Synthesis and evaluation of novel α-amino cyclic boronates as inhibitors of HCV NS3 protease

We have designed and synthesized a novel series of α-amino cyclic boronates and incorporated them successfully in several acyclic templates at the P1 position. These compounds are inhibitors of the HCV NS3 serine protease, and structural studies show that they inhibit the NS3 protease by trapping the Ser-139 hydroxyl group in the active site. Synthetic methodologies and SARs of this series of compounds are described.     

Reinnervation of hair cells by auditory neurons after selective removal of spiral ganglion neurons

Hearing loss can be caused by primary degeneration of spiral ganglion neurons or by secondary degeneration of these neurons after hair cell loss. The replacement of auditory neurons would be an important step in any attempt to restore auditory function in patients with damaged inner ear neurons or hair cells. Application of beta-bungarotoxin, a toxin derived from snake venom, to an explant of the cochlea eradicates spiral ganglion neurons while sparing the other cochlear cell types. The toxin was found to bind to the neurons and to cause apoptotic cell death without affecting hair cells or other inner ear cell types as indicated by TUNEL staining, and, thus, the toxin provides a highly specific means of deafferentation of hair cells. We therefore used the denervated organ of Corti for the study of neuronal regeneration and synaptogenesis with hair cells and found that spiral ganglion neurons obtained from the cochlea of an untreated newborn mouse reinnervated hair cells in the toxin-treated organ of Corti and expressed synaptic vesicle markers at points of contact with hair cells. These findings suggest that it may be possible to replace degenerated neurons by grafting new cells into the organ of Corti.     

Dopaquinone redox exchange with dihydroxyindole and dihydroxyindole carboxylic acid

A pulse radiolytic investigation has been conducted to establish whether a redox reaction takes place between dopaquinone and 5,6-dihydroxyindole (DHI) and its 2-carboxylic acid (DHICA) and to measure the rate constants of the interactions. To obviate possible confounding reactions, such as nucleophilic addition, the method employed to generate dopaquinone used the dibromide radical anion acting on dopa to form the semiquinone which rapidly disproportionates to dopaquinone. In the presence of DHI the corresponding indole-5,6-quinone (and/or tautomers) was also formed directly but, by judicious selection of suitable relative concentrations of initial reactants, we were able to detect the formation of additional indolequinone from the redox exchange reaction of DHI with dopaquinone which exhibited a linear dependency on the concentration of DHI. Computer simulation of the experimental time profiles of the absorption changes showed that, under the conditions chosen, redox exchange does proceed but not quite to completion, a forward rate constant of 1.4 x 10(6)/M/s being obtained. This is in the same range as the rate constants previously established for reactions of dopaquinone with cyclodopa and cysteinyldopa. In similar experiments carried out with DHICA, the reaction more obviously does not go to completion and is much slower, k (forward) =1.6 x 10(5)/M/s. We conclude that, in the eumelanogenic pathway, DHI oxidation may take place by redox exchange with dopaquinone, although such a reaction is likely to be less efficient for DHICA.     

A pulse--radiolysis approach to fast reductive cleavage of a disulfide bond to uncage enzyme activity

The essential thiol of the enzyme papain has been caged by linking to an aromatic thiol. The resulting caged protein is inactive but enzymatic activity is fully restored upon chemical cleavage of the protective disulfide bond. We have exploited the chemistry of this disulfide bond to uncage papain by pulse radiolysis. We have shown that up to 10% of the enzyme activity can be restored by reductive pulse radiolysis. This approach has been tested on a small-molecule model system, and experiments on this model compound show that pulse radiolysis of the mixed cysteine-aromatic disulfide results in selective reduction of the disulfide bond to generate a thiol in 10-20% yield, consistent with the radiolytically restored activity of the caged papain quantified by the biochemical assay.     

Characterization of formulated microbial products by denaturing gradient gel electrophoresis, total cellular fatty acid analysis, and DNA microarray analysis

Two commercial products, Biotize and Cycle, containing bacteria as an active ingredient were characterized for species identification and batch-to-batch variation by denaturing gradient gel electrophoresis (DGGE), total cellular fatty acid analysis (FAA), and a taxonomic DNA microarray. DGGE was useful at assessing the stability of consortia in different batches, and cluster analysis differentiated each batch even when only slight differences in species composition were observed. DGGE, FAA, and DNA microarray results indicated little batch-to-batch variation in Biotize and some batch variation in Cycle. The 3 methods agreed well with species identification in Biotize but generated conflicting results in the species composition of Cycle. This multi-method approach was useful in determining if the observed bacterial species present in the products matched the expected species composition.     

Site-specific interactions of copper(II) ions with heparin revealed with complementary (SRCD, NMR, FTIR and EPR) spectroscopic techniques

The interactions between Cu(II) ions and heparin were investigated using several complementary spectroscopic techniques. NMR indicated an initial binding phase involving specific coordination to four points in the structure that recur in slightly different environments throughout the heparin chain; the carboxylic acid group and the ring oxygen of iduronate-2-O-sulfate, the glycosidic oxygen between this residue and the adjacent (towards the reducing end) glucosamine and the 6-O-sulfate group. In contrast, the later binding phase showed little structural specificity. One- and two-dimensional correlated FTIR revealed that complex out of phase (asynchronous) conformational changes also occurred during the titration of Cu(II) ions into heparin, involving the CO and N-H stretches. EPR demonstrated that the environments of the Cu(II) ions in the initial binding phase were tetragonal (with slightly varied geometry), while the later non-specific phases exhibited conventional coordination. Visible spectroscopy confirmed a shift of the absorbance maximum. Titration of Cu(II) ions into a solution of heparin indicated (both by analysis of FTIR and EPR spectra) that the initial binding phase was complete by 15-20 Cu(II) ions per chain; thereafter the ions bound in the non-specific mode. Hetero-correlation spectroscopy (FTIR-CD) improved resolution and assisted assignment of the broad CD features from the FTIR spectra and indicated both in-phase and more complex out of phase (synchronous and asynchronous, respectively) changes in interactions within the heparin molecule during the titration of Cu(II) ions.     

Temporal analysis of gene expression in a field population of the Scleractinian coral Montastraea faveolata

Organisms maintain homeostasis and abate cellular damage by altering gene expression. Coral colonies have been shown to produce unique gene expression patterns in response to different environmental stimuli. In order to understand these induced changes, the natural variation in expression of genetic biomarkers needs to be determined. In this study, an array of genes isolated from Scleractinian coral was used to track changes in gene expression within a population of Montastraea faveolata from April to October 2001 in the Florida Keys. The profiles of genes observed in this study can be divided into two groups based on expression over this time period. In spring and early summer, May through July, most of the genes show little deviation from their average level of expression. In August and September, several genes show large deviations from their average level of expression. The physiological and environmental triggers for the observed changes in gene expression have not yet been identified, but the results show that our coral stress gene array can be used to track temporal changes in gene expression in a natural coral population.     

Uncertainties in structural determinations of oligosaccharide conformation, using measurements of nuclear Overhauser effects

A fundamental problem in the determination of molecular structure by n.m.r. spectroscopy is insufficient experimental constraints. This problem is particularly marked for oligosaccharides, where few constraints are available across glycosidic linkages. By calculating distances as a function of dihedral angle, it is shown that, in general, two n.O.e. constraints result in two possible conformations for each glycosidic linkage, one of which can usually be discarded on the basis of model building or energy calculations. Using these calculations, an estimate of the uncertainty in the structure can be obtained.