On the Modeling of Some Anti-inflammatory and Anti-thrombotic Drugs by AM1

Two families of autacoids from cell membrane phospholipids have been identified. The first, the icosanoids, which are formed from arachidonic acid, include prostaglandins and leukotrienes. The other includes modified phospholipids, as the platelet aggregating factor (PAF). These compounds are related to inflammatory and cardiovascular diseases. We review in this paper some of the work that has been done in our laboratories in the last few years relating to the modeling of new potential thromboxane synthase (TXS) and 5-lipoxygenase (5-LO) and cyclooxygenase (COX) inhibitors, and TXA₂ receptor antagonists derived from nitrogenated heterocycles. We include the results of the modeling of a group of proposed PAF antagonists, and compare their structures with PAF itself and with a recently proposed PAF antagonist model. This revised version was published online in June 2006 with corrections to the Cover Date.     

Nucleosides Having Quinolone Derivatives as Nitrogenated Base: Regiospecific and Stereospecific Ribosylation of 3-Carbethoxy-1,4-dihydro-4-oxoquinolines

Abstract

Ribosylation reactions of previously silylated 3-carbethoxy-8-methyl-1,4-dihydro-4-oxoquinoline (6a) and 3-carbethoxy-6-methyl-1,4-dihydro-4-oxoquinoline (6b) with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose (7), under Lewis acid catalysis, were studied. The method using hexamethyldisilazane (HMDS)/trimethylchlorosilane (TMCS) mixture for silylation and anhydrous stannic chloride as catalyst for ribosylation failed to give any nucleoside product. On the other hand, the protected nucleoside 3-carbethoxy-6-methyl-1-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)-1,4-dihydro-4-oxoquinoline (8b) was obtained in good yields using bis(trimethylsilyl)trifluoroacetamide (BSTFA) containing 1% of TMCS and the same catalyst. Compound 8b was more easily isolated in higher yields with an improvement of the later method by replacing stannic chloride with trimethylsilyl trifluoromethanesulfonate (TMSOTf).

De-O-benzoylation of 8b with methanolic sodium hydroxide solution afforded the free riboside 3-carbomethoxy-6-methyl-1-β-D-ribofuranosyl-1,4-dihydro-4-oxoquinoline (9b). The structures of the obtained products were confirmed by their LTV, MS, IR, ¹H and ¹³C-NMR data.     

Oxytocin Sustained Release Using Natural Rubber Latex Membranes

The demand for biomaterials with properties that provide sustained release of substances with pharmacological interest is constant. One candidate for applications in this area is the Natural Rubber Latex (NRL) extracted from the rubber tree Hevea brasiliensis. Recent studies indicate the NRL as a matrix for sustained release, showing promising results for biomedical applications such as: can stimulate natural angiogenesis and is capable of adhering cells on its surface, promoting the replacement and regeneration of tissue. So, the NRL is an excellent candidate to propitiate the sustained release of peptides of pharmacological interest such as oxytocin, a hormonal peptide which has the function to promote uterine muscle contractions and reduce bleeding during childbirth, and stimulate the release of breast milk. Results demonstrated that 90 μg mL^?1 (45 %) of the incorporated peptide in Natural Rubber Latex Biomedical (NRLb) functionalized membranes was released at 10 h in phosphate-buffered saline (PBS) solution. Swelling kinetics assay showed that the NRLb membranes are able to absorb over a period of 16 h up to 1.08 grams of water per grams of membrane. Scanning electron microscopy showed that the peptide was adsorbed on the surface and within NRLb membrane. Fourier transform infrared and Derivative Thermogravimetric analysis indicated that oxytocin did not interacted chemically with the membrane. Furthermore, hemolysis of erythrocytes, quantified spectrophotometrically using materials (Oxytocin, NRLb, and NRLb + Oxytocin) showed no hemolytic effects up to 100 μg mL^?1 (compounds and mixtures), indicating no detectable disturbance of the red blood cell membranes. Based on these results it was possible to conclude that the NRLb has shown effectiveness as a model in the release of peptides with pharmacological interest.     

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Interaction of Leptomonas wallacei with the intestinal tract of its natural host Oncopeltus fasciatus (Hemiptera: Lygaeidae)

While investigating the distribution of Leptomonas wallacei in the intestine of the insect host Oncopeltus fasciatus, promastigotes and cyst-like forms of L. wallacei were observed only in the midgut ventricles V(3) and V(4) and the hindgut. In video-microscopy, once contact had occurred, the parasites remained attached to the midgut epithelium. Scanning electron microscopy revealed the adhesion of flagellates and cyst-like forms to the midgut wall and to the rectal pads of the hindgut. Using transmission electron microscopy, we observed that adhesion occurred mainly between the flagellum and the perimicrovillar membranes secreted by the midgut epithelium. No modifications were observed either in the parasite or in the epithelial cells. In the hindgut, adhesion to the superficial wax layer of the epithelial cells of the rectal pads was via flagellum. Host cell morphology appeared unaffected by L. wallacei.     

Leptomonas wallacei shows distinct morphology and surface carbohydrates composition along the intestinal tract of its host Oncopeltus fasciatus (Hemiptera: Lygaeidae) and in axenic culture

Leptomonas wallacei is a monoxenic trypanosomatid that colonizes the digestive tract of the phytophagous hemipteran Oncopeltus fasciatus. This infection was specific and took place exclusively in midgut intestinal ventricles V3 and V4, and in the hindgut. Abundances of parasites in the hindgut were 54% less than those in the hindgut. Parasites in the hindgut were more slender and had a longer flagellum than those from the hindgut, which were rounded, with a shorter flagellum. Moreover, hindgut forms expressed sugar residues on the cell surface, recognized by the lectins from Griffonia simplicifolia-I (alpha-galactose, alpha-N-acetyl-galactosamine) and Helix pomatia (N-acetyl-galactosamine); those sugar residues were not present in protozoa from the midgut. In culture, parasites were morphologically similar to midgut forms, but differed from them because they did not express sugar residues that bind to lectin (beta-galactose(1-3) N-acetyl-galactosamine) from Arachis hypogaea.     

Granule-bound starch synthase: structure, function, and phylogenetic utility

Interest in the use of low-copy nuclear genes for phylogenetic analyses of plants has grown rapidly, because highly repetitive genes such as those commonly used are limited in number. Furthermore, because low- copy genes are subject to different evolutionary processes than are plastid genes or highly repetitive nuclear markers, they provide a valuable source of independent phylogenetic evidence. The gene for granule-bound starch synthase (GBSSI or waxy) exists in a single copy in nearly all plants examined so far. Our study of GBSSI had three parts: (1) Amino acid sequences were compared across a broad taxonomic range, including grasses, four dicotyledons, and the microbial homologs of GBSSI. Inferred structural information was used to aid in the alignment of these very divergent sequences. The informed alignments highlight amino acids that are conserved across all sequences, and demonstrate that structural motifs can be highly conserved in spite of marked divergence in amino acid sequence. (2) Maximum-likelihood (ML) analyses were used to examine exon sequence evolution throughout grasses. Differences in probabilities among substitution types and marked among-site rate variation contributed to the observed pattern of variation. Of the parameters examined in our set of likelihood models, the inclusion of among-site rate variation following a gamma distribution caused the greatest improvement in likelihood score. (3) We performed cladistic parsimony analyses of GBSSI sequences throughout grasses, within tribes, and within genera to examine the phylogenetic utility of the gene. Introns provide useful information among very closely related species, but quickly become difficult to align among more divergent taxa. Exons are variable enough to provide extensive resolution within the family, but with low bootstrap support. The combined results of amino acid sequence comparisons, maximum-likelihood analyses, and phylogenetic studies underscore factors that might affect phylogenetic reconstruction. In this case, accommodation of the variable rate of evolution among sites might be the first step in maximizing the phylogenetic utility of GBSSI.      

The function of communities in protein interaction networks at multiple scales

Background  

If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological modules and network communities in yeast and its relationship to the scale at which we probe the network.