Current Topics in Medicinal Chemistry - Volume 3, Issue 6, 2003

Cell motility is a central feature of a range of normal and pathological processes, including embryonic development, tissue repair, immune cell function, angiogenesis, and cancer metastasis. The dynamics of the actin cytoskeleton power cell migration. A large number of proteins are known or suspected to play roles in regulating actin dynamics. While there are now many available small molecules that target the actin cytoskeleton directly, there is a paucity of specific inhibitors of actin-binding proteins and other immediate regulators of actin dynamics and cell movement. This makes the field of exceptional interest as a meeting place between the goals of chemical biology and the needs of cell biology. Furthermore, while regulators of the cell cycle have been recognized for some time as targets for anti-cancer drug development, controlling actin dynamics and cell motility as a therapeutic approach has received scant attention in comparison until recently. This review deals with small-molecule inhibitors of actin dynamics as they relate to cell shape change and motility, from compounds targeting actin directly to those targeting proteins involved in the fundamental control of the actin cytoskeleton.

As the human genome sequence is nearly deciphered, it is important to turn the attention to the physiological functions of the genes. Thus, the study of the gene products, the proteins, is the next big challenge. The proteins, however, are not the final gene products in many cases. It has been shown that carbohydrates participate in posttranslational modifications and in many other functional regulations, hence the study of the glycome, the entire collection of carbohydrates is essential in order to determine the functions of all genes, and will greatly enhance the field of chemical genetics. Known biological function / targets of carbohydrates and combinatorial synthesis & structural analysis of natural / non-natural carbohydrates are surveyed in this review. Methods to search for new biological targets that include carbohydrate mimetics and carbohydrate scaffolds along with chip technology, are also presented.

Expression of the genome is primarily regulated at the level of transcription by gene-specific transcription factors, which recognize specific DNA sequences to activate or inhibit transcription. The ability to control gene expression at will would provide scientists with a powerful tool for biotechnology and drug-discovery research. Over the last decade or so, researchers have made great strides in our understanding of the structures and mechanisms of action of naturally occurring transcription factors. Such research has revealed that members of the Cys2-His2 zinc finger family of transcription factors consist of functional modules that recognize a wide variety of DNA sequences. This review describes recent advances in the development of novel methods to design and construct artificial transcription factors to control gene expression at will. The applications of artificial transcription factors in the areas of medicine and biotechnology are discussed.

Supertargeted chemistry is the study of how chemical structures localize or direct molecules to specific sub-cellular compartments in living cells. Supertargeting can be used to increase the activity or specificity of an inhibitor against its target, by concentrating the inhibitor in the particular organelle where the target is active. But, unlike structure-activity relationships, structure-localization relationships are not a simple function of compound concentration. Various aspects of mitochondrial physiology, proteomics and pharmacology have made this the organelle of choice for supertargeting studies. While exploration of supertargeting strategies to this and the other organelles has been limited, combinatorial chemical libraries of fluorescent molecules are beginning to illuminate new supertargeting mechanisms at the sub-cellular level. Moreover, predictive approaches that determine the relationship between a molecule's features and sub-cellular localization are being developed in the related field of functional genomics. Applied to the small molecules, such strategies could prove useful for predicting structure-localization relationships amongst large libraries of compounds.

The study of complex biological systems requires methods to perturb the system in complex yet controlled ways to elucidate mechanisms and dynamic interactions, and to recreate in vivo conditions in flexible in vitro set-ups. This paper reviews recent advances in the use of micro- and nanotechnologies in the study of complex biological systems and the advantages they provide in these two areas. Particularly useful for controlling the chemical and mechanical microenvironments of cells is a set of techniques called soft lithography, whereby elastomeric materials are used to transfer and generate micro- and nanoscale patterns. Examples of some of the capabilities of soft lithography include the use of elastomeric stamps to generate micropatterns of protein and the use of elastomeric channels to localize chemicals with subcellular spatial resolutions. These types of biological micro- and nanotechnologies combined with mathematical modeling will propel our understandings of cellular and subcellular physiology to new heights.

Latest microarray-based technologies, including small molecule-, peptide-, protein- and cell-based arrays, and their applications in the field of proteomics are reviewed.

The mechanism of mammalian gene regulation is highly complex, involving multiple layers of feedback control loops and dynamic chromatin remodeling. The current approach used to dissect the genetic circuitry of mammalian gene regulation utilizes somatic cells and protein fusion as a means to modulate protein interactions. This approach has several limitations that include (i) genome inaccessibility, (ii) high background interferences and, (iii) limited cellular phenotypes. Previously, the two broad fields of research “control of gene expression” and “stem cell biology” had been pursued separately by cell biologists; this review outlines evidence suggesting that integration of these two fields would provide a comprehensive platform for interdisciplinary research seeking to address mechanistic questions concerning gene regulationthat could have enormous implication for the development of therapeutic applications.