Current Topics in Medicinal Chemistry - Volume 2, Issue 3, 2002

The new millennium has ushered in an era of science that will revolutionize a great majority of our daily activities. That revolution is being experienced by a growing number of the population who are pushing the average life expectancy closer to the 80-year mark. The primary reason for this increase is the changes we have made in the last 2-3 decades both in how we live our lives as well as how we treat our maladies when they arise. The advent of new techniques in diagnostics and surgery have allowed many to survive debilitating illnesses when their chances would have been slim only a few years ago. In addition, several new therapeutic agents have been developed in the latter part of the 20th century that have improved our quality of life and increased our overall survival time. New medicines to treat cardiovascular, degenerative, infectious, and neoplastic diseases are rapidly being discovered in an effort to further lengthen our lifetimes. The processes used by academic and industrial scientist to discover new drugs has recently experienced a true renaissance with many new and exciting techniques being developed in only the past 5-10 years. In this review, we will attempt to outline these latest protocols that chemists and biomedical scientist are currently employing to rapidly bring new drugs to the clinic.

Increasing insight into the genetics and molecular biology of cancer has resulted in the identification of an increasing number of potential molecular targets for anti-cancer drug discovery and development. These targets can be approached through exploitation of emerging structural biology,”rational“ drug design, screening of chemical libraries, or a combination of these methods. In this article we discuss the application of high-throughput screening to anti-cancer drug discovery, with special reference to approaches used at the U.S. National Cancer Institute.

Structure-based drug design is an organized, multidisciplinary endeavor undertaken by scientists from many different scientific fields. The success of structurebased drug design was only made possible by advances in structure biology that provides the three-dimensional structure of the drug design target with which small molecular chemical ligands interact. Visualization of the conformation and interactions of a small molecule ligand bound to the protein target in the co-crystal structure of the protein ligand complex enables the design of new chemical compounds with improved binding affinity and specificity.With the advances in molecular biology, lab automation, and computational science, genomic data have now become available for the human genome, as well as various other organisms. The pharmaceutical industry is currently putting forth tremendous effort in the area of functional genomics and structural genomics in attempts to decipher functions and structures of protein encoded by genes, with the ultimate goal of identifying novel targets for drug discovery and development.This chapter discusses the significant impact made by recombinant DNA technology and protein engineering on structural biology and, more specifically, on structure-based drug design.

One of the major events occurring at biological interfaces is the specific recognition of bioactive ligands by their receptor proteins. The elucidation of interacting partners is an immediate entrance into the discovery of medicinal leads. The method of photoaffinity labeling enables the direct probing of target protein through a covalent bond introduced between a ligand and its specific receptor. Thus, the photoaffinity labeling is applied in two stages of drug discovery and development processes. First, the method is useful for the screening of early leads. If the binding site analysis of target protein is important for defining a particular pharmacophore, the photoaffinity labeling will give the structural information at the contact point of drugs with receptors. Second, emerging new technologies, combinatorial chemistry, recombinant DNA techniques,and high-throughput analysis, are extending the potential of photoaffinity labeling to become a rapid and more sensitive means for the identification of drug-receptor pairs as well as the elucidation of molecular recognition mechanism at drug-receptor interfaces. This review focuses on several recent impacts of photoaffinity labeling as a useful tool for drug discovery and developments.

Today, the majority of pharmaceuticals developed to treat cancers and viral / bacterial infections target cellular, bacterial or viral proteins known to be associated with a given pathology. Although proteins are the focus of most current drug discovery efforts, exciting new research has recently begun which aims to exploit ribonucleic acid (RNA) and RNP particles as novel targets for pharmaceutical development. These RNA-targeted research efforts have been fueled by an increased appreciation for the central role played by RNA and RNA-protein interactions in many biological processes and diseases, together with a better understanding of RNA structure and an improvement in biophysical / biochemical techniques available to study RNA. As for protein targets, genome sequencing is greatly accelerating the identification of human and microbial RNA transcripts for targeted drug discovery. With this explosion in the number of potential RNA and RNP targets, the effective development of specific small molecule RNA-based drugs requires robust and general approaches for detecting and quantifying RNA-ligand interactions, which can be used as high-throughput screens (HTS) and for obtaining rapid structural information to guide rational drug design. In this review, an overview of the potential for therapeutic intervention based on RNA and RNP targets is presented, together with recent efforts to develop generally useful nuclear magnetic resonance (NMR) and fluorescence binding assays for screening and optimizing drugs aimed at RNA and RNP targets.

This paper describes recent progress in the design, synthesis and biological evaluation of inhibitors for the enzyme protein farnesyltransferase (PFTase). This enzyme plays a critical role in the post-translational modification of a range of different intracellular proteins. In particular, PFTase attaches a farnesyl group to the GTPase Ras whose oncogenically mutated form is found in over 30% of human cancers. As a result PFTase inhibitors have been developed as potential cancer therapeutic drugs either by rational design based on the structure of the CAAX carboxyl terminus of Ras or random screening of chemical libraries or natural products. Some of these inhibitors show remarkable inhibition potency against PFTase at subnanomolar concentrations and >1000-fold selectivity compared to the related enzyme geranylgeranyltransferase-I. Certain of these compounds are highly effective at blocking the growth of human tumors in animal models and are now undergoing clinical trials. However, several issues in the research remain unsolved, including the mechanism by which PFTase inhibitors suppress tumor growth. Although it has been established that PFTase inhibitors block prenylation of Ras in vitro, the results in whole cells and animal studies suggest the possibility that proteins other than Ras are affected.

The choice of peptides as prototype modulators of biological function, is justified on the grounds that peptides are natural constituents of living systems. They exist as hormones, biochemical inhibitors,antigens, growth factors, transmembrane carriers and, indeed they are comprised of the building blocks of all proteins. As such, the natural and mutated analogs of these functional entities provide a rich variety of pharmacophore models for further development. Peptidomimetic modification of active peptides can provide biostable analogs. Moreover, cyclization of linear peptides is frequently used as an attractive venue to provide both conformationally more restricted as well as more biostable analogs. The objective of this review is to report an updated summary of the more recently developed methodologies for the design and synthesis of cyclized peptides, citing selected examples of the effect of cyclization on both proteolytic stability and biological activity.