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Srivastava Vikas - - 2010
Computational chemistry is playing an increasingly important role in drug design and discovery, structural biology, and quantitative structure-activity relationship studies. A series of 4(3H)-quinozolone derivatives were screened for two-dimensional quantitative structure-activity relationship studies and subsequently their absorption, distribution, metabolism, and excretion (ADME) properties with the use of soft modeling techniques ...
Caballero Julio - - 2010
Inhibitory activities of flavonoid derivatives against aldose reductase (AR) enzyme were modelled by using CoMFA, CoMSIA and GALAHAD methods. CoMFA and CoMSIA methods were used for deriving quantitative structure-activity relationship (QSAR) models. All QSAR models were trained with 55 compounds, after which they were evaluated for predictive ability with additional ...
Stojić Nataša - - 2010
In this work, a novel algorithm for optimization of counter-propagation artificial neural networks has been used for development of quantitative structure-activity relationships model for prediction of the estrogenic activity of endocrine-disrupting chemicals. The search for the best model was performed using genetic algorithms. Genetic algorithms were used not only for ...
Ekins Sean - - 2010
Drug-induced liver injury (DILI) is one of the most important reasons for drug development failure at both preapproval and postapproval stages. There has been increased interest in developing predictive in vivo, in vitro, and in silico models to identify compounds that cause idiosyncratic hepatotoxicity. In the current study, we applied ...
Virsdoia Vijay - - 2010
The resurgence of tuberculosis and the emergence of multidrug-resistant strains of Mycobacteria necessitate the search for new classes of antimycobacterial agents. We have synthesized a small library of 50 analogues of 4-(arylamino)coumarins with various aromatic amines at the C(4) - position of the coumarin scaffold. The compounds were evaluated for ...
Le-Thi-Thu Huong - - 2011
The present work is devoted to the development and application of a multi-agent Quantitative Structure-Activity Relationship (QSAR) classification system for tyrosinase inhibitor identification, in which the individual QSAR outputs are the inputs of a fusion approach based on the voting mechanism. The individual models are based on TOMOCOMD-CARDD (TOpological Molecular ...
Weber Karen C - - 2010
Two-dimensional and 3D quantitative structure-activity relationships studies were performed on a series of diarylpyridines that acts as cannabinoid receptor ligands by means of hologram quantitative structure-activity relationships and comparative molecular field analysis methods. The quantitative structure-activity relationships models were built using a data set of 52 CB1 ligands that can ...
Trifković Jelena - - 2010
A quantitative structure-retention relationship study has been performed to correlate the retention of 33 newly synthesized arylpiperazines with their molecular characteristics, using thin-layer chromatography. Principal component analysis followed by multiple linear regression (MLR), principal component regression (PCR) and partial least squares (PLS) was performed to identify the most important factors, ...
Ghavami Raouf - - 2010
High resolution gas chromatographic relative retention time (HRGC-RRT) models were developed to predict relative retention times of the 209 individual polychlorinated biphenyls (PCBs) congeners. To estimate and predict the HRGC-RRT values of all PCBs on 18 different stationary phases, a multiple linear regression equation of the form RRT = a(o) + a(1) (no. o-Cl) + a(2) ...
Rajak Harish - - 2010
A novel series of N'-{5-[(1H-indol-3-ylmethyl)-1,3,4-thiadiazol-2-yl}-N4-(4-substituted benzaldehyde)-semicarbazones, N1-{5-[(1H-indol-3-ylmethyl)-1,3,4-thiadiazol-2-yl}-N4-[1-(4-substituted phenyl)ethanone]-semicarbazones and N1-{5-[(1H-indol-3-ylmethyl)-1,3,4-thiadiazol-2-yl}-N4-[1-(4-substituted phenyl) (phenyl) methanone]-semicarbazones were synthesized and evaluated for their anticonvulsant potential using maximal electroshock seizure (MES) and subcutaneous pentylenetrtrazole (scPFZ) models. The minimal motor impairment (neurotoxicity) was determined by rotorod test. The results of the present study confirmed the requirements ...
Mahipal - - 2010
The article describes the development of a robust pharmacophore model and the investigation of structure activity relationship analysis of 48 aminophenyl benzamide derivatives reported for Histone Deacetylase (HDAC) inhibition using PHASE module of Schrodinger software. A five point pharmacophore model consisting of two aromatic rings (R), two hydrogen bond donors ...
Roy Kuldeep K - - 2011
The present study describes a systematic 3D-QSAR study consisting of pharmacophore modeling, docking, and integration of ligand-based and structure-based drug design approaches, applied on a dataset of 72 Hsp90 inhibitors as anti-cancer agents. The best pharmacophore model, with one H-bond donor (HBD), one H-bond acceptor (HBA), one hydrophobic_aromatic (Hy_Ar), and ...
Manoharan Prabu - - 2010
The ability to identify fragments that interact with a biological target is a key step in FBDD. To date, the concept of fragment based drug design (FBDD) is increasingly driven by bio-physical methods. To expand the boundaries of QSAR paradigm, and to rationalize FBDD using In silico approach, we propose ...
Ravichandran V - - 2011
Inhibition of human immunodeficiency virus 1 (HIV-1) protease is an important strategy for the treatment of HIV and acquired immune deficiency syndrome (AIDS). Therefore, HIV-1 protease inhibitory activity of dihydropyranone derivatives has been analyzed with different physico-chemical parameters. In the present work, QSAR studies were performed on a series of ...
Mishra Rama K - - 2010
Studies reported here are aimed to investigate the important structural features that characterize the human EP(3) antagonists. Based on the knowledge of low-energy conformation of the endogenous ligand, the initial hit analogs were prepared. Subsequently, a ligand-based lead optimization approach using pharmacophore model generation was utilized. A 5-point pharmacophore using ...
Warner Daniel J - - 2010
An algorithm to automatically identify and extract matched molecular pairs from a collection of compounds has been developed, allowing the learning associated with each molecular transformation to be readily exploited in drug discovery projects. Here, we present the application to an example data set of 11 histone deacetylase inhibitors. The ...
Gupta Amit K - - 2010
A pharmacophore model has been developed for determining the essential structural requirements for antimalarial activity from the eight series of substituted 1,2,4-trioxanes. The best pharmacophore model possessing two aliphatic hydrophobic, one aromatic hydrophobic, one hydrogen-bond (H-bond) acceptor, and one H-bond acceptor (lipid) feature for antimalarial activity showed an excellent correlation ...
Wawer Mathias - - 2010
An intuitive and generally applicable analysis method, termed similarity-potency tree (SPT), is introduced to mine structure-activity relationship (SAR) information in compound data sets of any source. Only compound potency values and nearest-neighbor similarity relationships are considered. Rather than analyzing a data set as a whole, in part overlapping compound neighborhoods ...
Escalera Sergio - - 2011
In this paper, we propose a circular blurred shape model descriptor to deal with the problem of symbol detection and classification as a particular case of object recognition. The feature extraction is performed by capturing the spatial arrangement of significant object characteristics in a correlogram structure. The shape information from ...
Mensch Jurgen - - 2010
This study examines whether algorithms to predict brain penetration of 88 drug candidates could benefit from inclusion of PAMPA data such as Peff, flux and membrane retention. Specifically the ability to fit experimentally derived LogBB data with PAMPA information and compound related physicochemical and structural parameters was assessed. Collected data ...
Li Fei - - 2010
Comprehension of the ligand-receptor interactions is a prerequisite for constructing mechanism based quantitative structure-activity relationship (QSAR) models on xenoestrogenic activity. Molecular docking was performed to simulate the interactions between anthraquinone derivative (AQs) molecules and the estrogen receptor alpha (ERalpha). Hydrogen bonding, hydrophobic, and pi-pi interactions were found to be the ...
Andrić Filip Lj - - 2010
In order to determine the soil-water partition coefficient for eleven mono- and poly-substituted phenolic compounds, for which there is still no literature data available, the possibility of using thin-layer chromatography (TLC) as a means for rapid and reliable logK(OC) estimation was examined. A series of chromatographically derived descriptors: R(M)(0), b, ...
Halder Amit Kumar - - 2010
Validated predictive QSAR modeling was done on some N-aryl-oxazolidinone-5-carboxamides for higher anti-HIV protease activities. Stepwise regression developed significant models showing importance of atom based descriptors like RTSA indices, Wang-Ford charges and different whole molecular descriptors. The true predictabilities of QSAR models were justified by challenging these against an external dataset. ...
Mitra Indrani - - 2010
The present work deals with the chemometric modeling of antioxidant molecules belonging to the class of flavone derivatives employing the quantitative structure-activity relationship (QSAR) technique. A QSAR model was initially built based on the Fujita-Ban method with the training set molecules. Due to the inability of the Fujita-Ban type model ...
Pirhadi Somayeh - - 2010
3D-QSAR studies namely CoMFA, CoMFA region focusing and CoMSIA have been carried out on a series (36 compounds) of HIV-1 entry inhibitors. An alignment rule for the compounds was defined using Distill in SYBYL 7.3. Models were validated using a data set obtained by dividing the data set into a ...
Goodarzi Mohammad - - 2010
Leishmaniasis is a neglected disease transmitted in many tropical and sub-tropical countries, with few studies devoted to its treatment. In this work, the activities of two antileishmanial compound classes were modeled using Dragon descriptors, and multiple linear (MLR) and support vector machines (SVM) as linear and nonlinear regression methods, respectively. ...
Gupta Rishi R - - 2010
Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using ...
Guerrieri Peter - - 2010
The solid-state properties of pharmaceutical salts, which are dependent on the counterion used to form the salt, are critical for successful development of a stable dosage form. In order to better understand the relationship between counterion and salt properties, 11 salts of procaine, which is a base, were synthesized and ...
Manallack David T - - 2010
The development of robust and predictive QSAR models is highly dependent on the use of molecular descriptors that contain information relevant to the property being modelled. Selection of these relevant features from a large pool of possibilities is difficult to achieve effectively. Modern Bayesian methods provide substantial advantages over conventional ...
Ma Bin - - 2010
Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 ...
Sârbu Costel - - 2010
The retention behavior of some food synthetic dyes has been studied by RP-HPLC on chemically bonded C18, C8, C16 and CN stationary phases. Using methanol-ammonium acetate (0.08 mol/L, pH=6.76) as mobile phase, a linear behavior of retention parameters throughout the methanol fraction variance was obtained in all cases (r>0.99). The ...
Lowe Edward W EW - - 2010
Positive allosteric modulation of the metabotropic glutamate receptor subtype 5 was studied by conducting a comparative molecular field analysis on 118 benzoxazepine derivatives. The model with the best predictive ability retained significant cross-validated correlation coefficients of q(2) = 0.58 (r(2) = 0.81) yielding a standard error of 0.20 in pEC(50) ...
Chen Beijing - - 2011
The derivation of moment invariants has been extensively investigated in the past decades. In this paper, we construct a set of invariants derived from Zernike moments which is simultaneously invariant to similarity transformation and to convolution with circularly symmetric point spread function (PSF). Two main contributions are provided: the theoretical ...
Salum Lívia Barros - - 2010
Alzheimer's disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. ...
Su Bo-Han - - 2010
Blockage of the human ether-a-go-go related gene (hERG) potassium ion channel is a major factor related to cardiotoxicity. Hence, drugs binding to this channel have become an important biological end point in side effects screening. A set of 250 structurally diverse compounds screened for hERG activity from the literature was ...
Yu Melvin J - - 2010
A conceptually simple, fully in silico model to predict total clearance of new compounds in humans is described. Based on the premise that similar molecules will exhibit similar pharmacokinetic properties, we used a k-nearest-neighbors (kNN) technique to predict total clearance by comparison with known reference agents. Molecular similarity was defined ...
Yan Shi-Kai - - 2010
Quantitative composition-activity relationship (QCAR) study makes it possible to discover active components in traditional Chinese medicine (TCM) and to predict the integral bioactivity by its chemical composition. In the study, 28 samples of Radix Tinosporae were quantitatively analyzed by high performance liquid chromatography, and their analgesic activities were investigated via ...
Borges de Melo Eduardo - - 2010
A quantitative structure-activity relationship (QSAR) study of twenty flavonoid derivatives with antimutagenic activity against 3-nitrofluoranthene (3-NFA) was performed by Partial Least Squares (PLS), using Ordered Predictors Selection (OPS) algorithm for variable selection. Four descriptors (PJI2, Mor27m, G1e and R4u+) were selected and a good model (n = 19; R(2) = ...
Morales-Bayuelo Alejandro - - 2010
Comparative molecular similarity indices analysis (CoMSIA) and comparative molecular field analysis (CoMFA) were performed on a series of bicyclo [4.1.0] heptanes derivatives as melanin-concentrating hormone receptor R1 antagonists (MCHR1 antagonists). Molecular superimposition of antagonists on the template structure was performed by database alignment method. The statistically significant model was established ...
Shahlaei Mohsen - - 2010
Quantitative relationships between molecular structure and methionine aminopeptidase-2 inhibitory activity of a series of cytotoxic anthranilic acid sulfonamide derivatives were discovered. We have demonstrated the detailed application of two efficient nonlinear methods for evaluation of quantitative structure-activity relationships of the studied compounds. Components produced by principal component analysis as input ...
Zambre Vishal P - - 2010
G-quadruplex structures of DNA represent a potentially useful target for anticancer drugs. Telomerase enzyme, involved in immortalization of cancer cells is inhibited by stabilization of G-quadruplex at the ends of chromosomes. Anthraquinone and acridone derivatives are promising G-quadruplex ligands as telomerase inhibitors. So far, optimization of these ligands remained hampered ...
Diao Jianxiong - - 2010
By partial least square regression, simple quantitative structure-activity relationship (QSAR) models were developed for the toxicity of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Quantum chemical descriptors computed by semi-empirical PM3 method were used as predictor variables. Three optimal QSAR models are developed for 25 PCDDs, 35 PCDFs, 25 PCDDs and 35 ...
Awate Suyash P - - 2010
This paper presents a novel statistical framework for human cortical folding pattern analysis that relies on a rich multivariate descriptor of folding patterns in a region of interest (ROI). The ROI-based approach avoids problems faced by spatial normalization-based approaches stemming from the deficiency of homologous features between typical human cerebral ...
Agrafiotis Dimitris K - - 2010
We introduce Scaffold Explorer, an interactive tool that allows medicinal chemists to define hierarchies of chemical scaffolds and use them to explore their project data. Scaffold Explorer allows the user to construct a tree, where each node corresponds to a specific scaffold. Each node can have multiple children, each of ...
Fernandes João Paulo S - - 2011
Histamine is an important biogenic amine, which acts with a group of four G-protein coupled receptors (GPCRs), namely H(1) to H(4) (H(1)R - H(4)R) receptors. The actions of histamine at H(4)R are related to immunological and inflammatory processes, particularly in pathophysiology of asthma, and H(4)R ligands having antagonistic properties could ...
Shah P - - 2010
3D-QSAR studies were carried out on a training set of 53 structurally highly diverse analogues of triclosan to investigate the correlation of the structural properties of triclosan derivatives with the inhibition of the activity of enoyl acyl carrier protein reductase in Plasmodium falciparum (PfENR) by employing Comparative Molecular Field Analysis ...
Bolboacă Sorana D - - 2010
The quantitative structure-activity relationship approach was applied to understand the relative binding affinity of triphenyl acrylonitriles to estrogen receptors. A sample of previously studied triphenyl acrylonitriles was divided into training (18 compounds) and test sets (7 compounds) using a stratified random approach. The molecular descriptor family on vertices cutting (MDFV) ...
Boethling R S - - 2010
Knowledge of the interpolative region or applicability domain (AD) of structure-activity relationships is believed to improve predictive accuracy. The present work was undertaken to characterize the AD of EPI Suite biotransformation models and evaluate the performance of selected AD assessment methods. AD methods were applied to the training sets of ...
Thareja Suresh - - 2010
A three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a series of 1, 3, 4-thiadiazole derivatives reported as anticonvulsant employing self-organizing molecular field analysis (SOMFA) techniques to investigate the structural requirements for the design of novel anticonvulsant. The training set composed of twenty two 1, 3, 4-thiadiazole derivatives that ...
Cunningham A R - - 2010
Previously, SAR models for carcinogenesis used descriptors that are essentially chemical descriptors. Herein we report the development of models with the cat-SAR expert system using biological descriptors (i.e., ligand-receptor interactions) rat mammary carcinogens. These new descriptors are derived from the virtual screening for ligand-receptor interactions of carcinogens, non-carcinogens, and mammary ...
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