The enzyme mechanism of sialidase from influenza virus has been investigated by kinetic isotope methods, NMR, and a molecular dynamics simulation of the enzyme-substrate complex. Comparison of the reaction rates obtained with the synthetic substrate 4-methylumbelliferyl-N-acetyl-a-~-neuraminic acid and the [3,3-'H]-substituted substrate revealed /!I-deuterium isotope effects for V/Km ranging over 1.09 -1 .I 5 in the pH range 6.0 -9.5, whereas the effects observed for V in this pH range increased from 0.979 to 1.07. In D'O, ODV/Km was slightly increased by 2% and 5% at pD 6.0 and 9.5 respectively, while ODV was unchanged. Solvent isotope effects of 1.74 were obtained for both ODV/Km and ODV at pD 9.5, with ODV/K, decreasing and ODV remaining constant at acidic pD. 'H-NMR experiments confirmed that the initial product of the reaction is the a-anomer of N-acetyl-oneuraminic acid. Molecular dynamics studies identified a water molecule in the crystal structure of the sialidase-N-acetyl-D-neuraminic acid complex which is hydrogen-bonded to Asp1 51 and is available to act as a proton donor source in the enzyme reaction. The results of this study lead us to propose a mechanism for the solvent-mediated hydrolysis of substrate by sialidase that requires the formation of an endocyclic sialosyl cation transition-state intermediate.Sialidases catalyse the hydrolysis of terminal sialic acids from a range of glycoprotein, glycolipid and oligosaccharide substrates [I]. A large number of important biological functions are associated with the actions of this class of enzyme, including receptor recognition and masking, antigenic expression, protein degradation and some infectious processes [2]. Although a great deal of structural information has been gathered from crystallographic studies of influenza virus sialidase [3,4] and from sequence studies of bacterial sialidases [5, 61, there is a lack of detailed mechanistic information. Our recent interest in the biochemistry of sialidase from influenza virus [7, 81, has prompted us to undertake a mechanistic study of this enzyme.Isotope effects have been successfully used to show that some glycosidase-catalysed reactions occur with glycosyl cation-like transition states [9-131. However the application of isotope effects to a mechanistic study of sialidase has not been previously reported. The present study reports p-deuterium and solvent isotope effects on the enzyme reaction of sialidase from influenza virus, as well as the pH dependence and mul- V, secondary P-deuterium isotope effect on V.Enzyme. Sialidase (EC 3.2.1.18).tiple isotope effects of these deuterium probes. The enzyme reaction was also investigated by 'H-NMR spectroscopy to determine the stereochemistry around the anomeric centre of the released product, N-acetyl-D-neuraminic acid (NeuSAc). The kinetic results have been related to a molecular dynamics simulation of the sialidase-N-acetylneuraminic-acid complex, enabling us to propose a more detailed mechanism for the action of sialidase from influenza virus. MATERIALS A...

The first paper in this series (see previous article) described structure-activity studies of carboxamide analogues of zanamivir binding to influenza virus sialidase types A and B and showed that inhibitory activity of these compounds was much greater against influenza A enzyme. To understand the large differences in affinities, a number of protein-ligand complexes have been investigated using crystallography and molecular dynamics. The crystallographic studies show that the binding of ligands containing tertiary amide groups is accompanied by the formation of an intramolecular planar salt bridge between two amino acid residues in the active site of the enzyme. It is proposed that the unexpected strong binding of these inhibitors is a result of the burial of hydrophobic surface area and salt-bridge formation in an environment of low dielectric. In sialidase from type A virus, binding of the carboxamide moeity and salt-bridge formation have only a minor effect on the positions of the surrounding residues, whereas in type B enzyme, significant distortion of the protein is observed. The results suggest that the decreased affinity in enzyme from influenza B is directly correlated with the small changes that occur in the amino acid residue interactions accompanying ligand binding. Molecular dynamics calculations have shown that the tendency for salt-bridge formation is greater in influenza A sialidase than influenza B sialidase and that this tendency is a useful descriptor for the prediction of inhibitor potency.

4-Amino- and 4-guanidino-4H-pyran-6-carboxamides 4 and 5 related to zanamivir (GG167) are a new class of inhibitors of influenza virus sialidases. Structure--activity studies reveal that, in general, secondary amides are weak inhibitors of both influenza A and B viral sialidases. However, tertiary amides, which contain one or more small alkyl groups, show much greater inhibitory activity, particularly against the influenza A virus enzyme. The sialidase inhibitory activities of these compounds correlate well with their in vitro antiviral efficacy, and several of the most potent analogues displayed useful antiviral activity in vivo when evaluated in a mouse model of influenza A virus infection. Carboxamides which were highly active sialidase inhibitors in vitro also showed good antiviral activity in the mouse efficacy model of influenza A infection when administered intranasally but displayed modest activity when delivered by the intraperitoneal route.

Small modifications of the molecular structure of a ligand sometimes cause strong gains in binding affinity to a protein target, rendering a weakly active chemical series suddenly attractive for further optimization. Our goal in this study is to better rationalize and predict the occurrence of such interaction hot-spots in receptor binding sites. To this end, we introduce two new concepts into the computational description of molecular recognition. First, we take a broader view of noncovalent interactions and describe protein–ligand binding with a comprehensive set of favorable and unfavorable contact types, including for example halogen bonding and orthogonal multipolar interactions. Second, we go beyond the commonly used pairwise additive treatment of atomic interactions and use a small world network approach to describe how interactions are modulated by their environment. This approach allows us to capture local cooperativity effects and considerably improves the performance of a newly derived empirical scoring function, ScorpionScore. More importantly, however, we demonstrate how an intuitive visualization of key intermolecular interactions, interaction networks, and binding hot-spots supports the identification and rationalization of tight ligand binding.

X-ray detection limit and sensitivity are important figure of merits for perovskite X-ray detectors, but literatures lack a valid mathematic expression for determining the lower limit of detection for a perovskite X-ray detector. In this work, we present a thorough analysis and new method for X-ray detection limit determination based on a statistical model that correlates the dark current and the X-ray induced photocurrent with the detection limit. The detection limit can be calculated through the measurement of dark current and sensitivity with an easy-to-follow practice. Alternatively, the detection limit may also be obtained by the measurement of dark current and photocurrent when repeatedly lowering the X-ray dose rate. While the material quality is critical, we show that the device architecture and working mode also have a significant influence on the sensitivity and the detection limit. Our work establishes a fair comparison metrics for material and detector development.

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A clustering method based on finding the largest set of disconnected fragments that two chemical compounds have in common is shown to be able to group structures in a way that is ideally suited to medicinal chemistry programs. We describe how markedly improved results can be obtained by using a similarity metric that accounts not just for the size of the shared fragments but also on their relative arrangement in the two parent compounds. The use of a physiochemical atom typing scheme is also shown to provide significant contributions. Results from calculations using a test set consisting of actives from nine different important biological target proteins demonstrate the strengths of our clustering method and the advantages over other approaches that are widely used throughout the pharmaceutical industry.

The role of vascular endothelial growth factor (VEGF) in endometrial angiogenesis was examined by measuring its production in human endometrial tissues from different stages of the menstrual cycle and relating these data to endothelial cell proliferation in the same tissues. Conditioned medium was collected from explant, and separated glandular epithelial and stromal cells cultured from 24 normal human endometrial biopsies and VEGF measured by enzyme-linked immunosorbent assay (ELISA). Immunohistochemistry was also used to assess VEGF and the percentage of proliferating microvessels in the samples. Wide variation in results between individual endometrial samples at each stage of the menstrual cycle was observed for all parameters measured. There was no significant difference in VEGF secretion by explant, glandular epithelial or stromal cell cultures across the menstrual cycle, or in the percentage of proliferating vessels. VEGF immunostaining in the stroma was elevated during the early proliferative stage (P = 0.03). Epithelial cells secreted more VEGF than stromal cells (1.76 +/- 0.46 versus 0.46 +/- 0.06 ng per 10(5) cells; P = 0.002). There was no correlation between VEGF secreted by cultured explants, epithelial or stromal cells, VEGF immunostaining and the proportion of proliferating microvessels. These results show that the majority of endometrial VEGF is produced by glands, but neither total glandular nor stromal VEGF is correlated with endometrial endothelial cell proliferation. There is still no clear understanding on the regulation of human endometrial angiogenesis.