. RECENT FINDINGS: Analyses of the chemical structures of low molecular weight organic compounds known to have caused occupational asthma has led to the development of mechanistic alerts usually based on electrophilic reaction chemistry and protein cross-linking potential...
February 7, 2017: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28177532/quantitative-structure-activity-relationships-for-the-nucleophilicity-of-trivalent-boron-compounds
#8
Jorge Juan Carbo, Diego García-López, Ruben Marqués, Jessica Cid, Elena Fernández
We describe the development of quantitative structure-activity relationships (QSAR) for the nucleophilicity of trivalent boron compounds covering boryl fragments bonded to alkali and alkali-earth metals, to transition metals, and to B(sp³) units in diboron reagents. We used the charge of the boryl fragment (q[B]) and the boron p/s-population ratio (p/s) to describe the electronic structure of boryl moieties, whereas the distance-weighted volume (VW) descriptor was used to evthe steric effects. The 3-terms easy-to-interpret QSAR model showed statistical significance and predictive ability (r²= 0...
February 8, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28176631/grid-based-continual-analysis-of-molecular-interior-for-drug-discovery-qsar-and-qspr
#9
A V Potemkin, M A Grishina, V A Potemkin
BACKGROUND: In 1979, R.D.Cramer and M.Milne made a first realization of the above mentioned principles attempting to compare molecules by aligning them in space and by mapping their molecular fields to a 3D grid. Further, this approach was developed as the DYLOMMS (DYnamic Lattice-Oriented Molecular Modelling System) approach. In 1984, H.Wold and S.Wold proposed the use of partial least squares (PLS) analysis, instead of principal component analysis, to correlate the field values with biological activities...
February 7, 2017: Current Drug Discovery Technologies
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
#10
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/28169452/in-vivo-toxicity-of-nitroaromatics-a-comprehensive-qsar-study
#11
Aminah Gooch, Natalia Sizochenko, Bakhtiyor Rasulev, Leonid Gorb, Jerzy Leszczynski
The toxicity data of 90 nitroaromatic compounds related to their 50% lethal dose concentration for rats (LD50 ) were analyzed to develop quantitative structure-activity relationship (QSAR) models. Quantum-chemically calculated descriptors together with molecular descriptors generated by DRAGON, PaDEL and HiT-QSAR software were utilized to build QSAR models. Quality and validity of the models were determined by internal and external validation techniques. The results of the study show that the toxicity of nitroaromatic compounds depends on various factors, such as the number of nitro-groups, the topological state, and the presence of certain structural fragments...
February 7, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28168765/prediction-of-anti-alzheimer-s-activity-of-flavonoids-targeting-acetylcholinesterase-in-silico
#12
Subrata Das, Monjur A Laskar, Satyajit D Sarker, Manabendra D Choudhury, Prakash Roy Choudhury, Abhijit Mitra, Shajarahtunnur Jamil, Siti Mariam A Lathiff, Siti Awanis Abdullah, Norazah Basar, Lutfun Nahar, Anupam D Talukdar
INTRODUCTION: Prenylated and pyrano-flavonoids of the genus Artocarpus J. R. Forster & G. Forster are well known for their acetylcholinesterase (AChE) inhibitory, anti-cholinergic, anti-inflammatory, anti-microbial, anti-oxidant, anti-proliferative and tyrosinase inhibitory activities. Some of these compounds have also been shown to be effective against Alzheimer's disease. OBJECTIVE: The aim of the in silico study was to establish protocols to predict the most effective flavonoid from prenylated and pyrano-flavonoid classes for AChE inhibition linking to the potential treatment of Alzheimer's disease...
February 7, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28168672/compilation-of-data-and-modelling-of-nanoparticle-interactions-and-toxicity-in-the-nanopuzzles-project
#13
Andrea-Nicole Richarz, Aggelos Avramopoulos, Emilio Benfenati, Agnieszka Gajewicz, Nazanin Golbamaki Bakhtyari, Georgios Leonis, Richard L Marchese Robinson, Manthos G Papadopoulos, Mark Td Cronin, Tomasz Puzyn
The particular properties of nanomaterials have led to their rapidly increasing use in diverse fields of application. However, safety assessment is not keeping pace and there are still gaps in the understanding of their hazards. Computational models predicting nanotoxicity, such as (quantitative) structure-activity relationships ((Q)SARs), can contribute to safety evaluation, in line with general efforts to apply alternative methods in chemical risk assessment. Their development is highly dependent on the availability of reliable and high quality experimental data, both regarding the compounds' properties as well as the measured toxic effects...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28165522/classification-of-baseline-toxicants-for-qsar-predictions-to-replace-fish-acute-toxicity-studies
#14
Monika Nendza, Martin Müller, Andrea Wenzel
Fish acute toxicity studies are required for environmental hazard and risk assessment of chemicals by national and international legislations such as REACH, the regulations of plant protection products and biocidal products, or the GHS (globally harmonised system) for classification and labelling of chemicals. Alternative methods like QSARs (quantitative structure-activity relationships) can replace many ecotoxicity tests. However, complete substitution of in vivo animal tests by in silico methods may not be realistic...
February 6, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28161994/conformation-dependent-qsar-approach-for-the-prediction-of-inhibitory-activity-of-bromodomain-modulators
#15
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/28161088/synthesis-and-qsar-study-of-novel-%C3%AE-methylene-%C3%AE-butyrolactone-derivatives-as-antifungal-agents
#16
Yong-Ling Wu, De-Long Wang, En-Hui Guo, Shuang Song, Jun-Tao Feng, Xing Zhang
Thirty-six new α-benzylidene-γ-lactone compounds based α-methylene-γ-butyrolactone substructure were prepared and characterized by spectroscopic analysis. All compounds were evaluated for antifungal activities in vitro against six plant pathogenic fungi and the half maximal inhibitory concentration (IC50) against Botrytis cinerea and Colletotrichum lagenarium were investigated. Compounds 5c-3 and 5c-5 with the halogen atom exhibited excellent fungicidal activity against B. cinerea (IC50=22.91, 18.89μM)...
January 13, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28157177/antiplasmodial-activity-cytotoxicity-and-structure-activity-relationship-study-of-cyclopeptide-alkaloids
#17
Emmy Tuenter, Karen Segers, Kyo Bin Kang, Johan Viaene, Sang Hyun Sung, Paul Cos, Louis Maes, Yvan Vander Heyden, Luc Pieters
Cyclopeptide alkaloids are polyamidic, macrocyclic compounds, containing a 13-, 14-, or 15-membered ring. The ring system consists of a hydroxystyrylamine moiety, an amino acid, and a β-hydroxy amino acid; attached to the ring is a side chain, comprised of one or two more amino acid moieties. In vitro antiplasmodial activity was shown before for several compounds belonging to this class, and in this paper the antiplasmodial and cytotoxic activities of ten more cyclopeptide alkaloids are reported. Combining these results and the IC50 values that were reported by our group previously, a library consisting of 19 cyclopeptide alkaloids was created...
February 2, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28155653/novel-group-based-qsar-and-combinatorial-design-of-ck-1%C3%AE-inhibitors-as-neuroprotective-agents
#18
Kopal Joshi, Sukriti Goyal, Sonam Grover, Salma Jamal, Aditi Singh, Pawan Dhar, Abhinav Grover
BACKGROUND: Tar DNA binding protein 43 (TDP-43) hyperphosphorylation, caused by Casein kinase 1 (CK-1) protein isoforms, is associated with the onset and progression of Amyotrophic Lateral Sclerosis (ALS). Among the reported isoforms and splice variants of CK-1 protein superfamily, CK-1δ is known to phosphorylate different serine and threonine sites on TDP-43 protein in vitro and thus qualifies as a potential target for ALS treatment. RESULTS: The developed GQSAR (group based quantitative structure activity relationship) model displayed satisfactory statistical parameters for the dataset of experimentally reported N-Benzothiazolyl-2-Phenyl Acetamide derivatives...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28155089/predicting-dpp-iv-inhibitors-with-machine-learning-approaches
#19
Jie Cai, Chanjuan Li, Zhihong Liu, Jiewen Du, Jiming Ye, Qiong Gu, Jun Xu
Dipeptidyl peptidase IV (DPP-IV) is a promising Type 2 diabetes mellitus (T2DM) drug target. DPP-IV inhibitors prolong the action of glucagon-like peptide-1 (GLP-1) and gastric inhibitory peptide (GIP), improve glucose homeostasis without weight gain, edema, and hypoglycemia. However, the marketed DPP-IV inhibitors have adverse effects such as nasopharyngitis, headache, nausea, hypersensitivity, skin reactions and pancreatitis. Therefore, it is still expected for novel DPP-IV inhibitors with minimal adverse effects...
February 2, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28154864/development-of-polyparameter-linear-free-energy-relationship-models-for-octanol-air-partition-coefficients-of-diverse-chemicals
#20
Xiaochen Jin, Zhiqiang Fu, Xuehua Li, Jingwen Chen
The octanol-air partition coefficient (KOA) is a key parameter describing the partition behavior of organic chemicals between air and environmental organic phases. As the experimental determination of KOA is costly, time-consuming and sometimes limited by the availability of authentic chemical standards for the compounds to be determined, it becomes necessary to develop credible predictive models for KOA. In this study, a polyparameter linear free energy relationship (pp-LFER) model for predicting KOA at 298...
February 3, 2017: Environmental Science. Processes & Impacts
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