Biospecific interaction analysis: a tool for drug discovery and development

Transcription factor decoy: a pre-transcriptional approach for gene downregulation purpose in cancer

Gene therapy as a therapeutic approach has been the dream for many scientists around the globe. Many strategies have been proposed and applied for this purpose, yet the void for a functional safe method is still apparent. Since most of the diseases are caused by undesirable upregulation (oncogenes) or downregulation (tumor suppressor genes) of genes, major gene therapy's techniques affect gene expression. Most of the methods are used in post-transcriptional level such as RNA inhibitory (RNAi) and splice-switching oligonucleotides (SSOs). RNAi blocks messenger RNA (mRNA) translation by mRNA degradation or interruption between attachments of mRNA with ribosomes' subunits. However, one of the novel methods is the usage of transcription factor targeted decoys. DNA decoys are the new generation of functional gene downregulatory oligonucleotides which compete with specific binding sites of transcription factors. Considering the exponential growth of this technique in both in vitro and in vivo studies, in this paper, we aim to line out the description, design, and application of decoys in research and therapy.

Label-free biosensors based on optically responsive nanocomposite layers: sensitivity and dynamic range

Core-shell nanoparticle layers have proven to be a promising tool for the label-free detection of binding events. Upon reflection of white light, they exhibit pronounced extinction peaks in the UV/vis and NIR regime of the electromagnetic spectrum, which shift to higher wavelengths when molecules are adsorbed. Beside drastic simplification of the instrumentation and related reduction in cost, a significantly stronger response toward alkanethiol adsorption has been observed in previous experiments than in conventional surface plasmon resonance (SPR). However, as the amount of molecules deposited onto the nanoparticle films was unknown, no quantitative relationship could be established between the measured wavelength shifts and the surface mass density of the adsorbate. In order to facilitate quantitative molecule detection, self-assembled monolayers (SAMs) of simple and ethylene glycol (EG) terminated alkanethiols with various chain lengths were prepared on the nanoparticle-coated substrates. The measured red-shift of the extinction spectrum upon molecule adsorption was related to the amount of adsorbate as determined by X-ray photoelectron spectroscopy (XPS). For the whole range of film thicknesses studied, a linear relationship is found yielding a sensitivity factor of 0.027 nm/(ng/cm (2)). As proven by enzyme-linked immunosorbent assay (ELISA), such determined sensitivity factor can also be used to correctly predict the amount of surface-bound protein in immunoreactions from the measured wavelength shifts. It is concluded that the decay length of the evanescent electric field associated with the nanoparticle sensors is more than 100 nm and, thus, significantly larger than that observed for localized surface plasmons excited in small isolated metal clusters.

Introduction to Chemical Proteomics for Drug Discovery and Development

A fundamental goal of chemical proteomics is to identify target proteins for bioactive small molecules and then apply them to drug discovery and development as valid and drugable targets. Here, we introduce integrated technologies for the rapid identification of target proteins, methodologies for validating them as drugable targets, and applications of chemical proteomics in drug discovery and development.

Characterisation of the RNA binding properties of the coronavirus infectious bronchitis virus nucleocapsid protein amino-terminal region

The coronavirus nucleocapsid (N) protein binds viral RNA to form the ribonucleocapsid and regulate RNA synthesis. The interaction of N protein with viral RNA was investigated using circular dichroism and surface plasmon resonance. N protein underwent a conformational change upon binding viral RNA and the data indicated electrostatic interactions were involved in the binding of the protein to RNA. Kinetic analysis suggested the amino-terminal region facilitates long-range non-specific interactions between N protein and viral RNA, thus bringing the RNA into close proximity to N protein allowing specific contacts to form via a 'lure' and 'lock' mechanism.

Proteomics in developmental toxicology

The objective of this presentation is to review the major proteomic technologies available to developmental toxicologists and, when possible, to provide examples of how various proteomic technologies have been used in developmental toxicology or toxicology in general. The field of proteomics is too broad for us to go into great depth about each technology, so we have attempted to provide brief overviews supplemented with many references that cover the subjects in more detail. Proteomics tools produce a global view of complex biological systems by examining complex protein mixtures using large-scale, high-throughput technologies. These technologies speed up the process of protein separation, quantification, and identification. As an important complement to genomics, proteomics allows for the examination of the entire complement of proteins in an organism, tissue, or cell-type. Current proteomics technologies not only identify protein expression, but also post-translational modifications and protein interactions. The field of proteomics is expanding rapidly to provide greater volume and quality of protein information to help understand the multifaceted nature of biological systems.

Selectins-an emerging target for drug delivery

Selectins are multifunctional adhesion molecules that mediate the initial interactions between circulating leukocytes and cells of the endothelium. First identified over a decade ago, selectins have provided insight into areas as diverse as normal lymphocyte homing, leukocyte recruitment during inflammatory responses, carbohydrate ligand biosynthesis and adhesion-mediated signalling. Of late, selectins were introduced as targets for drug delivery in the development of new anti-inflammatory therapeutics and in anti-cancer therapy. This review will examine the selectins and their ligands with a focus on recent findings on their role in physiology and pathophysiology as well as the emerging role of selectins as targets in controlled drug delivery.

Liposome-Based Nanocapsules

Here we present three different types of mechanically stable nanometer-sized hollow capsules. The common point of the currently developed systems in our laboratory is that they are liposome based. Biomolecules can be used to functionalize lipid vesicles to create a new type of intelligent material. For example, insertion of membrane channels into the capsule wall can modify the permeability. Covalent binding of antibodies allows targeting of the capsule to specific sites. Liposomes loaded with enzymes may provide an optimal environment for them with respect to the maximal turnover and may stabilize the enzyme. However, the main drawback of liposomes is their instability in biological media as well as their sensitivity to many external parameters such as temperature or osmotic pressure. To increase their stability we follow different strategies: 1) polymerize a two-dimensional network in the hydrophobic core of the membrane; 2) coat the liposome with a polyelectrolyte shell; or 3) add surface active polymers to form mixed vesicular structures.

Functional protein microarrays: ripe for discovery

The manufacture and use of protein microarrays with correctly folded and functional content presents significant challenges. Despite this, the feasibility and utility of such undertakings are now clear, and exciting progress has recently been demonstrated in the areas of content generation, printing strategies and protein immobilization. More importantly, we are now beginning to enjoy the fruits of these efforts as functional protein microarrays are being increasingly employed for biological discovery purposes. Recent examples of this include the characterization of autoantibody responses, antibody specificity profiling, protein-protein domain interaction profiling and a comprehensive characterization of coiled-coil interactions. The best, however, is yet to come.

Transcription factor decoy (TFD) in breast cancer research and treatment

Synthetic oligonucleotides have recently been the object of many investigations aimed to develop sequence-selective compounds able to modulate, either positively or negatively, transcription of eukaryotic and viral genes. Alteration of transcription could be obtained by using synthetic oligonucleotides mimicking target sites of transcription factors (the transcription factor decoy -TFD- approach). This could lead to either inhibition or activation of gene expression, depending on the biological functions of the target transcription factors. Since several transcription factors are involved in tumor onset and progression, this issue is of great interest in order to design anti-tumor compounds. In addition to oligonucleotides, peptide nucleic acids (PNA) can be proposed for the modulation of gene expression. In this respect, double-stranded PNA-DNA chimeras have been shown to be capable to exhibit strong decoy activity. In the case of treatment of breast cancer cells, decoy oligonucleotides mimicking CRE binding sites, promoter region of estrogen receptor alpha gene, NF-kB binding sites have been used with promising results. Therefore, the transcription factor decoy approach could be object of further studies to develop protocols for the treatment of breast cancer. In the future, transcription factors regulating cell cycle, hormone-dependent differentiation, tumor invasion and metastasis are expected to be suitable targets for transcription factor decoy.