Current Pharmaceutical Biotechnology - Volume 5, Issue 1, 2004

The collection of articles published under the motto “The way down from single genes and proteins to single molecules” is covering the results of groundbreaking developments of the recent years. They include single molecule detection yielding ultimate sensitivity and closely linked to the analysis of molecular noise by correlation spectroscopy. Several important examples from the field of nucleic acid as well as protein analysis as diagnostic tools are presented as well as the impact on the studies of single cells and biomembranes. The development of high sensitivity analysis at the single molecule level has in turn prompted the development of high-throughput protocols nowadays used in drug screening. In the attempt to make the vast and still growing knowledge of the human genome available for understanding the ultimate cause of disease and their therapy, these four special issues will fulfill a very important goal.

RNA interference (RNAi) has emerged as a powerful tool for the silencing of gene expression in animals and plants. RNAi is mediated by approximately 21-nt small interfering RNAs (siRNAs), which are originally produced from larger double stranded RNAs (dsRNAs) in vivo through the action of Dicer. Recently, many groups have reported systems designed to express siRNAs in mammalian cells through transfection of either oligonucleotides or plasmids encoding siRNAs. Although the use of siRNAs to silence genes in vertebrate cells was only reported three years ago, the emerging literature indicates that most vertebrate genes can be studied with this technology. This review summarizes some approaches to generate siRNAs, the delivery and application of siRNAs to target cells and the utility of siRNAs as analytical and potential therapeutic tools.

Immunoassays, or assays that are using antibodies as the specific binding reagents, have become one of the most common methodologies in diagnostic laboratories. In this paper we review different configurations of immunoassays as applied to a variety of analytes and sensitivity limits, along with common detection techniques and strategies. Progress in developing of ultra high affinity antibodies as a direction to improved immunoassays is also reviewed. Finally, we specifically concentrate on determination of antibody binding constants and performing immunoassays at the single molecule level using Fluorescence Correlation Spectroscopy (FCS). This technique has become a powerful tool in molecular binding characterizations and assay development, and possibly will grow into a quantitative analytical method suitable for diagnostic tests.

This paper reviews progress towards the customised generation of proteins for applications as therapeutics, diagnostics and in proteomics. It particularly focuses on combinatorial approaches where proteins with pre-defined biochemical and biophysical characteristics are selected from large variant libraries.

Peptides are key to modern drug discovery. This article reviews the requirements for bulk production of peptides and how it affects research and production of smaller scales. Peptides, as modern drugs, are currently produced in millions in mg-scale for research purpose, in order to better understand the function of biological systems. Some newly discovered sequences form the basis of modern drugs and are now produced in multi-tons. The most popular example is the T-20 peptide (Fuzeon), which is the first peptide produced at such scale by a combination of solid phase and solution phase methodologies. This particular peptide sequence has the ability to dock on the surface of the HIV virus and block the virus from entering into a human blood cell, helping patient life conditions. A multi-ton scale production was made necessary based on the high number of patients, the socio-economical importance of the disease and the strong support by governmental institutions such as the FDA. Fuzeon is the first peptide-based drug that is produced in multi-tons on solid support. This had revolutionary effects on the whole peptide synthesis techniques in general including the production of the starting materials. It also had a positive impact on the cost-effectiveness of peptides for research, as the standard technique for producing peptides in research quantities is solid phase chemistry. The decrease of the cost of all starting materials will lead to an increase of the number of produced peptides, which will certainly bring new interesting and effective sequences to be used as novel drugs.

The early diagnosis of cancer at a curable stage is crucial for the successful treatment of this disease. Most of the currently used tumor assays appear too late and rely on single biomarkers with high false-negative and/or falsepositive rates. As an additional burden for the patient, the traditional assays often require biopsy material instead of less invasively taken samples like serum. With the hope for more reliable DNA- and RNA-based screening tools, the research activities of the past 20 years have focused on the genomic characteristics of cancer cells. But, up to now, the output from this strategy has been disappointingly low and the disillusionment is paired with a return to proteins as the real key players in all physiological and pathological processes. Meanwhile, comparative protein profiling is generally acknowledged as a promising way for the detection of specific and predictive protein patterns reflecting certain stages of cancer without dependency on single markers. To meet the new technological demands, the ProteinChip® Biomarker System was developed for the Expression Difference Mapping™ - analysis of several hundreds of samples per day on a single, uncomplicated platform; with software support for the construction of multi-marker predictive models. The Interaction Discovery Mapping - platform is introduced as the next methodical step for investigations about protein binding partners of possible importance in diagnosis and therapy. This review summarizes the current state in cancer diagnosis, provides an introduction into the ProteinChip technology, and gives an update on publications and research collaborations in SELDI-based tumor marker discovery.

The most challenging and fruitful biomedical research endeavor of this decade will be the mapping of cell signaling systems and establishing their linkages to normal and disease-related processes. Amongst other things, the Human Genome Sequencing Project has greatly facilitated MALDI-TOF mass spectrometry identification of proteins that have been resolved by standard 2D gel electrophoresis. However, the low abundance of protein kinases and other signal transduction proteins has rendered their analyses particularly problematic without some means of purification and enrichment from cell and tissue lysates. Antibodies have been the most specific affinity probes for tracking target proteins, but their variable quality and high cost preclude their deployment in most discovery-based proteomics studies. Current multi-immunoblotting techniques can permit the probing of a single mini-SDS-PAGE gel with 50 or more antibodies at a time to monitor large changes in the expression and phosphorylation states of signaling proteins. The development of new affinity probes to replace antibodies is necessary to drive large scale proteomics studies. Such affinity probes could include short peptide antibody mimetics (PAM's) and oligonucleotide aptamers that when spotted in 2D array formats (e.g. membrane macroarrays, glass microarrays) or presented on specific beads (e.g. Luminex-beads) can capture target proteins for their specific enrichment. The bound target proteins can then be detected using reporter antibodies or other specific probes for their quantitation by high throughput systems. These new proteomics methodologies will accelerate assessment of specific protein expression, post-translational modification, protein-protein interactions and protein-drug interactions to provide a more holistic view of cellular operations and how they might be manipulated under pathological circumstances.

Proteomics technologies are under continuous improvements and new technologies are introduced. Nowadays high throughput acquisition of proteome data is possible. The young and rapidly emerging field of bioinformatics in proteomics is introducing new algorithms to handle large and heterogeneous data sets and to improve the knowledge discovery process. For example new algorithms for image analysis of two dimensional gels have been developed within the last five years Within mass spectrometry data analysis algorithms for peptide mass fingerprinting (PMF) and peptide fragmentation fingerprinting (PFF) have been developed. Local proteomics bioinformatics platforms emerge as data management systems and knowledge bases in Proteomics. We review recent developments in bioinformatics for proteomics with emphasis on expression proteomics.

So far, chemists, molecular biologists and biochemists have reaped the greatest benefits from mass spectrometry (Aebersold et al., 2003). This type of analysis could, however, be useful in many fields. Mass spectrometry is on its way to the doctor's office (Pusch et al., 2003; Foldes-Papp et al., 2002; Henry 1999). The article is focused on laser-activated microprobe mass analysis (LAMMA) and inductively coupled argon plasma mass spectrometry (ICP-MS). Potential applications of the two types of mass spectrometry are demonstrated in clinical medicine. It is the first comprehensive review on qualitative characterization of carbonaceous compounds in lung tissue samples in situ and quantitative trace element determination in body fluids.

Moderate hyperhomocysteinemia is associated with an increased risk of atherosclerosis, thrombosis and neurodegenerative diseases. Homocysteine accumulation in the blood can be due to many underlying causes, which may interact with each other, e.g. genetic disposition and B-vitamin status. The role of the sulfur-containing amino acid homocysteine in the pathogenesis of diseases remains unclear, even if many studies suggest a causal relationship between homocysteine-mediated processes like oxidative stress, NO-inactivation and endothelial deficiency and atherogenesis. Proposed mechanisms of action of homocysteine are discussed, and the question is addressed, whether effects that are attributed to homocysteine, are not rather the consequence of folate and vitamin B12-deficiency. Deficiency of these Bvitamins in parallel with moderate hyperhomocysteinemia is often found in patients with enhanced activation of the cellular immune system, like Alzheimer´s disease, rheumatoid arthritis and also vascular diseases. In patients with these diseases an association between homocysteine metabolism, oxidative stress and immune activation exists. On the one hand proliferation of immunocompetent cells having an enhanced demand for B-vitamins leads to the accumulation of homocysteine. On the other hand macrophages stimulated by TH1-type cytokine interferon-γ form reactive oxygen species (ROS), which oxidize antioxidants, lipoproteins and oxidation-sensitive B-vitamins. Thereby Th1-type immune response could contribute importantly to the development of hyperhomocysteinemia, and may also be a major determinant of disease progression.

Much research effort has been made to realize a single-molecule sequencing. Central to this project are two enzymatic tasks that challenged several biochemists during the last years. They searched for polymerases for copying a DNA target into completely fluorophore-labeled DNA as well as for handling this new DNA derivative. Furthermore, they studied exonucleases for the sequential hydrolysis of completely dye-labeled DNA and explored optimal conditions for future application on the single-molecule level. In this article, the recent advances will be summarized from the biochemist's point of view.