Recent advances in nanotechnology based drug delivery to the brain

Drug delivery into the brain was difficult due to the existence of blood brain barrier, which only permits some molecules to pass through freely. In past decades, nanotechnology has enabled many technical advances including drug delivery into the brain with high efficiency and accuracy. In the present paper, we summarize recent important advances in employing nanotechnology for drug delivery to the brain as well as controlled drug release.     

Regulation of μ binding sites after chronic administration of antibodies directed against specific anti-opiate peptides

There is some indication that anti-opiate peptides (AOP) modulate opioid receptor systems by altering μ-receptor density. To further characterize this phenomenon, we investigated the effects of continuous infusion of anti-AOP IgG on μ binding sites in the brains of rats. Specifically, male Sprague–Dawley rats received intracerebroventricular (ICV) infusions for 13 days of either control (rabbit) IgG or test IgGs: anti-dynorphin A IgG, anti-dynorphin A_1–8 IgG, anti-α-MSH IgG, or the monoclonal anti-NPFF IgG. Administration of anti-NPFF IgG or the anti-dynorphin_1–8 IgG significantly increased μ labeling by 40–70% in several brain regions at the caudate level. Contrary to these findings, anti-α-MSH IgG decreased (19–32%) [¹²⁵I]-DAMGO labeling in several thalamic nuclei. The results suggest that the density of μ-opioid receptors is regulated in part by anti-opiate peptides in the extracellular fluid of the brain.     

A novel specific binding site for anxiolytic homophthalazines in the rat brain.

Radioligand binding studies were performed in order to elucidate the mechanism of action of anxiolytic-neuroleptic homophthalazines. Rat striatal membrane preparations were found to bind 3H-EGIS 6775 [3H-GYKI-52 322, 3H-(1-(4-aminophenyl)-4-methyl-7,8-dimethoxy-5H-homophthalazine)] in a specific and displaceable manner. Several other brain regions tested were devoid of similar binding activity. Saturation analysis revealed that binding affinity was in the 10(-8)-10(-7) M range. Binding was enhanced by Mg2+ ions and, to a smaller extent by Ca2+ ions. The binding principle was sensitive to heat or trypsin treatment. This specific binding site appears, according to competition studies, different from the receptors whose presence in the rat striatum has been reported earlier.     

A novel approach to the generation of high affinity class II-binding peptides

We have found that if core regions crucial for class II binding are incorporated in multiple copies in the same peptide molecule ("reiterative motifs"), marked enhancement of the binding capacity occurs. Isotype specificity (IAd vs IEd binding capacities) is retained in all three antigenic determinants so far analyzed (lambda rep 12-26, OVA 323-339, and hen egg lysozyme 105-120). The mechanism involved in such an effect is not clear, but experiments involving introduction of a peptide spacer between two repeated core regions do not support the notion that the effect is mediated by cross-linking of more than one MHC molecule, favoring the possibility that conformational effects or distinct subsites of interaction on the MHC molecule may be involved. Based on reiterative structures, a peptide molecule composed of only two different amino acids (Ala and His) has been produced that still retains a very high binding affinity. An 125I-radiolabeled form of this peptide has been used to demonstrate that the high binding detected is mediated by the same binding site involved in the interaction of IAd and OVA 323-339. Inhibition of Ag presentation studies further supports the immunologic relevance of the phenomena observed. Finally, we observed naturally occurring clustered binding sites in proximity of immunodominant protein regions, raising the possibility that the phenomenon might have a physiologic counterpart.     

A new in vitro approach for investigating the MPTP effect on DA uptake

Previous studies have shown that dopamine (DA) uptake was decreased after preincubation of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) or 1-methyl-4-phenylpyridinium (MPP(+)) in in vitro slice and synaptosome models. The present study, conducted with and without preincubation, attempted to determine whether inhibition results from a direct effect of neurotoxins on neuronal DA transporter or from an alteration of the transporter secondary to other toxic events. DA uptake was inhibited about 50% in the presence of MPTP+O(2) or MPP(+) (0.1, 1 and 5 mM) in rat striatal slices and synaptosomes. Such inhibition was obtained in synaptosomes preincubated for 150 min with MPP(+) and then washed. Inhibition of DA uptake was lower in slices preincubated with MPTP (5 mM)+O(2) and then washed (30%). Experiments in synaptosomes prepared from slices preincubated with MPTP or MPP(+) showed greater inhibition of DA uptake with MPTP. The results suggest that the inhibition of DA uptake in vitro by MPTP or MPP(+) results initially from a direct effect on the transporter during its penetration in nerve endings and subsequently from a transporter alteration related to toxic events. Thus, the preincubation of striatal slices followed by DA uptake measurement in synaptosomes would appear to be a good in vitro model for studying the dopaminergic toxicity of MPTP.     

A novel approach to predict active sites of enzyme molecules

Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. Proteins 2004. © 2004 Wiley-Liss, Inc.     

Computer-based design of novel HIV-1 entry inhibitors: neomycin conjugated to arginine peptides at two specific sites

Aminoglycoside–arginine conjugates (AAC and APAC) are multi-target inhibitors of human immunodeficiency virus type-1 (HIV-1). Here, we predict new conjugates of neomycin with two arginine peptide chains binding at specific sites on neomycin [poly-arginine-neomycin-poly-arginine (PA-Neo-PA)]. The rationale for the design of such compounds is to separate two short arginine peptides with neomycin, which may extend the binding region of the CXC chemokine receptor type 4 (CXCR4). We used homology models of CXCR4 and unliganded envelope glycoprotein 120 (HIV-1_IIIB gp120) and docked PA-Neo-PAs and APACs to these using a multistep docking procedure. The results indicate that PA-Neo-PAs spread over two negatively charged patches of CXCR4. PA-Neo-PA–CXCR4 complexes are energetically more favorable than AACs/APAC–CXCR4 complexes. Notably, our CXCR4 model and docking procedure can be applied to predict new compounds that are either inhibitors of gp120–CXCR4 binding without affecting stromal cell-derived factor 1α (SDF-1α) chemotaxis activity, or inhibitors of SDF-1α–CXCR4 binding resulting in an anti-metastasis effect. We also predict that PA-Neo-PAs and APACs can interfere with CD4–gp120 binding in unliganded conformation. Figure The r5-Neo-r5-CXCR4 complex. CXCR4 is shown in CPK representation. The negatively charged residues are shown in red and positively charged residues in blue. The r5-Neo-r5 is shown in stick representation, neomycin core is colored yellow and arginine moieties are colored magenta. Two negatively charged patches separated by neutral and positively charged residues are visible.     

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

Background  

Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-coding intronic regions, especially in alu retrotransposable elements, but very few substrates that are site-selectively edited in coding regions. Known RNA edited substrates suggest, however, that site selective A-to-I editing is particularly important for normal brain development in mammals.     

Localization of binding sites for carboxyl terminal specific anti-rhodopsin monoclonal antibodies using synthetic peptides

The binding sites for four monoclonal antibodies, rho 1D4, rho 3C2, rho 3A6, and rho 1C5, have been localized within the C-terminal region of bovine rhodopsin: Asp18'-Glu-Ala16'-Ser-Thr-Thr-Val12'-Ser-Lys-Thr-Gl u8'-Thr-Ser-Gln-Val4'-Ala-Pr o -Ala1'. Antibody binding sites were localized by using synthetic C-terminal peptides in conjunction with solid-phase competitive inhibition assays and limited proteolytic digestion of rhodopsin in conjunction with electrophoretic immunoblotting techniques. Binding of the rho 1D4 and rho 3C2 antibodies to immobilized rhodopsin was inhibited with peptides of length 1'-8' and longer. Antibody rho 1D4 binding was not inhibited by peptides 2'-13' or 3'-18', indicating that the C-terminal alanine residue of rhodopsin was required. Similar competitive inhibition studies indicated that the antibody rho 3A6 required peptides of length 1'-12' and longer whereas rho 1C5 required peptide 1'-18'. Peptide 3'-18' was as effective as 1'-18' in inhibiting rho 3A6 binding to rhodopsin, but replacement of glutamic acid in position 8' with glutamine abolished competition. This substitution had little effect on the binding of antibody rho 1C5. Thus, Glu8' was essential for rho 3A6 binding but not for the binding of the rho 1C5 antibody. Cleavage of the seven amino acid C-terminus from rhodopsin and further cleavage to F1 (Mr 25 000) and F2 (Mr 12 000) fragments with Staphylococcus aureus V8 protease abolished binding of rho 1D4 antibody to the membrane-bound rhodopsin fragments.(ABSTRACT TRUNCATED AT 250 WORDS)     

A novel feature extraction approach for microarray data based on multi-algorithm fusion

Feature extraction is one of the most important and effective method to reduce dimension in data mining, with emerging of high dimensional data such as microarray gene expression data. Feature extraction for gene selection, mainly serves two purposes. One is to identify certain disease-related genes. The other is to find a compact set of discriminative genes to build a pattern classifier with reduced complexity and improved generalization capabilities. Depending on the purpose of gene selection, two types of feature extraction algorithms including ranking-based feature extraction and set-based feature extraction are employed in microarray gene expression data analysis. In ranking-based feature extraction, features are evaluated on an individual basis, without considering inter-relationship between features in general, while set-based feature extraction evaluates features based on their role in a feature set by taking into account dependency between features. Just as learning methods, feature extraction has a problem in its generalization ability, which is robustness. However, the issue of robustness is often overlooked in feature extraction. In order to improve the accuracy and robustness of feature extraction for microarray data, a novel approach based on multi-algorithm fusion is proposed. By fusing different types of feature extraction algorithms to select the feature from the samples set, the proposed approach is able to improve feature extraction performance. The new approach is tested against gene expression dataset including Colon cancer data, CNS data, DLBCL data, and Leukemia data. The testing results show that the performance of this algorithm is better than existing solutions.     

Binding sites for tachykinin peptides in the brain and stomach of the dogfish, Scyliorhinus canicula.

In membranes of dogfish brain and stomach, two binding sites for tachykinins were identified. One site specifically bound [125I]-Bolton-Hunter substance P (BH-SP) and the rank potency of tachykinins to compete for BH-SP binding revealed similarities with the rank potency of an NK1 receptor. The pharmacology of the other site, which specifically bound [125I]-Bolton-Hunter scyliorhinin II (BH-Scy II), did not resemble any of the mammalian tachykinin receptors. The rank potency to inhibit BH-Scy II binding to this second site was: scyliorhinin II approximately scyliorhinin I greater than eledoisin approximately substance P approximately neurokinin A greater than phyllomedusin approximately physalaemin greater than [Sar9Met(O2)11]substance P. Neurokinin B and senktide did not displace BH-Scy II binding. In addition, nucleotide analogues inhibited BH-SP binding but not BH-Scy II binding. Our binding data suggest the existence of a mammalian-like NK1 receptor and of a nonmammalian tachykinin receptor in the dogfish.     

A novel approach for assessing factors affecting biodiversity based on networks analysis

We propose in this work a novel approach aiming at assessing cause and effect relationships between variables that can affect target biodiversity issues. These cause–effect relations are used to build a network whose nodes represent variables linked by directed arcs. The arcs have associated a value that represents trends of cause–effect relations. An important novelty of this approach is the use of product and addition operations between trends of cause–effect relations for assessing factors that can affect target variables. For the analysis of the network we use the concept of paths. Paths are defined as sequences of cause–effect relations from source variables to target variables. For example, the path from population increment that causes effects on the increment of transport routes, which in turn causes effects on the loss of vegetation cover. This approach was applied to the assessment of vegetation cover in the Morelos State, México during the period 2000–2010. The results show a promising practical alternative to assess the potential effects on biodiversity issues based on the analysis of the paths represented in the network.     

Protein A–calmodulin fusions: a novel approach for investigating calmodulin function in yeast

A novel gene fusion approach which may be of more general use has been developed for investigating the function of calmodulin in the budding yeast Saccharomyces cerevisiae. By fusing a portion of the Staphylococcus aureus spa gene (encoding protein A) to CMD1, the S. cerevisiae gene encoding calmodulin, we have generated a yeast calmodulin with an affinity tag able to bind immunoglobulins. The chimaeric protein A-calmodulin (ProtA-CaM) polypeptide functions in vivo and shows Ca(2+)-dependent binding to calmodulin target proteins. The spa-CMD1 fusion has been used (i) to prepare (by affinity chromatography) a fraction of yeast proteins which interact with calmodulin, (ii) to isolate genes encoding calmodulin target proteins by direct screening of an expression library, and (iii) to visualize calmodulin-binding proteins in crude extracts by Western blot analysis.     

Characterization of aPY-like peptides in anglerfish brain using a novel radioimmunoassay for aPY-Gly

Anglerfish peptide YG (aPY) was isolated from pancreatic islets of the anglerfish. Subsequent immunohistochemical and biochemical analyses demonstrated that anglerfish islet cells synthesize aPY. We have now developed and characterized a radioimmunoassay (RIA) for aPY and have examined extracts of anglerfish brain for aPY-like peptides. Brain extracts were subjected to gel filtration and high performance liquid chromatography (HPLC). Fractions from HPLC eluates were analyzed in the aPY RIA and also in a neuropeptide Y (NPY) RIA. A single peak of aPY-like immunoreactivity eluted from HPLC columns. The elution position of this aPY-like peptide coincided exactly with the aPY-Gly marker under several gradient conditions. Results from the NPY RIA confirmed the presence of several molecular forms of NPY-like immunoreactive peptides in the anglerfish brain. These results demonstrate the utility of the newly developed aPY RIA for studies of anglerfish brain peptides and extend our previous immunohistochemical demonstration of aPY-like staining in the anglerfish brain.