Current Medicinal Chemistry - Volume 11, Issue 16, 2004

During the last two decades, the number of sequence-known proteins has increased rapidly. In contrast, the corresponding increment for structure-known proteins is much slower. The unbalanced situation has critically limited our ability to understand the molecular mechanism of proteins and conduct structurebased drug design by timely using the updated information of newly found sequences. Therefore, it is highly desired to develop an automated method for fast deriving the 3D (3-dimensional) structure of a protein from its sequence. Under such a circumstance, the structural bioinformatics was emerging naturally as the time required. In this review, three main strategies developed in structural bioinformatics, i.e., pure energetic approach, heuristic approach, and homology modeling approach, as well as their underlying principles, are briefly introduced. Meanwhile, a series of demonstrations are presented to show how the structural bioinformatics has been applied to timely derive the 3D structures of some functionally important proteins, helping to understand their action mechanisms and stimulating the course of drug discovery. Also, the limitation of these approaches and the future challenges of structural bioinformatics are briefly addressed.

Tremendous progress in DNA sequencing has yielded the genomes of a host of important organisms. The utilisation of these resources requires understanding of the function of each gene. Standard methods of functional assignment involve sequence alignment to a gene of known function; however such methods often fail to find any significant matches. Here we discuss a number of recent alternative methods that may be of use when sequence alignment fails. Function can be defined in a number of ways including E.C. number and MIPS and KEGG functional classes. Phylogenetic profiles show the pattern of presence or absence of a protein between genomes. Protein-protein interactions can be identified by searching for interacting pairs of proteins that are fused to a single protein chain in another organism. The gene neighbour method uses the observation that if the genes that encode two proteins are close on a chromosome, the proteins tend to be functionally related. More general methods use sequence properties such as amino acid composition, mean hydrophobicity, predicted secondary structure and post-translational modification sites. Data mining methods devise rules in the form of IF... THEN statements that make predictions of function using sequence based attributes, predicted secondary structure and sequence similarity. Finally, structural features can be used, after modelling the structure of a protein from its sequence or solving its structure. Protein fold class can be strongly indicative of function, while other structural features, such as secondary structure content, cleft size and 3D structural motifs are also useful.

DNA microarrays are devices capable of detecting the identity and abundance of numerous DNA or RNA segments in samples. They are used for analyzing gene expressions, identifying genetic markers and detecting mutations on a genomic scale. The fundamental chemical mechanism of DNA microarrays is the hybridization between probes and targets due to the hydrogen bonds of nucleotide base pairing. Since the cross hybridization is inevitable, and probes or targets may form undesirable secondary or tertiary structures, the microarray data contain noise and depend on experimental conditions. It is crucial to apply proper statistical algorithms to obtain useful signals from noisy data. After we obtained the signals of a large amount of probes, we need to derive the biomedical information such as the existence of a transcript in a cell, the difference of expression levels of a gene in multiple samples, and the type of a genetic marker. Furthermore, after the expression levels of thousands of genes or the genotypes of thousands of single nucleotide polymorphisms are determined, it is usually important to find a small number of genes or markers that are related to a disease, individual reactions to drugs, or other phenotypes. All these applications need careful data analyses and reliable algorithms.

P-selectin (CD62P) is a member of the selectin family of cell adhesion molecules. It is expressed on stimulated endothelial cells and activated platelets and mediates leukocyte rolling on stimulated endothelial cells and heterotypic aggregation of activated platelets onto leukocytes. It also mediates heterotypic aggregation of activated platelets to cancer cells and adhesion of cancer cells to stimulated endothelial cells. Using P-selectin knockout mice, the importance of P-selectin-mediated cell adhesive interactions in the pathogeneses of inflammation, thrombosis, growth and metastasis of cancers has been clearly demonstrated. Here we will summarize the current knowledge and highlight the important progress in the biomedical research of P-selectin biology, providing a suitable target for therapeutic interventions developed through both experimental and bioinformatic approaches.

Iron is essential for all human cells as well as neoplastic cells and invading microbes. Natural and synthetic iron chelators could affect biological processes involving iron and other metal ions in health and disease states. Iron overload is the most common metal toxicity condition worldwide. There are currently two iron chelating drugs, which are mostly used for the treatment of thalassaemia and other conditions of transfusional iron overload. Deferoxamine was until recently the only approved iron chelating drug, which is effective but very expensive and administered parenterally resulting in low compliance. Deferiprone (L1 or 1,2- dimethyl-3-hydroxypyrid-4-one) is the world's first and only orally active iron chelating drug, which is effective and inexpensive to synthesise thus increasing the prospects of making it available to most thalassaemia patients in third world countries who are not currently receiving any form of chelation therapy. Deferiprone has equivalent iron removal efficacy and comparable toxicity to deferoxamine. There are at least four other known iron chelators, which are currently being developed. Even if successful, these are not expected to become available for clinical use in the next five years and to be as inexpensive as deferiprone. The variation in the chemical, biological, pharmacological, toxicological and other properties of the chelating drugs and experimental chelators provide evidence of the difference in the mode of action of chelators and the need to identify and select molecular structures and substituents based on structure / activity correlations for specific pharmacological activity. Such information may increase the prospects of designing new chelating drugs, which could be targeted and act on different tissues, organs, proteins and iron pools that play important role not only in the treatment of iron overload but also in other diseases of iron and other metal imbalace and toxicity including free radical damage. Chelating drugs could also be designed, which could modify the enzymatic activity of iron and other metal containing enzymes, some of which play a key role in many diseases such as cancer, inflammation and atherosclerosis. Other applications of iron chelating drugs could involve the detoxification of toxic metals with similar metabolic pathways to iron such as Al, Cu, Ga, In, U and Pu.

The term protein glycation summarizes non-enzymatic reactions between amino groups of proteins and sugars or sugar degradation products, leading to early glycation products (intact sugar attached) and advanced glycation end-products (AGEs). Protein glycation is involved in the progression of several diseases, such as diabetes, uremia, and atherosclerosis. However, qualitative and quantitative analysis of in vitro or in vivo glycated proteins is still a challenging task. The introduction of matrix-assisted laser desorption ionization time-of-flight technique (MALDI-TOF) changed mass spectrometry (MS) into a valuable tool for biomedical analysis, because the soft ionization procedure allows the measurement of proteins up to 100 kDa. In the last few years, MALDI-TOF-MS was applied to the investigation of glycation processes: the analyses of plasma proteins from diabetic or uremic patients allowed a precise determination of the average number of sugar residues attached to serum albumin or immunoglobulins of each patient. Thus, a more individualized diagnosis of each patient was achieved by MALDI-TOF-MS than by other diagnostic tools. In a similar way, the glycation rate of hemoglobin, isolated from diabetic blood and of β-2-microglobulin isolated from amyloid plaques from uremic patients was determined. The application of MALDI-TOF-MS for in vitro studies revealed important new insights into glycation mechanisms. Whereas the measurement of the intact proteins allows the determination of the average glycation rate, peptide mapping prior to MALDI-TOF-MS can reveal the exact structures of the glycation products and the glycation site. Furthermore, when the unmodified peptide is used as internal standard, MALDI-TOF-MS can also be used for reliable, site specific relative quantification of defined glycation products.

A number of studies have demonstrated that malignant transformation is associated with an increase in glycolytic flux and in anaerobic and aerobic cellular lactate excretion. Using quantitative bioluminescence imaging in various primary carcinomas in patients (uterine cervix, head and neck, colorectal region) at first diagnosis of the disease, we showed that lactate concentrations in tumors in vivo could be relatively low or extremely high (up to 40 μmol / g) in different individual tumors or within the same lesion. In all tumor entities investigated, high molar concentrations of lactate were correlated with a high incidence of distant metastasis already in an early stage of the disease. Low lactate tumors (< median of approx. 8 μmol / g) were associated with both a longer overall and disease free survival compared to high lactate lesions (lactate > approx. 8 μmol / g). Lactate dehydrogenase was found to be upregulated in most of these tumors compared to surrounding normal tissue. Numerous recent reports support these data by demonstrating various biological activities of lactate that can enhance the malignant behavior of cancer cells. These mechanisms include the activation of hyaluronan synthesis by tumor-associated fibroblasts, upregulation of VEGF and of HIF-1alpha, and direct enhancement of cellular motility which generates favorable conditions for metastatic spread. Thus, lactate accumulation not only mirrors but also actively enhances the degree of tumor malignancy. We propose that determination of lactate in primary tumors may serve as a basis for a novel metabolic classification which can lead to an improvement of prognosis and therapy in clinical oncology.

TNF is a major proinflammatory cytokine, which exerts its effects through two different receptors known as TNF-R1 and TNF-R2. Whereas TNF-R1 induced signaling pathways have been very well characterized during the past years, TNF-R2 has been much less well studied. Nevertheless, the function of TNF-R2 should not be underestimated, the more because this receptor shows a much more restricted but inducible expression. Several inflammatory diseases and cancers show upregulated levels of soluble TNF-R2 or are associated with TNF-R2 polymorphisms, implicating an important role for TNF-R2 as a therapeutic target. Here we will review the mechanisms that regulate TNF-R2 expression, as well as discuss TNF-R2 induced signal transduction and cross-talk with TNF-R1.

The development of bacterial resistance is a significant problem in the treatment of infection, and the importance of research directed toward the discovery of novel agents to treat infections cannot be underestimated. In the past, discovery programs have focused on modification of natural products or existing classes of marketed antibacterial agents. A significant period of time lapsed between the introduction of the nalidixic acid-based quinolones and the next novel antibacterial agent (Zyvox™). However, the advent of the “genomics era” has provided a wealth of new targets that afford the opportunity to discover novel antibacterial agents. This review reports on the state of antibacterial research directed toward the development of novel antibacterial agents with novel mechanisms of action for the calendar year, 2002. While variations on existing drug classes continue to appear, we have chosen to limit our discussion to novel classes of antibacterial agents which have not yet been marketed.