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https://www.readbyqxmd.com/read/28319747/integration-of-in-silico-methods-and-computational-systems-biology-to-explore-endocrine-disrupting-chemical-binding-with-nuclear-hormone-receptors
#1
P Ruiz, A Sack, M Wampole, S Bobst, M Vracko
Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28317396/3d-qsar-studies-pharmacophore-modeling-and-virtual-screening-of-diarylpyrazole-benzenesulfonamide-derivatives-as-a-template-to-obtain-new-inhibitors-using-human-carbonic-anhydrase-ii-as-a-model-protein
#2
Yeganeh Entezari Heravi, Hassan Sereshti, Ali Akbar Saboury, Jahan Ghasemi, Marzieh Amirmostofian, Claudiu T Supuran
A 3D-QSAR modeling was performed on a series of diarylpyrazole-benzenesulfonamide derivatives acting as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). The compounds were collected from two datasets with the same scaffold, and utilized as a template for a new pharmacophore model to screen the ZINC database of commercially available derivatives. The datasets were divided into training, test, and validation sets. As the first step, comparative molecular field analysis (CoMFA), CoMFA region focusing and comparative molecular similarity indices analysis (CoMSIA) in parallel with docking studies were applied to a set of 41 human (h) CA II inhibitors...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28314269/quantitative-structure-cytotoxicity-relationship-of-chalcones
#3
Hiroshi Sakagami, Yoshiko Masuda, Mineko Tomomura, Satoshi Yokose, Yoshihiro Uesawa, Naruhiko Ikezoe, Daiki Asahara, Koichi Takao, Taisei Kanamoto, Shigemi Terakubo, Hajime Kagaya, Hideki Nakashima, Yoshiaki Sugita
BACKGROUND: Fifteen chalcones were subjected to quantitative structure-activity relationship (QSAR) analysis based on their cytotoxicity and tumor specificity, in order to find their new biological activities. MATERIALS AND METHODS: Cytotoxicity against four human oral squamous cell carcinoma cell lines and three oral mesenchymal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor specificity (TS) was evaluated by the ratio of the mean 50% cytotoxic concentration (CC50) against normal cells to that against tumor cell lines...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28302310/design-synthesis-and-anti-diabetic-activity-of-triazolotriazine-derivatives-as-dipeptidyl-peptidase-4-dpp-4-inhibitors
#4
Bhumika D Patel, Shraddha V Bhadada, Manjunath D Ghate
Type 2 diabetes mellitus (T2DM) is one of the major global metabolic disorders characterized by insulin resistance and chronic hyperglycemia. Inhibition of the enzyme, dipeptidyl peptidase-4 (DPP-4) has been proved as successful and safe therapy for the treatment of T2DM since last decade. In order to design novel DPP-4 inhibitors, various in silico studies such as 3D-QSAR, pharmacophore modeling and virtual screening were performed and on the basis of the combined results of them, total 50 triazolo[5,1-c][1,2,4]triazine derivatives were designed and mapped on the best pharmacophore model...
March 6, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28302016/validation-of-tzd-scaffold-as-potential-aris-pharmacophore-modelling-atom-based-3d-qsar-and-docking-studies
#5
Lalita Dahiya, Manoj Kumar Mahapatra, Ramandeep Kaur, Vipin Kumar, Manoj Kumar
Metabolic disorders associated with diabetic patients are a serious concern. Aldose reductase (ALR2) has been identified as first rate-limiting enzyme in the polyol pathway which catalyzes the reduction of glucose to sorbitol. It represents one of the validated targets to develop potential new chemical entities for the prevention and subsequent progression of microvascular diabetic complications. In order to further understand the intricate structural prerequisites of molecules to act as ALR2 inhibitors, ligand-based pharmacophore model, atom-based 3D-QSAR and structure based drug design studies have been performed on a series of 2,4-thiazolidinedione derivatives with ALR2 inhibitory activity...
March 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28299833/unsupervised-pharmacophore-modeling-combined-with-qsar-analyses-revealed-novel-low-micromolar-sirt2-inhibitors
#6
Mohammad A Khanfar, Mutasem O Taha
Situin 2 (SIRT2) enzyme is a histone deacetylase that has important role in neuronal development. SIRT2 is clinically validated target for neurodegenerative diseases and some cancers. In this study, exhaustive unsupervised pharmacophore modeling was combined with quantitative structure-activity relationship (QSAR) analysis to explore the structural requirements for potent SIRT2 inhibitors using 146 known SIRT2 ligands. A computational workflow that combines genetic function algorithm with k-nearest neighbor or multiple linear regression was implemented to build self-consistent and predictive QSAR models based on combinations of pharmacophores and physicochemical descriptors...
March 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28299584/combined-molecular-docking-and-qsar-study-of-fused-heterocyclic-herbicide-inhibitors-of-d1-protein-in-photosystem-ii-of-plants
#7
Simona Funar-Timofei, Ana Borota, Luminita Crisan
Cinnoline, pyridine, pyrimidine, and triazine herbicides were found be inhibitors of the D1 protein in photosystem II (D1 PSII) electron transport of plants. The photosystem II inhibitory activity of these herbicides, expressed by experimental [Formula: see text] values, was modeled by a docking and quantitative structure-activity relationships study. A conformer ensemble for each of the herbicide structure was generated using the MMFF94s force field. These conformers were further employed in a docking approach, which provided new information about the rational "active conformations" and various interaction patterns of the herbicide derivatives with D1 PSII...
March 16, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28296049/qsar-and-molecular-docking-studies-on-designing-inhibitors-of-the-perforin
#8
Fucheng Song, Lianhua Cui, Jinmei Piao, Hui Liang, Hongzong Si, Yunbo Duan, Honglin Zhai
Quantitative structure-activity relationship (QSAR) studies were performed on a series of 5-Arylidene-2thioxoimidazolidin-4-ones derivatives as the inhibitors of perforin, and to gain insights about the structural determinants for designing new drug molecules. The heuristic method (HM) could explore the descriptors responsible for bioactivity and gain a best linear model with R(2) 0.82. Gene expression programming (GEP) method generated a novel nonlinear function model with R(2) 0.92 for training set, and R(2) 0...
March 14, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28294055/therapeutic-molecular-and-computational-aspects-of-novel-monoamine-oxidase-mao-inhibitors
#9
M Ramesh, Yussif M Dokurugu, Michael D Thompson, Mahmoud Soliman
Due to the limited number of MAOs inhibitors in the clinic and several research efforts are aimed at the discovery of novel MAOs inhibitors. At present, high specificity and a reversible mode of inhibition of MAO-A/B are cited as desirable traits in drug discovery process. This will help to reduce the probability of causing target disruption and may increase the duration of action. Most of the existing MAO inhibitors lead to side effects due to lack of affinity and selectivity. Therefore, there is an urgent need to design novel, potent, reversible and selective inhibitors for MAO-A/B...
March 10, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28294050/an-integrated-multi-qsar-modeling-approach-for-designing-knoevenagel-type-indoles-with-enhancing-cytotoxic-profiles
#10
Sk Abdul Amin, Nilanjan Adhikari, Tarun Jha, Shovanlal Gayen
BACKGROUND: Unconventional Knoevenagel-type indoles have been the topic of interest of many synthetic chemists because of its promising efficacy in different diseases including in cancer. OBJECTIVE: To explore the structural requirements of Knoevenagel-type cytotoxic indoles for higher efficacy. METHODS: Multi-QSAR modeling (MLR, ANN, SVM, Bayesian classification, HQSAR and Topomer CoMFA) was performed on these analogs. RESULTS: All these modeling techniques were validated individually and interpreted with the experimental SAR observations...
March 9, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28293683/qsars-and-computational-chemistry-methods-in-environmental-chemical-sciences
#11
EDITORIAL
Kathrin Fenner, Paul G Tratnyek
No abstract text is available yet for this article.
March 15, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28293633/combined-ligand-structure-based-virtual-screening-and-molecular-dynamics-simulations-of-steroidal-androgen-receptor-antagonists
#12
Yuwei Wang, Rui Han, Huimin Zhang, Hongli Liu, Jiazhong Li, Huanxiang Liu, Paola Gramatica
The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR), are the main endocrine therapies for prostate cancer (PCa). But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28291352/understanding-the-molecular-determinant-of-reversible-human-monoamine-oxidase-b-inhibitors-containing-2h-chromen-2-one-core-structure-based-and-ligand-based-derived-3-d-qsar-predictive-models
#13
Milan Mladenovic, Alexandros Patsilinakos, Adele Pirolli, Manuela Sabatino, Rino Ragno
Monoamine oxidase B (MAO B) catalyzes the oxidative deamination of aryalkylamines neurotransmitters with concomitant reduction of oxygen to hydrogen peroxide. Consequently, the enzyme's malfunction can induce oxidative damage to mitochondrial DNA and mediates development of Parkinson's disease. Thus, MAO B emerges as a promising target for developing pharmaceuticals potentially useful to treat this vicious neurodegenerative condition. Aiming to contribute to the development of drugs with the reversible mechanism of MAO B inhibition only, herein, an extended in silico-in vitro procedure for the selection of novel MAO B inhibitors is demonstrated, including: (1) definition of optimized and validated structure-based (SB) 3-D QSAR models derived from available co-crystallized inhibitor-MAO B complexes; (2) elaboration of structure-activity relationships (SAR) features for either irreversible or reversible MAO B inhibitors to characterize and improve coumarin-based inhibitor activity (Protein Data Bank ID: 2V61) as the most potent reversible lead compound; (3) definition of structure-based (SB) and ligand-based (LB) alignment rules assessments by which virtually any untested potential MAO B inhibitor might be evaluated; (4) predictive ability validation of the best 3-D QSAR model through SB/LB modeling of four coumarin-based external test sets (267 compounds); (5) design and SB/LB alignment of novel coumarin-based scaffolds experimentally validated through synthesis and biological evaluation in vitro...
March 14, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28290085/oxidation-of-indometacin-by-ferrate-vi-kinetics-degradation-pathways-and-toxicity-assessment
#14
Junlei Huang, Yahui Wang, Guoguang Liu, Ping Chen, Fengliang Wang, Jingshuai Ma, Fuhua Li, Haijin Liu, Wenying Lv
The oxidation of indometacin (IDM) by ferrate(VI) (Fe(VI)) was investigated to determine the reaction kinetics, transformation products, and changes in toxicity. The reaction between IDM and Fe(VI) followed first-order kinetics with respect to each reactant. The apparent second-order rate constants (k app) decreased from 9.35 to 6.52 M(-1) s(-1), as the pH of the solution increased from 7.0 to 10.0. The pH dependence of k app might be well explained by considering the species-specific rate constants of the reactions of IDM with Fe(VI)...
March 13, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28288354/pharmacophore-based-3d-qsar-modeling-virtual-screening-and-docking-for-identification-of-potential-inhibitors-of-%C3%AE-secretase
#15
Ravichand Palakurti, Ramakrishna Vadrevu
The enzyme β-secretase-1 is responsible for the cleavage of the amyloid precursor protein, a vital step in the process of the formation of amyloid-β peptides which are known to lead to neurodegeneration causing Alzheimer's disease. Challenges associated with toxicity and blood brain permeation inability of potential inhibitors, continue to evade a successful therapy, thus demanding the search and development of highly active and effective inhibitors. Towards these efforts, we used a ligand based pharmacophore model generation from a dataset of known inhibitors whose activities against β-secretase hovered in the nano molar range...
March 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28276287/benzimidazole-based-derivatives-as-privileged-scaffold-developed-for-the-treatment-of-the-rsv-infection-a-computational-study-exploring-the-potency-and-cytotoxicity-profiles
#16
Elena Cichero, Michele Tonelli, Federica Novelli, Bruno Tasso, Ilenia Delogu, Roberta Loddo, Olga Bruno, Paola Fossa
Respiratory syncytial virus (RSV) has been identified as a main cause of hospitalisation in infants and children. To date, the current therapeutic arsenal is limited to ribavirin and palivizumab with variable efficacy. In this work, starting from a number of in-house series of previously described anti-RSV agents based on the benzimidazole scaffold, with the aim at gaining a better understanding of the related chemical features involved in potency and safety profiles, we applied a computational study including two focussed comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28275924/2d-sar-and-3d-qsar-analyses-for-acetylcholinesterase-inhibitors
#17
Bing Niu, Manman Zhao, Qiang Su, Mengying Zhang, Wei Lv, Qin Chen, Fuxue Chen, Dechang Chu, Dongshu Du, Yuhui Zhang
Alzheimer's disease (AD) accounts for almost three quarters of dementia patients and interferes people's normal life. Great progress has been made recently in the study of Acetylcholinesterase (AChE), known as one of AD's biomarkers. In this study, acetylcholinesterase inhibitors (AChEI) were collected to build a two-dimensional structure-activity relationship (2D-SAR) model and three-dimensional quantitative structure-activity relationship (3D-QSAR) model based on feature selection method combined with random forest...
March 9, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28274840/systemic-qsar-and-phenotypic-virtual-screening-chasing-butterflies-in-drug-discovery
#18
REVIEW
Maykel Cruz-Monteagudo, Stephan Schürer, Eduardo Tejera, Yunierkis Pérez-Castillo, José L Medina-Franco, Aminael Sánchez-Rodríguez, Fernanda Borges
Current advances in systems biology suggest a new change of paradigm reinforcing the holistic nature of the drug discovery process. According to the principles of systems biology, a simple drug perturbing a network of targets can trigger complex reactions. Therefore, it is possible to connect initial events with final outcomes and consequently prioritize those events, leading to a desired effect. Here, we introduce a new concept, 'Systemic Chemogenomics/Quantitative Structure-Activity Relationship (QSAR)'. To elaborate on the concept, relevant information surrounding it is addressed...
March 6, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28273884/2d-qsar-and-3d-qsar-comsia-studies-on-a-series-of-r-2-2-1h-indol-2-yl-ethyl-amino-1-phenylethan-1-ol-with-human-%C3%AE-%C3%A2-adrenergic-activity
#19
Gastón Apablaza, Luisa Montoya, Cesar Morales-Verdejo, Marco Mellado, Mauricio Cuellar, Carlos F Lagos, Jorge Soto-Delgado, Hery Chung, Carlos David Pessoa-Mahana, Jaime Mella
The β₃ adrenergic receptor is raising as an important drug target for the treatment of pathologies such as diabetes, obesity, depression, and cardiac diseases among others. Several attempts to obtain selective and high affinity ligands have been made. Currently, Mirabegron is the only available drug on the market that targets this receptor approved for the treatment of overactive bladder. However, the FDA (Food and Drug Administration) in USA and the MHRA (Medicines and Healthcare products Regulatory Agency) in UK have made reports of potentially life-threatening side effects associated with the administration of Mirabegron, casting doubts on the continuity of this compound...
March 5, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28271914/monte-carlo-method-based-qsar-modelling-of-natural-lipase-inhibitors-using-hybrid-optimal-descriptors
#20
A Kumar, S Chauhan
Obesity is one of the most provoking health burdens in the developed countries. One of the strategies to prevent obesity is the inhibition of pancreatic lipase enzyme. The aim of this study was to build QSAR models for natural lipase inhibitors by using the Monte Carlo method. The molecular structures were represented by the simplified molecular input line entry system (SMILES) notation and molecular graphs. Three sets - training, calibration and test set of three splits - were examined and validated. Statistical quality of all the described models was very good...
March 8, 2017: SAR and QSAR in Environmental Research
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