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Relative Binding Affinities (relative + binding_affinity)
Selected AbstractsModeling 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] Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2007Suncerae I. Smith Abstract Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding. Copyright © 2007 John Wiley & Sons, Ltd. [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] The contribution of hepatic steroid metabolism to serum estradiol and estriol concentrations in nonylphenol treated MMTVneu mice and its potential effects on breast cancer incidence and latencyJOURNAL OF APPLIED TOXICOLOGY, Issue 5 2005Ricardo Acevedo Abstract The two major pathways for the metabolism of estradiol-17, (E2) are the 2- and 16-hydroxylase pathways. Research has suggested that the increased production of the estrogenically active 16-hydroxy products such as estriol (E3) may be involved in increased susceptibility to breast cancer. 4-Nonylphenol (4-NP) is an environmental estrogen that also can activate the pregnane-X receptor (PXR) and induce P-450 enzymes responsible for the production of E3. It is hypothesized that 4-NP may act in part as an environmental estrogen by increasing E3 production. Based on its affinity for the estrogen receptor (ER) alone, 4-NP may be more potent than predicted at increasing mammary cancer incidence in the MMTVneu mouse. Female mice were treated per os for 7 days at 0, 25, 50 or 75 mg kg,1 day,1 4-NP to investigate the effects of 4-NP on hepatic estrogen metabolism after an acute treatment. 4-Nonylphenol increased the hepatic formation of E3 in a dose-dependent manner. However, serum E3 concentrations were only increased at 25 mg kg,1 day,1 presumably due to direct inhibition of E3 formation by 4-NP. MMTVneu mice were then treated for 32 weeks at 0, 30 or 45 mg kg,1 day,1 4-NP to determine its effects on mammary cancer formation and estrogen metabolism. 4-Nonylphenol increased mammary cancer formation in the MMTVneu mice at 45 mg kg,1 day,1 but not at 30 mg kg,1 day,1. Mice treated with an equipotent dose of E2, 10 µg kg,1 day,1, based on the relative binding affinities of nonylphenol and estradiol for ER,, did not develop mammary cancer. This suggests that nonylphenol is more potent than predicted based on its affinity for the estrogen receptor. However, no changes in serum E3 concentrations or hepatic E3 production were measured after the chronic treatment. Changes in E3 formation were correlated with increased CYP2B levels after the 7 day 4-NP treatment, and repression of CYP2B and CYP3A after 32 weeks of 4-NP treatment. Microarray analysis and Q-PCR of liver mRNA from the mice treated for 32 weeks demonstrated a decrease in RXR,, the heterodimeric partner of the PXR, which may in part explain the repressed transcription of the P450s measured. In conclusion, 4-NP treatment for 32 weeks increased mammary cancer formation at a dose of 45 mg kg,1 day,1. However, chronic treatment with 4-NP did not increase hepatic E3 formation or serum E3 concentrations. The transient induction by 4-NP of hepatic E3 formation and serum concentrations is most likely not involved in the increased incidence of mammary cancer in MMTVneu mice since E3 serum concentrations were only increased at 25 mg kg,1 day,1, a dose that was not sufficient to induce mammary tumor formation. Nevertheless, the induced hepatic E3 production in the acute exposures to 4-NP was indicative of an increase in mammary cancer incidence after the chronic exposure. Copyright © 2005 John Wiley & Sons, Ltd. [source] Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2007Ravichandra Mutyala Abstract The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this article, the importance of hydrophobic and hydrophilic residues to the binding of adenosine monophosphate (AMP) to the fructose 1,6-bisphosphatase (FBPase), a target enzyme for type-II diabetes, was examined by FEP method. Five mutations were made to the FBPase enzyme with AMP inhibitor bound: 113Tyr , 113Phe, 31Thr , 31Ala, 31Thr , 31Ser, 177Met , 177Ala, and 30Leu , 30Phe. These mutations test the strength of hydrogen bonds and van der Waals interactions between the ligand and enzyme. The calculated relative free energies indicated that: 113Tyr and 31Thr play an important role, each via two hydrogen bonds affecting the binding affinity of inhibitor AMP to FBPase, and any changes in these hydrogen bonds due to mutations on the protein will have significant effect on the binding affinity of AMP to FBPase, consistent to experimental results. Also, the free energy calculations clearly show that the hydrophilic interactions are more important than the hydrophobic interactions of the binding pocket of FBPase. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2002Sonja M. Schwarzl Abstract The prediction of a ligand binding constant requires generating three-dimensional structures of the complex concerned and reliably scoring these structures. Here, the scoring problem is investigated by examining benzamidine-like inhibitors of trypsin, a system for which errors in the structures are small. Precise and consistent binding free energies for the inhibitors are determined experimentally for this test system. To examine possible improvement of scoring methods, we test the suitability of continuum electrostatics to account for solvation effects and use an ideal-gas entropy correction to account for the changes in the degrees of freedom of the ligand. The small observed root-mean-square deviation of 0.55 kcal/mol of the calculated relative to the experimental values indicates that the essentials of the binding process have been captured. Even though all six ligands make the same salt bridge and H-bonds to the protein, the electrostatic contribution varies among the ligands by as much as 2 kcal/mol. Moreover, although the ligands are rigid and similar in size, the entropic terms also significantly affect the relative binding affinities (by up to 2.7 kcal/mol). The present approach to solvation and entropy may allow the ranking of the ligands to be considerably improved at a cost that makes the method applicable to the optimization of lead compounds or to the screening of small collections of ligands. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1143,1149, 2002 [source] Synthesis, Structural Evaluation, and Estrogen Receptor Interaction of 4, 5-Bis(4-hydroxyphenyl)imidazolesARCHIV DER PHARMAZIE, Issue 10 2002Ronald Gust Abstract 4, 5-Bis(4-hydroxyphenyl)imidazoles with 2, 2,-H (1), 2, 2,-F (2), 2, 2,-Cl (3), and 2, 2,6-Cl (4) substituents in the aromatic rings were synthesized by oxidation of the respective methoxy-substituted (R, S)/(S, R)-4, 5-diaryl-2-imidazolines with MnO2 and subsequent ether cleavage with BBr3. N -alkylation of 1 and 3 with ethyl iodide yielded the compounds 5 and 6. The imidazoles were characterized by NMR spectroscopy and tested for estrogen receptor binding in a competition experiment with [3H]estradiol using calf uterine cytosol. Gene activation was verified in a luciferase assay using estrogen receptor positive MCF-7-2a cells stably transfected with the plasmid EREwtcluc. All halide substituted imidazoles competed with estradiol for the binding site at the estrogen receptor. The N -ethyl derivative 6 showed the highest relative binding affinity of 1.26 %. Treatment of MCF-7-2a cells, however, did not lead to gene activation. The relative activation of 6 amounted only to 10 % at 1,M compared to E2 (100 %). [source] | ||||||||||