A bioinformatic approach to check the spatial epitope structure of an immunogenic protein coded by DNA vaccine plasmids.

In this study, we used an approach to check the Hemagglutinin antigen-antibodies interactions after fusion of one or two gene segments to Hemagglutinin gene in some influenza DNA vaccines. We designed different DNA vaccine constructs containing Hemagglutinin 9 (H9) gene fused to four or eight 29 amino acids of C3d (4/8P29C3d) and/or 3, 4 domains of the Fc part of IgY (FcIgY) coding sequences. As there are receptors for P29C3d and FcIgY on the immune cells, fused H9 are targeted to these cells. Three dimensional (3D) structures of the DNA vaccine coded proteins were modeled and docked with two antibodies (1KEN, 1QFU) to evaluate the effect of the H9 gene fusion to the other gene segments (4, 8 P29C3d and FcIgY) on the interaction of two H9 spatial epitopes. Also, we docked DNA vaccine proteins containing Fc IgY to its receptor (CHIR AB1) and compare interaction affinity of Fc IgY alone with affinity of DNA vaccines containing Fc IgY. The average of 1KEN and 1QFU interface scores were 94.89 and 93.09% of H9 DNA vaccine-antibodies interface scores, respectively. These percentages showed a little change in the H9 immunogenic parts. Also, because of spatial freedom of H9 part in all DNA vaccine proteins, added parts may not interfere with antibody-antigen interactions. Once, H9+FcIgY and CHIR AB1 affinity decreased in comparison with affinity of Fc IgY alone and CHIR AB1, affinity of H9+8P29C3d+FcIgY and CHIR AB1 increased to 132%. So, this would be expectable that despite of loss of affinity in H9 and its antibodies in the H9+8P29C3d+FcIgY, dramatic increase of Fc IgY and CHIR AB1 affinity in this group, could repair the loss of H9 affinity and may lead to a better immunogenicity.

Bioinformatics Analysis of Upstream Region and Protein Structure of Fungal Phytase Gene.

Phytase increases the bioavailability of phytate phosphorus in seed-based animal feeds and reduces the phosphorus pollution of animal waste. Since most animal feeds for pellets are heated up to 65-80 °C, the production of a thermostable structure for phytase can be useful. In this study, we sought to perform bioinformatics analysis of the upstream region and protein structure of fungal phytase to improve its expression and thermostability properties. We used bioinformatics methods such as similarity search, multiple alignment, statistical analysis of physicochemical properties of amino acids, pattern recognition, and protein modeling to find out the effective factors in heat resistance of phytase. Change in Gibbs free energy (ΔG) of the best pattern promoter resulting from the interaction between RNA polymerase and the promoter sequences of modified genes of phytase was equal to -9 kcalmol-1, which is lower compared to other interactions. The evaluation of the three-dimensional structure of new phytases showed that amino acid substitutions aimed at improving thermostability did not change the form and structure of the protein. The results of Prochek, Whatcheck, and ERRAT for structural analysis and verification were 84, 72, and 70, respectively, that were satisfactory.

Chlorhexidine effects on membrane lipid domains of human buccal epithelial cells.

The effect of chlorhexidine gluconate on the adherence of Candida albicans to human buccal epithelial cells (BEC) and drug-induced alterations in BEC membrane-lipid packing order were examined. Treatment of BEC with attached yeasts with 0.1 and 0.2% chlorhexidine resulted in significant yeast detachment after 90 and 60 min, respectively. Following pre-treatment of BEC with greater than 0.1% chlorhexidine, yeast adherence was inhibited by greater than 80%. In parallel experiments, the fluorescence anisotropy of BEC labeled with fluorescent membrane probes--diphenylhexatriene (DPH) and trimethylammonium DPH--was assessed following exposure to chlorhexidine. The fluorescence anisotropy decreased with increasing concentrations of chlorhexidine, which indicated that the drug decreased epithelial-cell membrane-lipid packing order. Chlorhexidine concentrations that altered epithelial-cell membrane-lipid packing order, particularly in superficial regions, were similar to those drug concentrations required for detachment of adherent yeasts. Similar results were obtained with a second antifungal, nystatin A. While the effects of chlorhexidine on the buccal-cell membrane-lipid packing order were not reversed by multiple washings, the opposite situation occurred with nystatin A. The results suggest that chlorhexidine-induced alterations of BEC membrane-lipid order may be involved in the antifungal actions of the drug.

A comparison of aminopeptidases from excised human buccal epithelium and primary cultures of hamster pouch buccal epithelium.

Aminopeptidase activity associated with human buccal tissue and primary cultures of hamster buccal epithelium homogenates was assayed fluorometrically using 4-methoxy-2-naphthylamides of leucine, alanine, and arginine. Kinetic parameters, Km and Vmax, for all substrates were estimated. Aminopeptidase parameters for human tissue were similar to those for the in-vitro system and reported literature values for rodent buccal tissue aminopeptidases. Aminopeptidases of both tissues were also found to be similarly sensitive to typical inhibitors, bestatin and puromycin. Overall results suggest that appropriate in-vitro systems derived from animal tissues may be useful in assessing the role and localization of peptidases associated with buccal tissue.

Comparison of binding interactions of lomefloxacin to serum albumin and serum transferrin by resonance light scattering and fluorescence quenching methods.

The interaction between lomefloxacin (LMF) and two drug carrier proteins, human serum albumin (HSA) and serum transferrin (TF), were studied and compared by fluorescence quenching, resonance light scattering (RLS), and circular dichroism (CD) spectroscopic along with molecular modeling. Fluorescence data show that LMF has a stronger quenching effect on HSA than on TF. The binding constant and the number of binding sites were calculated as 6.00 x 10(5) M(-1) and 0.77 for HSA, and 4.66 x 10(5) M(-1) and 1.02, for TF, respectively. Also, these binding parameters were calculated by RLS data, as a novel approach and were compared to that obtained from fluorescence. The micro-environment changes of Trp residues were evident in both proteins. The quantitative analysis of the secondary structure in both proteins further confirmed the drug-induced conformational changes. The distance (r) between donors (HSA and TF) and acceptor (LMF) were obtained by fluorescence resonance energy transfer (FRET) theory and found to be 1.83 nm and 1.71 nm for HSA and TF respectively. Moreover, molecular modeling studies suggested the sub-domain IB in HSA and N-lobe in TF as the candidate place for the formation of the binding site of LMF on these proteins.

Design and synthesis of pyrimido[4,5-b][1,4]benzothiazine derivatives, as potent 15-lipoxygenase inhibitors.

A group of 2-substituted pyrimido[4,5-b][1,4]benzothiazines were designed, synthesized, and evaluated as potential inhibitors of 15-lipoxygenase (15-LO). Compounds 4d and 4e showed the best IC50 of 15-LO inhibition (IC50=18 and 34 microM, respectively). All compounds were docked into 15-LO. As a result the sulfur atom was oriented toward the iron atom of the active site of 15-LO. We suggest the interaction of the iron atom is essential for the activity of the inhibitors.

Cultured buccal epithelium: an in vitro model derived from the hamster pouch for studying drug transport and metabolism.

Hamster pouch buccal epithelium (HPBE) was isolated and grown in primary cultures on rat-tail collagen-coated growth surfaces. The cultured pouch buccal epithelium (CPBE) was characterized morphologically with electron microscopy as stratified multilayers of epithelial cells with well-developed tonofibrillar-desmosomal complexes. Only the superficial layer of the cultured cells exhibited evidence of terminal differentiation. Alkaline phosphatase, alcohol dehydrogenase, and aminopeptidase activities in the primary cultured cells were determined by biochemical assays and found to be similar to those of homogenates of freshly excised hamster pouch epithelium. In addition, by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE), keratins and total proteins associated with the cultured cells were similar to those of freshly excised HPBE. The permeability characteristics of the cultured cells was determined by placing cultured cells grown on permeable polycarbonate disks in a Side-Bi-Side diffusion apparatus and quantitating the transcellular flux of tritium-labeled water, fluorescein, and fluorescein isothiocyanate dextrans (MW 3800 to 150,000). The cultured cells were least permeable on the third day of culture and were not permeable to substances with a MW greater than about 18,000. Our results indicate that primary cultures of hamster pouch epithelium exhibit biochemical properties similar to those of the excised hamster pouch epithelium from which they were derived. The morphological and permeability characteristics of cultured hamster epithelium were similar to those of nonkeratinized stratified oral epithelia typical of buccal mucosa in man, rabbit, and other species. CPBE, as described here, represents a potentially useful tool for in vitro drug transport, metabolism, pharmacology, and toxicology studies.