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Binding Data (binding + data)
Selected AbstractsStructure,activity relationships for gene activation oestrogenicity: Evaluation of a diverse set of aromatic chemicalsENVIRONMENTAL TOXICOLOGY, Issue 1 2002T. Wayne Schultz Abstract Structure,activity relationships for oestrogenicity were developed based on 120 aromatic chemicals evaluated in the Saccharomyces cerevisiae -based Lac -Z reporter assay. Relative gene activation was compared to 17,-estradiol and varied over eight orders of magnitude. Analysis of the data compared to 17,-estradiol identified three structural criteria that were related to xenoestrogen activity and potency: (1) the hydrogen-bonding ability of the phenolic ring mimicking the A-ring, (2) a hydrophobic centre similar in size and shape to the B- and C-rings, and (3) a hydrogen-bond donor mimicking the 17,-hydroxyl moiety of the D-ring, especially with an oxygen-to-oxygen distance similar to that between the 3- and 17,-hydroxyl groups of 17,-estradiol. Binding data were segregated into activity clusters including strong, moderate, weak, and detectable gene expression, and those compounds that were inactive. The hydrogen-bonding ability of hydroxy group in the 3-position on 17,-estradiol was observed to be essential for gene activation. Compounds with a 4-hydroxyl substituted benzene ring and a hydrophobic moiety of size and shape equivalent to the B-ring of 17,-estradiol were generally observed to be weakly active compounds. Moderately active compounds have a 4-hydroxyl substituted benzene ring with a hydrophobic moiety equivalent in size and shape to the B- and C-ring of 17,-estradiol, or have a high hydrogen-bond donor capacity owing to the presence of halogens on a nonphenolic ring. Strongly active compounds, similar to 4,4,-diethylethylene bisphenol (DES), possess the same hydrophobic ring structure as described for moderately active compounds and an additional hydroxyl group with an oxygen-to-oxygen distance close to that exhibited by the 3- and 17-hydroxyl groups of 17,-estradiol. © 2002 by Wiley Periodicals, Inc. Environ Toxicol 17: 14,23, 2002 [source] Peptide based vaccine design: Synthesis and immunological characterization of branched polypeptide conjugates comprising the 276,284 immunodominant epitope of HSV-1 glycoprotein DJOURNAL OF PEPTIDE SCIENCE, Issue 3 2002Gábor Mez Abstract The importance of the length and conjugation site of a protective epitope peptide (276SALLEDPVG284) from glycoprotein D of herpes simplex virus in branched polypeptide conjugates has been investigated. A new set of peptides, with a single attachment site and truncated sequences, was prepared. The immunogenicity of conjugates and the specificity of antibody responses elicited were investigated in BALB/c, C57/Bl/6 and CBA mice. It was found that the covalent coupling of the peptide comprising the 276,284 sequence of gD through its Asp residue at position 281 did not influence the immunogenic properties of the epitope, while involvement of the side chain of Glu at position 280 almost completely abolished immunogenicity. These results clearly indicated that the conjugation site of the epitope peptide influenced the intensity and specificity of antibody responses. Comparison of the immunological properties of conjugates containing truncated gD peptides revealed the presence of two epitopes within the 276,284 region. One of the proposed epitopes is situated at the N -terminal (276,281) region, while the other is located at the C -terminal end of the sequence (279,284). Binding data demonstrated that some of the peptides comprising these epitopes induced gD-specific responses in their conjugated form and also elicited an immune response that conferred protection against lethal HSV-1 infection. The correlation of peptide- and gD-specific antibody responses with the protective effect of the immune response is discussed. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Interaction of bovine coagulation factor X and its glutamic-acid-containing fragments with phospholipid membranesFEBS JOURNAL, Issue 12 2002A surface plasmon resonance study The interaction of blood coagulation factor X and its Gla-containing fragments with negatively charged phospholipid membranes composed of 25 mol% phosphatidylserine (PtdSer) and 75 mol% phosphatidylcholine (PtdCho) was studied by surface plasmon resonance. The binding to 100 mol% PtdCho membranes was negligible. The calcium dependence in the membrane binding was evaluated for intact bovine factor X (factor X) and the fragment containing the Gla-domain and the N-terminal EGF (epidermal growth factor)-like domain, Gla,EGFN, from factor X. Both proteins show the same calcium dependence in the membrane binding. Calcium binding is cooperative and half-maximum binding was observed at 1.5 mm and 1.4 mm, with the best fit to the experimental data with three cooperatively bound calcium ions for both the intact protein and the fragment. The dissociation constant (Kd) for binding to membranes containing 25 mol% PtdSer decreased from 4.6 µm for the isolated Gla-domain to 1 µm for the fragments Gla,EGFN and Gla,EGFNC (the Gla-domain and both EGF-like domains) fragments and to 40 nm for the entire protein as zymogen, activated enzyme or in the active-site inhibited form. Analysis of the kinetics of adsorption and desorption confirmed the equilibrium binding data. [source] Transgenic Drosophila reveals a functional in vivo receptor for the Bacillus thuringiensis toxin Cry1Ac1INSECT MOLECULAR BIOLOGY, Issue 6 2002Michael Gill Abstract The bacterium Bacillus thuringiensis synthesizes toxins (,-endotoxins) that are highly specific for insects. Once ingested, the activated form of the toxin binds to a specific receptor(s) located on the midgut epithelial cells, inserts into the membrane causing the formation of leakage pores and eventual death of the susceptible insect larvae. Manduca sexta larvae are highly susceptible to Cry1Ac1, a toxin that is believed to bind M. sexta Aminopeptidase N, a glycoprotein located on the apical membrane. However, the binding data obtained to date only support the interaction of Cry1Ac1 with APN in vitro. To explore the in vivo role of APN, we have utilized the GAL4 enhancer trap technique to drive the expression of M. sexta APN in both midgut and mesodermal tissues of Cry1Ac1 insensitive Drosophila larvae. Transgenic Drosophila fed the toxin were now killed, demonstrating that APN can function as a receptor for Cry1Ac1 in vivo. [source] Electronic and charge aspects of potential endocrine disruptors: Applications to pharmacological clusteringINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2003James W. King Abstract Quantitative structure,activity relationships in a series of 37 substituted indoles with endocrine disruptor potential were performed using the structural indices FTe (electronic) and FTc (charge), in conjunction with a clustering technique, to relate substitution patterns to reported relative binding affinities for the calf estrogen receptor. Data clusters were generated by a primary numerically descending sort of the structure indices with a concurrent secondary numerically descending sort of the binding data. Reversal of the numerical descent of the latter served to delineate cluster boundaries. Analysis within the clusters defined the effect of substituents and their molecular positions on the pharmacological data. These results confirmed in detail a similar previous study in the same series using the more general FTm index and again suggested the same structure of a molecule with greater receptor binding ability than any in the database. The methodology used in these studies permits a rational presentation and subsequent interpretation of data that initially appear to be totally random and devoid of recoverable information content. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003 [source] Regulation and Expression of Progesterone Receptor mRNA Isoforms A and B in the Male and Female Rat Hypothalamus and Pituitary Following Oestrogen TreatmentJOURNAL OF NEUROENDOCRINOLOGY, Issue 3 2002R. E. M. Scott Abstract Progesterone receptors play a central role in neuroendocrine and behavioural regulation. To gain insight into the sex- and tissue-specific regulation of progesterone receptors, protein binding on a progesterone receptor-oestrogen response element and mRNA levels for progesterone receptor (PR)-A and PR-B were compared between female and male rats following oestradiol benzoate replacement treatment in hypothalamic and pituitary tissue. Both male and female pituitary protein extracts demonstrated an increase in nuclear protein binding activity to a progesterone receptor-oestrogen response element following oestradiol benzoate treatment. However, there was a greater difference in total binding activity seen in the female pituitary extracts compared to male pituitary protein extracts. In both cases, reflecting the binding data, oestradiol benzoate pretreatment led to an increase in pituitary PR-B messenger RNA, although this increase was significantly larger in females than in males. Oestradiol benzoate treatment also led to a significant increase in specific binding of hypothalamic nuclear proteins to the progesterone receptor oestrogen response element from both females and male hypothalamic extracts. In addition, PR-B messenger RNA was induced by oestradiol benzoate treatment in the female rat hypothalamus, under circumstances where no PR-A could be detected. The male also demonstrated an increase in PR-B messenger RNA following oestradiol benzoate treatment, with undetectable levels of PR-A, although to a lesser degree than that seen in the female. The predominance of PR-B over PR-A messenger RNA in rat hypothalamus and pituitary, and the quantitative differences between female and male rats, could both contribute to the greater responsiveness of female rats to progesterone with respect to control over luteinizing hormone release from the pituitary, and lordosis behaviour regulated by hypothalamic neurones. [source] Sparse partial least squares regression for simultaneous dimension reduction and variable selectionJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 1 2010Hyonho Chun Summary., Partial least squares regression has been an alternative to ordinary least squares for handling multicollinearity in several areas of scientific research since the 1960s. It has recently gained much attention in the analysis of high dimensional genomic data. We show that known asymptotic consistency of the partial least squares estimator for a univariate response does not hold with the very large p and small n paradigm. We derive a similar result for a multivariate response regression with partial least squares. We then propose a sparse partial least squares formulation which aims simultaneously to achieve good predictive performance and variable selection by producing sparse linear combinations of the original predictors. We provide an efficient implementation of sparse partial least squares regression and compare it with well-known variable selection and dimension reduction approaches via simulation experiments. We illustrate the practical utility of sparse partial least squares regression in a joint analysis of gene expression and genomewide binding data. [source] Role of two arginine residues in domain II, loop 2 of Cry1Ab and Cry1Ac Bacillus thuringiensis,-endotoxin in toxicity and binding to Manduca sexta and Lymantria dispar aminopeptidase NMOLECULAR MICROBIOLOGY, Issue 2 2000Mi Kyong Lee Two arginine residues (368,369) of Cry1Ab and Cry1Ac were mutated to alanine, glutamic acid and lysine by site-directed mutagenesis. Insecticidal activities of the mutant toxins on Manduca sexta and Lymantria dispar larvae were examined. Cry1Ac mutant toxins (c)RR-AA and (c)RR-EE and Cry1Ab mutant toxins (b)RR-AA and (b)RR-EE showed great reductions in toxicity against both insects. In contrast, conservatively changed (c)RR-KK and (b)RR-KK mutants did not alter toxicity to either insect. Binding assays with brush border membrane vesicles (BBMVs) prepared from L. dispar midguts demonstrated that (c)RR-AA, (c)RR-EE, (b)RR-AA and (b)RR-EE bound with lower affinities compared with their respective wild-type toxins. To M. sexta BBMVs, (c)RR-AA and (c)RR-EE showed great reductions in BBMV binding. However, (b)RR-AA and (b)RR-EE did not alter BBMV competition patterns, despite their reduced toxicity. Further binding assays were performed with aminopeptidase N (APN) purified from L. dispar and M. sexta BBMVs using surface plasmon resonance (BIAcore). Direct correlation between toxicity and APN binding was observed for the mutant toxins using this technique. The inconsistency between BBMV and APN binding data with Cry1Ab to M. sexta suggests the possibility of a different Cry1Ab toxin-binding mechanism or the importance of another receptor in M. sexta. [source] Comparative analysis of neonicotinoid binding to insect membranes: II.PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 10 2004An unusual high affinity site for [3H]thiamethoxam in Myzus persicae, Aphis craccivora Abstract Neonicotinoids represent a class of insect-selective ligands of nicotinic acetylcholine receptors. Imidacloprid, the first commercially used neonicotinoid insecticide, has been studied on neuronal preparations from many insects to date. Here we report first intrinsic binding data of thiamethoxam, using membranes from Myzus persicae Sulzer and Aphis craccivora Koch. In both aphids, specific binding of [3H]thiamethoxam was sensitive to temperature, while the absolute level of non-specific binding was not affected. In M persicae, binding capacity (Bmax) for [3H]thiamethoxam was ca 450 fmol mg,1 of protein at 22 °C and ca 700 fmol mg,1 of protein at 2 °C. The negative effect of increased temperature was reversible and hence not due to some destructive process. The affinity for [3H]thiamethoxam was less affected by temperature: Kd was ca 11 nM at 2 °C and ca 15 nM at 22 °C. The membranes also lost binding sites for [3H]thiamethoxam during prolonged storage at room temperature, and upon freezing and thawing. In A craccivora, [3H]thiamethoxam was bound with a capacity of ca 1000 fmol mg,1 protein and an affinity of ca 90 nM, as measured at 2 °C. Overall, the in vitro temperature sensitivity of [3H]thiamethoxam binding was in obvious contrast to the behaviour of [3H]imidacloprid studied in parallel. Moreover, the binding of [3H]thiamethoxam was inhibited by imidacloprid in a non-competitive mode, as shown with M persicae. In our view, these differences demonstrate that thiamethoxam and imidacloprid, which represent different structural sub-classes of neonicotinoids, do not share the same binding site or mode. This holds also for other neonicotinoids, as we report in a companion article. Copyright © 2004 Society of Chemical Industry [source] Systematic interpretation of cyclic nucleotide binding studies using KinetXBasePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2008Sonja Schweinsberg Abstract Functional proteomics aims to describe cellular protein networks in depth based on the quantification of molecular interactions. In order to study the interaction of adenosine-3,,5,-cyclic monophosphate (cAMP), a general second messenger involved in several intracellular signalling networks, with one of its respective target proteins, the regulatory (R) subunit of cAMP dependent protein kinase (PKA), a number of different methods was employed. These include fluorescence polarisation (FP), isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), amplified luminescence proximity homogeneous assay (ALPHA-screen), radioligand binding or activity-based assays. Kinetic, thermodynamic and equilibrium binding data of a variety of cAMP derivatives to several cAMP binding domains were integrated in a single database system, we called KinetXBase, allowing for very distinct data formats. KinetXBase is a practical data handling system for molecular interaction data of any kind, providing a synopsis of data derived from different technologies. This supports ongoing efforts in the bioinformatics community to devise formal concepts for a unified representation of interaction data, in order to enable their exchange and easy comparison. KinetXBase was applied here to analyse complex cAMP binding data and highly site-specific cAMP analogues could be identified. The software package is free for download by academic users. [source] The effect of streptozotocin-induced diabetes on cardiac ,-adrenoceptor subtypes in the ratAUTONOMIC & AUTACOID PHARMACOLOGY, Issue 1 2001D. J. Sellers 1,The present study investigates the effect of short-term experimental diabetes of 14-days duration on the ,-adrenoceptor subtypes of the rat heart. 2,,-adrenoceptor-mediated functional responses to submaximal doses of isoprenaline were enhanced in Langendorff-perfused hearts from diabetic rats, manifested as greater changes in tension, heart rate and rates of tension development (+dT/dt) and decline (,dT/dt). 3,Radioligand binding data demonstrated that total cardiac ,-adrenoceptor density and affinity for [3H]-dihydroalprenolol was unchanged by diabetes, although a decrease in ,1 -adrenoceptor density and increase in ,2 -adrenoceptor density was observed. 4,In conclusion, hearts from 14-day streptozotocin-induced diabetic rats demonstrate a number of alterations within the ,-adrenoceptor system. However, the enhanced ,-adrenoceptor-mediated responses to isoprenaline were not caused by an overall increase in density of ,-adrenoceptors, but were accompanied by changes in the ratio of the ,-adrenoceptor subtypes. [source] Influence of nonspecific brain and plasma binding on CNS exposure: implications for rational drug discoveryBIOPHARMACEUTICS AND DRUG DISPOSITION, Issue 8 2002J. Cory Kalvass Abstract Relative plasma, brain and cerebrospinal fluid (CSF) exposures and unbound fractions in plasma and brain were examined for 18 proprietary compounds in rats. The relationship between in vivo brain-to-plasma ratio and in vitro plasma-to-brain unbound fraction (fu) was examined. In addition, plasma fu and brain fu were examined for their relationship to in vivo CSF-to-plasma and CSF-to-brain ratios, respectively. Findings were delineated based on the presence or absence of active efflux. Finally, the same comparisons were examined in FVB vs. MDR 1a/1b knockout mice for a selected P-glycoprotein (Pgp) substrate. For the nine compounds without indications of active efflux, predictive correlations were observed between ratios of brain-to-plasma exposure and plasma-to-brain fu (r2 = 0.98), CSF-to-brain exposure vs. brain fu (r2 = 0.72), and CSF-to-plasma exposure vs. plasma fu (r2 = 0.82). For the nine compounds with indications of active efflux, nonspecific binding data tended to over predict the brain-to-plasma and CSF-to-plasma exposure ratios. Interestingly, CSF-to-brain exposure ratio was consistently under predicted by brain fu for this set. Using a select Pgp substrate, it was demonstrated that the brain-to-plasma exposure ratio was identical to that predicted by plasma-to-brain fu ratio in MDR 1a/1b knockout mice. In FVB mice, plasma-to-brain fu over predicted brain-to-plasma exposure ratio to the same degree as the difference in brain-to-plasma exposure ratio between MDR 1a/1b and FVB mice. Consistent results were obtained in rats, suggesting a similar kinetic behavior between species. These data illustrate how an understanding of relative tissue binding (plasma, brain) can allow for a quantitative examination of active processes that determine CNS exposure. The general applicability of this approach offers advantages over species- and mechanism-specific approaches. Copyright © 2002 John Wiley & Sons, Ltd. [source] Revisiting the neighbor exclusion model and its applicationsBIOPOLYMERS, Issue 1 2010Marcio S. Rocha Abstract We review the neighbor exclusion model and some of its applications to analyze the binding data of DNA-ligand complexes. We revisit the closed form of the model developed by McGhee and von Hippel in 1974, showing that this classic model can be used to help studying the behavior of DNA contour and persistence lengths when interacting with intercalating ligands. We present methods to quantitatively analyze the variation of these two quantities, allowing one to determine important parameters of the interaction such as the intrinsic binding constant and the exclusion number of the ligand. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 1,7, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Characterization of the Interaction of TZT-1027, a Potent Antitumor Agent, with TubulinCANCER SCIENCE, Issue 7 2000Tsugitaka Natsume TZT-1027, a derivative of dolastatin 10 isolated from the Indian Ocean sea hare Dolabella auricularia in 1987 by Pettit et al., is a potent antimicrotubule agent. We have compared the activity of TZT-1027 with that of dolastatin 10 as well as the vinca alkaloids vinblastine (VLB), vincristine (VCR) and vindesine (VDS). TZT-1027 and dolastatin 10 inhibited microtubule polymerization concentration-dependently at 1,100 ,M with IC50 values of 2.2±0.6 and 2.3±0.7 ,M, respectively. VLB, VCR and VDS inhibited microtubule polymerization at 1,3 ,M with IC50 values of 2.7±0.6, 1.6±0.4 and 1.6±0.2 ,M, respectively, but showed a slight decrease in inhibitory effect at concentrations of 10 ,M or more. TZT-1027 also inhibited monosodium glutamate-induced tubulin polymerization concentration-dependently at 0.3,10 ,M, with an IC50 of 1.2 ,M, whereas VLB was only effective at 0.3,3 ,M, with an IC50 of 0.6 ,M, and caused so-called "aggregation" of tubulin at 10 ,M. Scatchard analysis of the binding data for [3H]VLB suggested one binding site (Kd 0.2±0.04 ,M and Bmax 6.0±0.26 nM/mg protein), while that for [3H]TZT-1027 suggested two binding sites, one of high affinity (Kd 0.2±0.01 ,M and Bmax 1.7±0.012 nM/mg protein) and the other of low affinity (Kd 10.3±1.46 ,M, and Bmax 11.6±0.83 nM/mg protein). [3H]TZT-1027 was completely displaced by dolastatin 10 but only incompletely by VLB. [3H]VLB was completely displaced by dolastatin 10 and TZT-1027. Furthermore, TZT-1027 prevented [3H]VLB from binding to tubulin in a non-competitive manner according to Lineweaver-Burk analysis. TZT-1027 concentrationdependently inhibited both [3H]guanosine 5,-triphosphate (GTP) binding to and GTP hydrolysis on tubulin. VLB inhibited the hydrolysis of GTP on tubulin concentration-dependently to a lesser extent than TZT-1027, but no inhibitory effect of VLB on [3H]GTP binding to tubulin was evident even at 100 ,M. Thus, TZT-1027 affected the binding of VLB to tubulin, but its binding site was not completely identical to that of VLB. TZT-1027 had a potent inhibitory effect on tubulin polymerization and differed from vinca alkaloids in its mode of action against tubulin polymerization. [source] Synthesis and Stability in Biological Media of 1H -Imidazole-1-carboxylates of ROS203, an Antagonist of the Histamine H3 ReceptorCHEMISTRY & BIODIVERSITY, Issue 1 2008Mirko Rivara Abstract A series of carbamate derivatives of the H3 antagonist ROS203 (1) were prepared, and their lipophilicity and steric hindrance were modulated by introducing linear or branched alkyl chains of various lengths. In vitro stability studies were conducted to evaluate how structural modulations affect the intrinsic reactivity of the carbamoyl moiety and its recognition by metabolic enzymes. Linear alkyl carbamates were the most susceptible to enzymatic hydrolysis, with bioconversion rates being higher in rat liver and plasma. Chain ramification significantly enhanced the enzymatic stability of the set, with two derivatives (1g and 1h) being more stable by a factor of 8,40 than the ethyl carbamate 1a. Incubation with bovine serum albumin (BSA) showed a protective role of proteins on chemical and porcine-liver esterase (PLE)-catalyzed hydrolysis. Ex vivo binding data after i.v. administration of 1h revealed prolonged displacement of the labeled ligand [3H]-(R)- , -methylhistamine ([3H]RAMHA) from rat-brain cortical membranes, when compared to 1. However, the high rates of bioconversion in liver, as well as the chemical instability of 1h, suggest that further work is needed to optimize the enzymatic and chemical stability of these compounds. [source] Prospective Validation of a Comprehensive In silico hERG Model and its Applications to Commercial Compound and Drug DatabasesCHEMMEDCHEM, Issue 5 2010Munikumar Abstract Ligand-based in silico hERG models were generated for 2,644 compounds using linear discriminant analysis (LDA) and support vector machines (SVM). As a result, the dataset used for the model generation is the largest publicly available (see Supporting Information). Extended connectivity fingerprints (ECFPs) and functional class fingerprints (FCFPs) were used to describe chemical space. All models showed area under curve (AUC) values ranging from 0.89 to 0.94 in a fivefold cross-validation, indicating high model consistency. Models correctly predicted 80,% of an additional, external test set; Y-scrambling was also performed to rule out chance correlation. Additionally models based on patch clamp data and radioligand binding data were generated separately to analyze their predictive ability when compared to combined models. To experimentally validate the models, 50 of the predicted hERG blockers from the Chembridge database and ten of the predicted non-hERG blockers from an in-house compound library were selected for biological evaluation. Out of those 50 predicted hERG blockers, tested at a concentration of 10,,M, 18 compounds showed more than 50,% displacement of [3H]astemizole binding to cell membranes expressing the hERG channel. Ki values of four of the selected binders were determined to be in the micromolar and high nanomolar range (Ki (VH01)=2.0,,M, Ki (VH06)=0.15,,M, Ki (VH19)=1.1,,M and Ki (VH47)=18 ,M). Of these four compounds, VH01 and VH47 showed also a second, even higher affinity binding site with Ki values of 7.4,nM and 36,nM, respectively. In the case of non-hERG blockers, all ten compounds tested were found to be inactive, showing less than 50,% displacement of [3H]astemizole binding at 10,,M. These experimentally validated models were then used to virtually screen commercial compound databases to evaluate whether they contain hERG blockers. 109,784 (23,%) of Chembridge, 133,175 (38,%) of Chemdiv, 111,737 (31,%) of Asinex and 11,116 (18,%) of the Maybridge database were predicted to be hERG blockers by at least two of the models, a prediction which could, for example, be used as a pre-filtering tool for compounds with potential hERG liabilities. [source] | |||||||||||||||||||||||||