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Binding Affinity (binding + affinity)
Kinds of Binding Affinity Selected AbstractsQuantitative Structure,Activity Relationship Studies for the Binding Affinities of Imidazobenzodiazepines for the ,6 Benzodiazepine Receptor Isoform Utilizing Optimized Blockwise Variable Combination by Particle Swarm Optimization for Partial Least Squares ModelingMOLECULAR INFORMATICS, Issue 1 2007Leqian Hu Abstract Binding affinities of a series of substituted imidazobenzodiazepines for the ,6 Benzodiazepine Receptor (BzR) isoform are investigated by the Optimized Blockwise Variable Combination (OBVC) by Particle Swarm Optimization (PSO) based on Partial Least Squares (PLS) modeling. The QSAR analysis result showed that MolRef, AlogP, MRCM**-3, Rotatable bonds (Rotlbonds), Hydrogen Bond Acceptors (Hbond acceptor), five Jurs descriptors, two Shadow indices descriptors and principal moment of inertia are the most important descriptors among all the investigated descriptors. One can change the molar refractivity, the polar interactions between molecules, the shape of the molecules, the principal moments of inertia about the principal axes of a molecule, the hydrophobic character of the molecule, the number of Rotlbonds and Hbond acceptors of the compounds to adjust the binding affinities of imidazobenzodiazepine for the ,6 BzR isoform. The Quantitative Structure,Activity Relationship (QSAR) analysis result was also compared with MLR, PLS, and hierarchical PLS algorithms. It has been demonstrated that OBVC by PSO for PLS modeling shows satisfactory performance in the QSAR analysis. [source] Modeling the Inhibitor Activity and Relative Binding Affinities in Enzyme-Inhibitor-Protein Systems: Application to Developmental Regulation in a PG-PGIP SystemBIOTECHNOLOGY PROGRESS, Issue 3 2004Wayne W. Fish Within a number of classes of hydrolytic enzymes are certain enzymes whose activity is modulated by a specific inhibitor-protein that binds to the enzyme and forms an inactive complex. One unit of a specific inhibitor-protein activity is often defined as the amount necessary to inhibit one unit of its target enzyme by 50 %. No objective quantitative means is available to determine this point of 50 % inhibition in crude systems such as those encountered during purification. Two models were derived: the first model is based on an irreversible binding approximation, and the second, or equilibrium, model is based on reversible binding. The two models were validated using the inhibition data for the polygalacturonase-polygalacturonase-inhibiting protein (PG-PGIP) system. Theory and experimental results indicate that the first model can be used for inhibitor protein activity determination and the second model can be used for inhibitor protein activity determination as well as for comparison of association constants among enzymes and their inhibitor-proteins from multiple sources. The models were used to identify and further clarify the nature of a differential regulation of expression of polygalacturonase-inhibiting protein in developing cantaloupe fruit. These are the first relations that provide for an objective and quantitative determination of inhibitor-protein activity in both pure and crude systems. Application of these models should prove valuable in gaining insights into regulatory mechanisms and enzyme-inhibitor-protein interactions. [source] ChemInform Abstract: Synthesis of Functionalized Benzoxazoles and Their Binding Affinities to A,42 Fibrils.CHEMINFORM, Issue 5 2009Young Shin Chun Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Structure-Based Calculation of Binding Affinities of ,2A -Adrenoceptor AgonistsCHEMMEDCHEM, Issue 6 2007Balázs Balogh An atomic resolution structure of ,2a -adrenoceptor was constructed and 15 known agonists were docked into the optimized model and experimental binding free energies were estimated. The figure shows the binding of the agonist clonidine (sticks) to the core binding pocket of the adrenoceptor (blue cartoon, key residues are marked with sticks). [source] New Nonhydrolyzable Mimetics of Sialyl Lewis X and Their Binding Affinity to P-SelectinHELVETICA CHIMICA ACTA, Issue 5 2004Frédéric Carrel Wittig olefination of (2S,3R,5S,6R)-5-(acetyloxy)-tetrahydro-6-[(methoxymethoxy)methyl]-3-(phenylthio)- 2H -pyran-2-acetaldehyde ((+)- 10) with {2-[(2S,3R,4R,5R,6S)-tetrahydro-3,4,5-tris(methoxymethoxy)-6-methyl- 2H -pyran-2-yl]ethyl}triphenylphosphonium iodide ((,)- 11) gave a (Z)-alkene derivative (+)- 12 that was converted into (,R,2R,3S,4R,5R,6S)-tetrahydro- ,,3-dihydroxy-2-(hydroxymethyl)-5-(phenylthio)-6-{(2Z)-4-[(2S,3S,4R,5S,6S)-tetrahydro-3,4,5-trihydroxy-6-methyl-2H -pyran-2-yl]but-2-enyl}2H -pyran-4-acetic acid (8), (,R,2R,3S,4R,6S)-tetrahydro- ,,3-dihydroxy-2-(hydroxymethyl)-6-{4-[(2S,3S,4R,5S,6S)-tetrahydro-3,4,5-trihydroxy-6-methyl-2H -pyran-2-yl]butyl}-2H -pyran-4-acetic acid (9), and simpler analogues without the hydroxyacetic side chain such as (2S,3S,4R,5S,6S)-tetrahydro-6-methyl-2-{(2Z)-4-[(2S,3R,5S,6R)-tetrahydro-5-hydroxy-6-(hydroxymethyl)-3-(phenylthio)-2H -pyran-2-yl]but-2-enyl}-2H -pyran-3,4,5-triol (30), (2S,3S,4R,5S,6S)-tetrahydro-6-methyl-2-{[(2S,5S,6R)-tetrah dro-5-hydroxy-6-(hydroxymethyl)-2H -pyran-2-yl]butyl}-2H -pyran-3,4,5- triol ((,)- 41) and (2S,3S,4R,5S,6S)-tetrahydro-6-methyl-2-{(2Z/E))-4-[(2R,5S,6R)-tetrahydro-5-hydroxy-6-(hydroxymethyl)-2H -pyran-2-yl]but-2-enyl}-2H -pyran-3,4,5-triol (43). The key intermediates (+)- 10 and (,)- 11 were derived from isolevoglucosenone and from L -fucose, respectively. The following IC50 values were measured in a ELISA test for the affinities of sialyl Lewis x tetrasaccharide, 8, 9, 30, (,)- 41, and 43 toward P-selectin: 0.7, 2.5,2.8, 7.3,8.0, 5.3,5.9, 5.0,5.2, and 3.4,4.1,mM, respectively. [source] Further Data are Required to Assure that the Discrepant Binding Affinity is Explained by Different Receptor ConformationsJOURNAL OF BONE AND MINERAL RESEARCH, Issue 3 2000Charles A. Frolik No abstract is available for this article. [source] Efficient Encapsulation of Plasmid DNA in pH-Sensitive PMPC,PDPA Polymersomes: Study of the Effect of PDPA Block Length on Copolymer,DNA Binding AffinityMACROMOLECULAR BIOSCIENCE, Issue 5 2010Hannah Lomas Abstract We report the self-assembly of a series of amphiphilic diblock copolymers comprising a biocompatible, hydrophilic block, poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) and a pH-sensitive block, poly(2-(diisopropylamino)ethyl methacrylate) (PDPA), into a dispersion of colloidally stable, nanometer-sized polymersomes at physiological pH and salt concentration. The pH-sensitivity of the PDPA block affords the electrostatic interaction of these block copolymers with nucleic acids at endocytic pH, as a result of the protonation of its tertiary amine groups at pH values below its pKa. Herein we investigate the effect of PDPA block length on the binding affinity of the block copolymer to plasmid DNA. [source] Classical QSAR Modeling of CCR5 Receptor Binding Affinity of Substituted BenzylpyrazolesMOLECULAR INFORMATICS, Issue 6 2004Thomas Leonard Abstract CCR5 receptor binding affinity of a series of substituted benzylpyrazole derivatives was subjected to QSAR study using Fujita-Ban type analysis and a mixed approach based on Hansch and Fujita-Ban analyses. Apart from appropriate indicator variables encoding different group contributions, different physicochemical variables like hydrophobicity (,), electronic (Hammett ,) and steric (molar refractivity, STERIMOL values) parameters of phenyl ring substituents of the benzyl moiety of the compounds were used as predictor variables. Additionally, Wang-Ford charges of the common atoms of the compounds calculated from molecular electrostatic potential surface of AM1 optimized geometries of the compounds and various topological parameters were used as additional descriptors. The variables for the multiple regression analyses were selected based on principal component factor analysis and generated equations were statistically validated using leave-one-out technique and predicting the binding affinities of test set compounds. The analysis explores the substitutional requirements of the phenyl nucleus of the benzylpyrazole moiety of the compounds for effective binding with CCR5 receptor. [source] Fentanyl Derivatives Bearing Aliphatic Alkaneguanidinium Moieties: A New Series of Hybrid Molecules with Significant Binding Affinity for ,-Opioid Receptors and I2 -Imidazoline Binding Sites.CHEMINFORM, Issue 16 2004Christophe Dardonville No abstract is available for this article. [source] ChemInform Abstract: Diaryl-Dialkyl-Substituted Pyrazoles: Regioselective Synthesis and Binding Affinity for the Estrogen Receptor.CHEMINFORM, Issue 30 2002Gisele A. Nishiguchi Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Towards a Tunable Tautomeric Switch in Azobenzene Biomimetics: Implications for the Binding Affinity of 2-(4,-Hydroxyphenylazo)benzoic Acid to StreptavidinCHEMISTRY - A EUROPEAN JOURNAL, Issue 7 2008Joan-Antoni Farrera Dr. Abstract The tautomeric equilibria of 2-(4,-hydroxyphenylazo)benzoic acid (HABA) and 2-(3,,5,-dimethyl-4,-hydroxyphenylazo)benzoic acid (3,,5,-dimethyl-HABA) have been studied by a combination of spectroscopic and computational methods. For neutral HABA in solvents of different polarity (toluene, chloroform, DMSO, DMF, butanol, and ethanol) the azo tautomer (AT) is largely predominant. For monoanionic HABA, the hydrazone tautomer (HT) is the only detected species in apolar solvents such as toluene and chloroform, while the AT is the only detected species in water and a mixture of both tautomers is detected in ethanol. Comparison of the results obtained for HABA and its 3,,5,-dimethylated derivative shows that dimethylation of the hydroxybenzene ring shifts the tautomeric preferences towards the hydrazone species. These findings have been used to examine the differences in binding affinity to streptavidin, as the lower affinity of HABA can be explained in terms of the larger energetic cost associated with the tautomeric shift to the bioactive hydrazone species. Overall, these results suggest that a balanced choice of chemical substituents, embedding environment, and pH can be valuable for exploitation of the azo,hydrazone tautomerism of HABA biomimetics in biotechnological applications. [source] The Effect of an Amino-Acid Bridge on Binding Affinity and Cleavage Efficiency of Pyrenyl-Macrocyclic Polyamine Conjugates toward DNACHEMISTRY & BIODIVERSITY, Issue 8 2009Qiao-Sen Lu Abstract A series of pyrenyl-macrocyclic polyamines 5a,5c have been prepared and characterized. Their DNA-cleavage properties were examined under physiological conditions. Without the presence of other additives, the DNA cleavage ability of 5a,5c showed the order of 5c>5a>5b. Absorption and fluorescence experiments showed the binding affinity of 5a,5c to DNA. The interactions of 5a,5c with CT-DNA indicated that the DNA binding ability followed an order according to their cleavage efficiency. All the results indicated that the structures of amino-acid bridge in the ligands may affect the DNA binding and cleavage ability. The cleavage-mechanism studies indicated that singlet oxygen and superoxide free radicals were involved in the catalytic DNA cleavage process. [source] Docking Studies of Structurally Diverse Antimalarial Drugs Targeting PfATP6: No Correlation between in,silico Binding Affinity and in,vitro Antimalarial Activity.CHEMMEDCHEM, Issue 9 2009Fatima Bousejra-El Garah Abstract PfATP6, a calcium-dependent ATPase of Plasmodium falciparum, is considered the putative target of the antimalarial drug artemisinin and its derivatives. Herein, the 3D structure of PfATP6 was modeled on the basis of the crystal structure of SERCA,1a, the mammalian homologue. Model validation was achieved using protein structure checking tools. AutoDock4 was used to predict the binding affinities of artemisinin (and analogues) and various other antimalarial agents for PfATP6, for which in,vitro activity is also reported. No correlation was found between the affinity of the compounds for PfATP6 predicted by AutoDock4 and their antimalarial activity. [source] Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitorsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2008Kitiyaporn Wittayanarakul Abstract Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Quantitative Structure,Activity Relationship Studies for the Binding Affinities of Imidazobenzodiazepines for the ,6 Benzodiazepine Receptor Isoform Utilizing Optimized Blockwise Variable Combination by Particle Swarm Optimization for Partial Least Squares ModelingMOLECULAR INFORMATICS, Issue 1 2007Leqian Hu Abstract Binding affinities of a series of substituted imidazobenzodiazepines for the ,6 Benzodiazepine Receptor (BzR) isoform are investigated by the Optimized Blockwise Variable Combination (OBVC) by Particle Swarm Optimization (PSO) based on Partial Least Squares (PLS) modeling. The QSAR analysis result showed that MolRef, AlogP, MRCM**-3, Rotatable bonds (Rotlbonds), Hydrogen Bond Acceptors (Hbond acceptor), five Jurs descriptors, two Shadow indices descriptors and principal moment of inertia are the most important descriptors among all the investigated descriptors. One can change the molar refractivity, the polar interactions between molecules, the shape of the molecules, the principal moments of inertia about the principal axes of a molecule, the hydrophobic character of the molecule, the number of Rotlbonds and Hbond acceptors of the compounds to adjust the binding affinities of imidazobenzodiazepine for the ,6 BzR isoform. The Quantitative Structure,Activity Relationship (QSAR) analysis result was also compared with MLR, PLS, and hierarchical PLS algorithms. It has been demonstrated that OBVC by PSO for PLS modeling shows satisfactory performance in the QSAR analysis. [source] Sequence-dependent Interactions of Cationic Naphthalimides and PolynucleotidesPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2007Sun McMasters The binding interactions of three naphthalimide derivatives with heteropoly nucleic acids have been evaluated using fluorescence, absorption and circular dichroism spectroscopies. Mono- and bifunctionalized naphthalimides exhibit sequence-dependent variations in their affinity toward DNA. The heteropoly nucleic acids, [Poly(dA-dT)]2 and [Poly(dG-dC)]2, as well as calf thymus (CT) DNA, were used to understand the factors that govern binding strength and selectivity. Sequence selectivity was addressed by determining the binding constants as a function of polynucleotide composition according to the noncooperative McGhee,von Hippel binding model. Binding affinities toward [poly(dA-dT)]2 were the largest for spermine-substituted naphthalimides (Kb = 2,6 × 106 m,1). The association constants for complex formation between the cationic naphthalmides and [poly(dG-dC)]2 or CT DNA (58% A-T content) were 2,500 times smaller, depending on the naphthalmide,polynucleotide pair. The binding modes were also assessed using a combination of induced circular dichroism and salt effects to determine whether the naphthalimides associate with DNA through intercalative, electrostatic or groove-binding. The results show that the monofunctionalized spermine and pyridinium-substituted naphthalimides associate with DNA through electrostatic interactions. In contrast, intercalative interactions are predominant in the complex formed between the bifunctionalized spermine compound and all of the polynucleotides. [source] Folate receptor , as a potential delivery route for novel folate antagonists to macrophages in the synovial tissue of rheumatoid arthritis patientsARTHRITIS & RHEUMATISM, Issue 1 2009Joost W. Van Der Heijden Objective To determine the expression of folate receptor , (FR,) in synovial biopsy tissues and peripheral blood lymphocytes from rheumatoid arthritis (RA) patients and to identify novel folate antagonists that are more selective in the targeting and internalization of FR, than methotrexate (MTX). Methods Immunohistochemistry and computer-assisted digital imaging analyses were used for the detection of FR, protein expression on immunocompetent cells in synovial biopsy samples from RA patients with active disease and in noninflammatory control synovial tissues. FR, messenger RNA (mRNA) levels were determined by reverse transcription,polymerase chain reaction analysis. Binding affinities of FR, for folate antagonists were assessed by competition experiments for 3H-folic acid binding on FR,-transfected cells. Efficacy of FR,-mediated internalization of folate antagonists was evaluated by assessment of antiproliferative effects against FR,-transfected cells. Results Immunohistochemical staining of RA synovial tissue showed high expression of FR, on macrophages in the intimal lining layer and synovial sublining, whereas no staining was observed in T cell areas or in control synovial tissue. Consistently, FR, mRNA levels were highest in synovial tissue extracts and RA monocyte-derived macrophages, but low in peripheral blood T cells and monocytes. Screening of 10 new-generation folate antagonists revealed 4 compounds for which FR, had a high binding affinity (20,77-fold higher than for MTX). One of these, the thymidylate synthase inhibitor BCG 945, displayed selective targeting against FR,-transfected cells. Conclusion Abundant FR, expression on activated macrophages in synovial tissue from RA patients deserves further exploration for selective therapeutic interventions with high-affinity,binding folate antagonists, of which BCG 945 may be a prototypical representative. [source] Sympathectomy reveals ,1A - and ,1D -adrenoceptor components to contractions to noradrenaline in rat vas deferensBRITISH JOURNAL OF PHARMACOLOGY, Issue 6 2004Linda Cleary We have previously demonstrated that contractions of rat vas deferens to exogenous noradrenaline involve predominantly ,1A -adrenoceptors, but that contractions to endogenous noradrenaline involve predominantly ,1D -adrenoceptors. In this study, we have examined the effects of sympathectomy on the subtypes of ,1 -adrenoceptor in rat vas deferens in radioligand binding and functional studies. In vehicle-treated tissues, antagonist displacement of [3H]prazosin binding to ,1 -adrenoceptors was consistent with a single population of ,1 -adrenoceptors. Binding affinities for a range of ,1 -adrenoceptor antagonists were expressed as pKi values and correlated with known affinities for ,1 -adrenoceptor subtypes. The correlation was significant only with ,1A -adrenoceptors. In tissues from rats sympathectomised with 6-hydroxy-dopamine (2 × 100 mg kg,1 i.p.), binding affinity for the ,1D -adrenoceptor antagonist BMY 7378 fitted best with a two-site model. In functional studies, the potency of noradrenaline at producing total (phasic plus tonic) but not tonic contractions was increased in tissues from sympathectomised rats. Results obtained from sympathectomised rats suggest that phasic contractions are mainly ,1D -adrenoceptor mediated, whereas tonic contractions are mainly ,1A -adrenoceptor mediated, based on the effects of BMY 7378 and the ,1A -adrenoceptor antagonist RS 100329. It is concluded that the predominant ,1 -adrenoceptor in vehicle-treated rat vas deferens is the ,1A -adrenoceptor, both in terms of ligand binding and contractions to exogenous agonists. The ,1D -adrenoceptor is only detectable by ligand binding following chemical sympathectomy, but is involved in noradrenaline-evoked contractions, particularly phasic contractions, of rat vas deferens. British Journal of Pharmacology (2004) 143, 745,752. doi:10.1038/sj.bjp.0705987 [source] Prostromelysin-1 (proMMP-3) stimulates plasminogen activation by tissue-type plasminogen activatorFEBS JOURNAL, Issue 21 2000Begońa Arza Matrix metalloproteinase-3 (MMP-3 or stromelysin-1) specifically binds to tissue-type plasminogen activator (t-PA), without however, hydrolyzing the protein. Binding affinity to proMMP-3 is similar to single chain t-PA, two chain t-PA and active site mutagenized t-PA (Ka of 6.3 × 106 to 8.0 × 106 m,1), but is reduced for t-PA lacking the finger and growth factor domains (Ka of 2.0 × 106 m,1). Activation of native Glu-plasminogen by t-PA in the presence of proMMP-3 obeys Michaelis,Menten kinetics; at saturating concentrations of proMMP-3, the catalytic efficiency of two chain t-PA is enhanced 20-fold (kcat/Km of 7.9 × 10,3 vs. 4.1 × 10,4 µm,1·s,1). This is mainly the result of an enhanced affinity of t-PA for its substrate (Km of 1.6 µm vs. 89 µm in the absence of proMMP-3), whereas the kcat is less affected (kcat of 1.3 × 10,2 vs. 3.6 × 10,2 s,1). Activation of Lys-plasminogen by two chain t-PA is stimulated about 13-fold at a saturating concentration of proMMP-3, whereas that of miniplasminogen is virtually unaffected (1.4-fold). Plasminogen activation by single chain t-PA is stimulated about ninefold by proMMP-3, whereas that by the mutant lacking finger and growth factor domains is stimulated only threefold. Biospecific interaction analysis revealed binding of Lys-plasminogen to proMMP-3 with 18-fold higher affinity (Ka of 22 × 106 m,1) and of miniplasminogen with fivefold lower affinity (Ka of 0.26 × 106m,1) as compared to Glu-plasminogen (Ka of 1.2 × 106m,1). Plasminogen and t-PA appear to bind to different sites on proMMP-3. These data are compatible with a model in which both plasminogen and t-PA bind to proMMP-3, resulting in a cyclic ternary complex in which t-PA has an enhanced affinity for plasminogen, which may be in a Lys-plasminogen-like conformation. Maximal binding and stimulation require the N-terminal finger and growth factor domains of t-PA and the N-terminal kringle domains of plasminogen. [source] A3 domain residue Glu1829 contributes to A2 subunit retention in factor VIIIaJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 5 2007H. WAKABAYASHI Summary.,Background:,Factor VIII (FVIII) is activated by thrombin to the labile FVIIIa, a heterotrimer of A1, A2 and A3C1C2 subunits, which serves as a cofactor for FIXa. A primary reason for the instability of FVIIIa is the tendency for the A2 subunit to dissociate from FVIIIa leading to an inactive cofactor and consequent loss of FXase activity. Objective:,Based on our finding of low-specific activity and a fast decay rate for a FVIII point mutation of Glu1829 to Ala (E1829A), we examined whether residue Glu1829 in the A3 subunit is important for A2 subunit retention. Results:,The rate of activity decay of E1829A was ,fourteenfold faster than wild-type (wt) FVIIIa and this rate was reduced in the presence of added A2 subunit. Specific activity values for E1829A measured by one-stage and two-stage assays were ,14% and ,11%, respectively, compared with wt FVIII. Binding affinity for the A1 subunit to E1829A-A3C1C2 was comparable to wt A3C1C2 (Kd = 20.1 ± 3.4 nm for E1829A, 15.3 ± 3.7 nm for wt), whereas A2 subunit affinity for the A1/A3C1C2 dimer forms was reduced by ,3.6-fold as a result of the mutation (Kd = 526 ± 107 nm for E1829A, 144 ± 21 nm for wt). Conclusion:,As modeling data suggest that Glu1829 is located at the A2-A3 domain interface these results are consistent with Glu1829 contributing to the interactions involved with A2 subunit retention in FVIIIa. [source] Combinatorial expression patterns of heparan sulfate sulfotransferases in zebrafish: II.DEVELOPMENTAL DYNAMICS, Issue 12 2006The 6- O -sulfotransferase family Abstract Heparan sulfate (HS) is an unbranched chain of repetitive disaccharides, which specifically binds ligands when attached to the cell surface or secreted extracellularly. HS chains contain sulfated domains termed the HS fine structure, which gives HS specific binding affinities for extracellular ligands. HS 6- O -sulfotransferases (6-OST) catalyze the transfer of sulfate groups to the 6- O position of glucosamine residues of HS. We report here the characterization and developmental expression analysis of the 6-OST gene family in the zebrafish. The zebrafish 6-OST gene family consists of four conserved vertebrate orthologues, including a gene duplication specific to zebrafish. We examined the mRNA expression patterns in several tissues/organs throughout early zebrafish development, including early cleavage stages, eyes, somites, brain, internal organ primordial, and pectoral fin development. Members of the 6-OST gene family have spatially and temporally distinct restricted expression, suggesting in vivo functional differences exist between members of this family. Developmental Dynamics 235:3432,3437, 2006. © 2006 Wiley-Liss, Inc. [source] Appraising the mitogenicity of insulin analogues relative to human insulin,response to: Weinstein D, Simon M, Yehezkel E, Laron Z, Werner H. Insulin analogues display IGF-I-like mitogenic and anti-apoptotic activity in cultured cancer cells.DIABETES/METABOLISM: RESEARCH AND REVIEWS, Issue 3 2010Diabetes Metab Res Rev 2009; 25(1): 4 Abstract Interest in mitogenic and potentially carcinogenic effects of insulin and insulin analogues has been renewed by several recent publications that have examined the relationship between cancer and insulin analogues. Actions mediated through the insulin-like growth factor-I receptor in a hyperinsulinaemic state have been implicated mechanistically. Both type 2 diabetes and endogenously elevated insulin-like growth factor-I have been epidemiologically linked to malignancies. Therefore, in vitro mitogenic effects and binding affinities of the various analogues have been analysed. A recent publication by Weinstein et al. studied the in vitro mitogenic and anti-apoptotic activities of insulin analogues, and their conclusion asserts that insulins glargine, detemir, and lispro displayed proliferative and anti-apoptotic effects in a number of malignant cell lines. However, their conclusions are not supported by the data which are not complete and lack clear statistical significance. This data should be interpreted cautiously in light of all other presently available scientific evidence. Prospective, randomized clinical trials will best address any direct relationship between insulin analogues and cancer. Until those studies are designed and completed, clinicians should consider the demonstrated strong benefit of glycaemic control in balance with any alleged risk. Copyright © 2010 John Wiley & Sons, Ltd. [source] Structure,activity relationships of isoeugenol-based chlorophenylpiperazine derivatives on serotonergic/adrenergic receptor, platelet aggregation, and lipid peroxidationDRUG DEVELOPMENT RESEARCH, Issue 5 2010Kuo-Ping Shen Abstract Three isoeugenol-based eugenosedin chlorphenylpiperazine derivatives, Eu-A, Eu-B, and Eu-C, were synthesized and tested for their serotonergic, adrenergic antagonist, antioxidant, and anti-aggregation activities. In radioligand binding assays, all three agents displayed significant binding affinities on ,1, ,2, ,1, 5-HT1B, and 5-HT2A receptors. In human platelet, they inhibited epinephrine and 5-HT-induced aggregation, and in human platelet with ,2 and 5-HT2A receptors they had a competitive binding effect. Eu-B and Eu-C were more potent than Eu-A. All compounds had antioxidant effects derived from aryloxypropanolamine. Eu- A, Eu-B, or Eu-C (1, 3, 5,mg/kg iv) given to normotensive Wistar rats produced a dose-dependent decrease in mean arterial blood pressure and heart rate and when injected into the cisternum, Eu-A, Eu-B, or Eu-C (0.3, 0.03,µmol) increased blood pressure within 15,min. Pretreatment with any of the three agents inhibited clonidine (38,pmol)-induced hypotension. In vitro experiments, Eu-A, Eu-B, or Eu-C (1, 10, and 100,µM) competitively antagonized norepinephrine-, clonidine-, and 5-HT (10,8,10,4,M)-induced vasocontraction in isolated rat aorta, and competitively antagonized isoproterenol (10,8,10,4,M)-induced positive inotropic effects in a concentration-dependent manner in the isolated rat left atrium. In isolated rabbit ear arteries sensitized with 16,mM K+, all three agents antagonized 5-nonyloxytryptamine- and 5-HT-induced vasocontractions. These findings show that Eu-A, Eu-B, and Eu-C possess functional ,1, ,2, ,1, 5-HT1B, and 5-HT2A receptor blocking activities. In conclusion, the changes in the position of chloride at phenylpiperazine influenced the serotonergic receptor, adrenoceptor antagonistic activities, but not anti-aggregation and antioxidant activities. Drug Dev Res 71:1,9, 2010. © 2010 Wiley-Liss, Inc. [source] Competitive binding comparison of endocrine-disrupting compounds to recombinant androgen receptor from fathead minnow, rainbow trout, and humanENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 9 2007Vickie S. Wilson Abstract Typically, in vitro hazard assessments for the identification of endocrine-disrupting compounds (EDCs), including those outlined in the Endocrine Disruptor Screening and Testing Advisory Committee (EDSTAC) Tier 1 Screening protocols, utilize mammalian receptors. Evidence, however, exists that fish sex steroid hormone receptors differ from mammalian receptors both structurally and in their binding affinities for some steroids and environmental chemicals. Most of the binding studies to date have been conducted using cytosolic preparations from various tissues. In the present study, we compare competitive binding of a set of compounds to full-length recombinant rainbow trout androgen receptor , (rtAR), fathead minnow androgen receptor (fhAR), and human androgen receptor (hAR), each expressed in COS cells. Saturation binding and subsequent Scatchard analysis using [3H]R1881, a high-affinity synthetic androgen, revealed an equilibrium dissociation constant (Kd) of 0.11 nM for the rtAR, 1.8 nM for the fhAR, and 0.84 nM for the hAR. Compounds, including endogenous and synthetic steroids, known mammalian antiandrogens, and environmental compounds, were tested for competitive binding to each of the three receptors. Overall, agreement existed across receptors as to binding versus nonbinding for all compounds tested in this study. Minor differences, however, were found in the relative order of binding of the compounds to the individual receptors. Studies such as these will facilitate the identification of EDCs that may differentially affect specific species and aid in the development and support of future risk assessment protocols. [source] Differential binding of endogenous steroids and chemicals to androgen receptors in rainbow trout and goldfishENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 8 2000Kelly Wells Abstract Androgen receptors (ARs) from fish were characterized in order to evaluate differences in the binding affinities of steroids and environmental chemicals between mammals and fish, among species offish, and among target tissues within a species of fish. High-affinity, low-capacity ARs were identified in cytosolic fractions of rainbow trout brains (Oncorhynchus mykiss) and the brains, ovaries, and testes of goldfish (Carassius auratus) using [3H]testosterone. The binding specificities of endogenous steroids to the ARs did not differ between goldfish tissues but did differ between goldfish and rainbow trout. Interspecies differences in binding specificities were also seen using cyproterone acetate, which bound to the ARs in the goldfish tissues, but not in the rainbow trout brains. The mammalian antiandrogens flutamide, vinclozolin and its metabolites 2-(((3,5)-dichlorophenyl-carbamo-yl)oxy)-2-methyl-3-butenoic acid and 3,,5,-dichloro-2-hydroxy-2-methylbut-3-enanilide, along with procymidone did not bind to the ARs in any of the fish tissues tested. However, other mammalian antiandrogens including methoxychlor and its metabolite 2,2-bis(p -hydroxyphenyl)-1,1,1-trichloroethane, o,p,-DDT, o,p,-dichlorodiphenyldichloroethylene (DDE) and p,p,-DDE did bind to the fish ARs, but only in the goldfish testes, demonstrating tissue differences in AR binding specificities of environmental chemicals. These results may be due to the presence of multiple AR isoforms in the different fish species and tissues. This study supports the growing evidence of species differences in the potency and actions of endocrine-disrupting chemicals and suggests that multiple species need to be tested when screening the receptor binding ability of potential endocrine-disrupting chemicals. [source] Effect of the disease-causing mutations identified in human ribonuclease (RNase) H2 on the activities and stabilities of yeast RNase H2 and archaeal RNase HIIFEBS JOURNAL, Issue 19 2008Muhammad S. Rohman Eukaryotic ribonuclease (RNase) H2 consists of one catalytic and two accessory subunits. Several single mutations in any one of these subunits of human RNase H2 cause Aicardi,Goutičres syndrome. To examine whether these mutations affect the complex stability and activity of RNase H2, three mutant proteins of His-tagged Saccharomyces cerevisiae RNase H2 (Sc-RNase H2*) were constructed. Sc-G42S*, Sc-L52R*, and Sc-K46W* contain single mutations in Sc-Rnh2Ap*, Sc-Rnh2Bp*, and Sc-Rnh2Cp*, respectively. The genes encoding the three subunits were coexpressed in Escherichia coli, and Sc-RNase H2* and its derivatives were purified in a heterotrimeric form. All of these mutant proteins exhibited enzymatic activity. However, only the enzymatic activity of Sc-G42S* was greatly reduced compared to that of the wild-type protein. Gly42 is conserved as Gly10 in Thermococcus kodakareansis RNase HII. To analyze the role of this residue, four mutant proteins, Tk-G10S, Tk-G10A, Tk-G10L, and Tk-G10P, were constructed. All mutant proteins were less stable than the wild-type protein by 2.9,7.6 °C in Tm. A comparison of their enzymatic activities, substrate binding affinities, and CD spectra suggests that the introduction of a bulky side chain into this position induces a local conformational change, which is unfavorable for both activity and substrate binding. These results indicate that Gly10 is required to make the protein fully active and stable. [source] Migraine Headache Recurrence: Relationship to Clinical, Pharmacological, and Pharmacokinetic Properties of TriptansHEADACHE, Issue 4 2003Gilles Géraud MD Background and Objectives.,Triptan use is associated with headache recurrence, and this has been cited as an important reason for patient dissatisfaction with the treatment. The mechanism by which recurrence occurs is not clear, and the incidence of recurrence varies with the triptan used. In order to explore the pharmacological and physiological interaction of triptans and migraine headache recurrence further, some specific clinical, pharmacological, and pharmacokinetic factors that might influence migraine recurrence were evaluated in a review of the major efficacy data for the drugs in the triptan class. These factors were 5-HT1B and 5-HT1D receptor activities, the pharmacokinetic elimination half-life of each triptan, and the clinical efficacy of each compound, determined by the proportion of patients with headache relief and the therapeutic gain over placebo. Methods.,Clinical data were derived from 31 triptan, placebo-controlled, major efficacy studies used in a previous meta-analysis. The mean recurrence rate, mean headache response, and therapeutic gain were calculated using the results from the individual clinical studies. Mean headache response and therapeutic gain were calculated at the time point used to define recurrence in each study. Data for binding affinity and potency were taken from a direct-comparison in vitro pharmacology study, and the elimination half-life quoted in the data sheet for each triptan was used. Rank correlation with recurrence rate was performed for each of the test parameters. Results.,Mean headache recurrence rates ranged from 17% for frovatriptan 2.5 mg to 40% for rizatriptan. Elimination half-life and recurrence were inversely correlated (r = ,1.0, P = .0016). There was also a significant inverse correlation between 5-HT1B receptor potency and recurrence (r = ,0.68, P = .034), but 5-HT1D receptor potency was not correlated with recurrence (r = ,0.20, P = .54). In addition, the binding affinities for the 5-HT1B and 5-HT1D receptors were not correlated to headache recurrence. Importantly, it also was demonstrated that initial clinical efficacy was not correlated to headache recurrence. The correlation coefficient for headache response was 0.18 (P = .53) and for therapeutic gain, ,0.11 (P = .71). Conclusion.,The incidence of migraine headache recurrence varies between drugs in the triptan class. Migraine recurrence does not appear to be related to initial clinical efficacy, but is influenced by the pharmacological and pharmacokinetic properties of the individual triptans. The triptans with longer half-lives and greater 5-HT1B receptor potency had the lowest rates of headache recurrence. [source] Synthetic dsDNA-Binding Peptides Using Natural Compounds as ModelHELVETICA CHIMICA ACTA, Issue 6 2006Filip Borgions Abstract We have developed a series of short DNA-binding peptides containing newly synthesized, unnatural as well as natural amino acid building blocks. By a combinatorial-library approach, oligopeptides were developed with moderate dsDNA-binding affinities. Two strategies were used to further enhance the binding affinity of the lead peptides: Ac-Arg-Ual-Sar-Chi-Chi-Chi-Arg-NH2 and Ac-Arg-Cbg-Cha-Chi-Chi-Tal-Arg-NH2. Site-selective amino acid substitutions increased the binding affinities up to 2,×,10,5,M. Further enhancement of the binding affinities could be achieved by coupling of an acridine intercalating unit, using linker arms of different length and flexibility. With the introduction of a new lysine-based acridine unit, different types of oligopeptide,acridine conjugates were designed using known dsDNA-binding ligands as model compounds. The binding capacities of these new oligopeptide,acridine conjugates have been investigated by a fluorescent intercalator (ethidium bromide) displacement (FID) assay. With the synthesis of the dipeptide,acridine conjugates, binding affinities in the low micromolar range were obtained (6.4,×,10,6,M), which is similar to the binding strength of the well-known DNA binder Hoechst 33258. [source] Glyconanomaterials: Synthesis, Characterization, and Ligand PresentationADVANCED MATERIALS, Issue 17 2010Xin Wang Abstract Glyconanomaterials, nanomaterials carrying surface-tethered carbohydrate ligands, have emerged and demonstrated increasing potential in biomedical imaging, therapeutics, and diagnostics. These materials combine the unique properties of nanometer-scale objects with the ability to present multiple copies of carbohydrate ligands, greatly enhancing the weak affinity of individual ligands to their binding partners. Critical to the performance of glyconanomaterials is the proper display of carbohydrate ligands, taking into consideration of the coupling chemistry, the type and length of the spacer linkage, and the ligand density. This article provides an overview of the coupling chemistry for attaching carbohydrate ligands to nanomaterials, and discusses the need for thorough characterization of glyconanomaterials, especially quantitative analyses of the ligand density and binding affinities. Using glyconanoparticles synthesized by a versatile photocoupling chemistry, methods for determining the ligand density by colorimetry and the binding affinity with lectins by a fluorescence competition assay are determined. The results show that the multivalent presentation of carbohydrate ligands significantly enhances the binding affinity by several orders of magnitude in comparison to the free ligands in solution. The effect is sizeable even at low surface ligand density. The type and length of the spacer linkage also affect the binding affinity, with the longer linkage promoting the association of bound ligands with the corresponding lectins. [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] | |||||||||||||||||||||||||||||||||||||||||||