Current Topics in Medicinal Chemistry - Volume 4, Issue 7, 2004

Combinatorial chemistry has had a major impact on the discovery and optimisation of potential lead compounds. This review details some of the fundamental principles behind combinatorial chemistry and describes a variety of methods employed in the search for new therapeutically interesting compounds including the concept of dynamic combinatorial chemistry as a method of selecting active compounds from a mixture. It also outlines methods used to analyse resin bound products and describes how solution phase library generation may be aided by the use of resin bound reagents and scavengers.

The implementation of appropriate automation can make a significant improvement in productivity at each stage of the drug discovery process, if it is incorporated into an efficient overall process. Automated chemistry has evolved rapidly from the 'combinatorial' techniques implemented in many industrial laboratories in the early 1990's which focused primarily on the hit discovery phase, and were highly dependent on solid-phase techniques and instrumentation derived from peptide synthesis. Automated tools and strategies have been developed which can impact the hit discovery, hit expansion and lead optimization phases, not only in synthesis, but also in reaction optimization, work-up, and purification of compounds. This article discusses the implementation of some of these techniques, based especially on experiences at Millennium Pharmaceuticals Research and Development Ltd.

With the number of protein-ligand complexes available in the Protein Data Bank constantly growing, structure-based approaches to drug design and screening have become increasingly important. Alongside this explosion of structural information, a number of molecular docking methods have been developed over the last years with the aim of maximally exploiting all available structural and chemical information that can be derived from proteins, from ligands, and from protein-ligand complexes. In this respect, the term 'guided docking' is introduced to refer to docking approaches that incorporate some degree of chemical information to actively guide the orientation of the ligand into the binding site. To reflect the focus on the use of chemical information, a classification scheme for guided docking approaches is proposed. In general terms, guided docking approaches can be divided into indirect and direct approaches. Indirect approaches incorporate chemical information implicitly, having an effect on scoring but not on orienting the ligand during sampling. In contrast, direct approaches incorporate chemical information explicitly, thus actively guiding the orientation of the ligand during sampling. Direct approaches can be further divided into protein-based, mapping-based, and ligandbased approaches to reflect the source used to derive the features capturing the chemical information inside the protein cavity. Within each category, a representative list of docking approaches is discussed. In view of the limitations of current scoring functions, it was generally found that making optimal use of chemical information represents an efficient knowledge-based strategy for improving binding affinity estimations, ligand binding-mode predictions, and virtual screening enrichments obtained from protein-ligand docking.

In vitro assays developed for the evaluation of drug-like properties can accelerate the drug development process. The key assays are those for the evaluation of bioavailability, metabolic stability, drug-drug interaction potential, and toxicity. For bioavailability, the human colon carcinoma derived Caco-2 assay is the most widely used, allowing the evaluation of multiple pathways of intestinal absorption including paracellular uptake, transcellular uptake, and transporter-mediated uptake and efflux. For metabolic stability and drug-drug interactions, human liver microsomes, hepatocytes, and cDNA-expressed microsomes are commonly used, with human hepatocytes representing the most complete system, containing all metabolic enzymes and cofactors at physiological level and an intact plasma membrane to allow the modeling of intracellular drug concentrations. Primary human cells from target organs (e.g., human hepatocytes for human hepatotoxicity) should represent the best experimental system for the evaluation of human drug toxicity. These assays, when applied intelligently with their limitations, should greatly facilitate the selection of drug candidates with a high probability of clinical success.

This article reviews the current and future applications of micro reactors in the field of chemistry, biochemistry and drug discovery. The fabrication and physical characterisation of micro reactors, together with details of their use and operation is described. Liquid and gas phase reactions have been used to illustrate the advantages of performing chemical reactions in micro reactors. A brief evaluation of the possible advantages that micro fabrication could offer in developing biological applications, based on miniaturized devices is also presented.

This review provides an introduction to three of the most well-developed solvent replacement strategies currently under investigation for synthetic chemistry: Ionic liquids, fluorous phase techniques, and supercritical carbon dioxide. They are all fascinating reaction media, and have considerable potential for use in pharmaceutical synthesis. However, this has to be balanced with problems and limitations of the new methods. This review aims to provide an overall account of recent advances in the use of unusual media for synthetic chemistry, with an emphasis on highlighting potential benefits, but also limitations, of each of the methods described.

Microwave assisted organic synthesis (MAOS) is rapidly gaining acceptance as a valuable tool for relieving some of the bottlenecks in the drug discovery process. This article outlines the basic principles behind the technology and summarizes recent trends and areas in drug discovery where microwave technology has made an impact.