Will combinatorial chemistry deliver real medicines?

Human P450 Microarrays for In Vitro Toxicity Analysis: Toward Complete Automation of Human Toxicology Screening

The development of a tool that can provide early-stage predictive toxicology data may accelerate the identification of safer drug candidates, and thereby improve the clinical progression of drug candidates to pharmaceuticals. Such a system would require an accurate and reliable technique that is amenable to the large number of drug candidates that must be screened in the lead discovery and optimization stages of drug development. A key component of predictive toxicology is the ability to harness the metabolite-generating capacity of human cytochromes P450, which are involved in first-pass drug metabolism function of the liver. We have miniaturized P450 catalysis into a microarray format consisting of up to 11,200 isolated P450 reactions, each in 5 nL sol-gel spots, on a single functionalized glass microscope-size biochip. This dramatic scale down from more conventional 96 and 384-well plate scales (at least a 1000-fold reduction in volume) did not adversely affect P450 catalytic activity. Based on the functionality of the P450-containing microarray, we developed the metabolizing enzyme toxicology assay Chip (MetaChip), which combines high-throughput P450 catalysis with cell-based screening on a microscale platform. Proof of concept was demonstrated using anticancer prodrugs cyclophosphamide and Tegafur, as well as the analgesic acetaminophen. The MetaChip may provide a high-throughput microscale alternative to currently used in vitro methods for human metabolism and toxicology screening.

Triggers and cues that activate antibiotic production by actinomycetes

Actinomycetes are a rich source of natural products, and these mycelial bacteria produce the majority of the known antibiotics. The increasing difficulty to find new drugs via high-throughput screening has led to a decline in antibiotic research, while infectious diseases associated with multidrug resistance are spreading rapidly. Here we review new approaches and ideas that are currently being developed to increase our chances of finding novel antimicrobials, with focus on genetic, chemical, and ecological methods to elicit the expression of biosynthetic gene clusters. The genome sequencing revolution identified numerous gene clusters for natural products in actinomycetes, associated with a potentially huge reservoir of unknown molecules, and prioritizing them is a major challenge for in silico screening-based approaches. Some antibiotics are likely only expressed under very specific conditions, such as interaction with other microbes, which explains the renewed interest in soil and marine ecology. The identification of new gene clusters, as well as chemical elicitors and culturing conditions that activate their expression, should allow scientists to reinforce their efforts to find the necessary novel antimicrobial drugs.

Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening

The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition.

Metabolomics for bioactivity assessment of natural products

Natural products historically have been a rich source of lead molecules in drug discovery, based on their capability to create unique and diverse chemical structures. However, it is also true that the vast number of metabolites typically present in natural products and their huge dynamic range results in the loss of many possibly bioactive natural compounds, becoming an inextricable obstacle for drug development. Recently, new strategies which favour a holistic approach as opposed to the traditional reductionist methods used previously, have been introduced with the purpose of overcoming the bottlenecks in natural product research. This approach is based on the application of new technologies, including metabolomics, for example. Metabolomics allows a systematic study of a complex mixture such as a phytochemical preparation, which can be linked to observations obtained through biological testing systems without the need for isolating active principles. This may put drug discovery from natural products back in the limelight again. In this review paper, the description of some examples of successful metabolomics applications in several important fields related to drug discovery from natural sources aims at raising the potential of metabolomics in reducing the gap between natural products (NP) and modern drug discovery demand.

Shape Signatures: speeding up computer aided drug discovery

Identifying potential lead molecules is becoming a more automated process. We review Shape Signatures, a tool that is effective and easy to use compared with most computer aided drug design techniques. Laboratory researchers can apply this in silico technique cost-effectively without the need for specialized computer backgrounds. Identifying a potential lead molecule requires database screening, and this becomes rate-limiting once the database becomes too large. The use of Shape Signatures eliminates this concern and offers molecule screening rates that are in advance of any currently available method. Shape Signatures provides a conduit for researchers to conduct rapid identification of potential active molecules, and studies with this tool can be initiated with only one bioactive lead or receptor site.

Metabolizing enzyme toxicology assay chip (MetaChip) for high-throughput microscale toxicity analyses

The clinical progression of new chemical entities to pharmaceuticals remains hindered by the relatively slow pace of technology development in toxicology and clinical safety evaluation, particularly in vitro approaches, that can be used in the preclinical and early clinical phases of drug development. To alleviate this bottle-neck, we have developed a metabolizing enzyme toxicology assay chip (MetaChip) that combines high-throughput P450 catalysis with cell-based screening on a microscale platform. The MetaChip concept is demonstrated by using sol-gel encapsulated P450s to activate the prodrug cyclophosphamide, which is the major constituent of the anticancer drug Cytoxan, as well as other compounds that are activated by P450 metabolism. The MetaChip provides a high-throughput microscale alternative to currently used in vitro methods for human metabolism and toxicology screening based on liver slices, cultured human hepatocytes, purified microsomal preparations, or isolated and purified P450s. This technology creates opportunities for rapid and inexpensive assessment of ADME/Tox (absorption, distribution, metabolism, excretion/toxicology) at very early phases of drug development, thereby enabling unsuitable candidates to be eliminated from consideration much earlier in the drug discovery process.

The role of natural product chemistry in drug discovery

Although traditionally natural products have played an important role in drug discovery, in the past few years most Big Pharma companies have either terminated or considerably scaled down their natural product operations. This is despite a significant number of natural product-derived drugs being ranked in the top 35 worldwide selling ethical drugs in 2000, 2001, and 2002. There were 15 new natural product-derived drugs launched from 2000 to 2003, as well as 15 natural product-derived compounds in Phase III clinical trials or registration at the end of 2003. Recently, there has been a renewed interest in natural product research due to the failure of alternative drug discovery methods to deliver many lead compounds in key therapeutic areas such as immunosuppression, anti-infectives, and metabolic diseases. To continue to be competitive with other drug discovery methods, natural product research needs to continually improve the speed of the screening, isolation, and structure elucidation processes, as well addressing the suitability of screens for natural product extracts and dealing with issues involved with large-scale compound supply.

Targeting signal transduction with large combinatorial collections

The large-scale application of combinatorial chemistry to drug discovery is an endeavor that is now more than ten years old. The growth of chemical libraries together with the influx of novel genomic targets has led to a reconstruction of the drug-screening paradigm. The drug discovery industry faces a post-genomic world where the interplay between tens-of-thousands of proteins must be addressed. To compound this complexity, there now exists the ability to screen millions of compounds against a single target. This review focuses on the practice and use of selecting individual compounds from large chemical libraries that act on targets relevant to signal transduction.

Combinatorial computational method gives new picomolar ligands for a known enzyme

Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct conformations. The experiments verified that computational predictions concerning the binding affinities and the binding modes were correct for both isomers. The designed R isomer is the best-known inhibitor (K(d) approximately 30 pM) of human carbonic anhydrase II.

A versatile and inexpensive apparatus for rapid parallel synthesis on solid support: description and synthesis illustration

A new inexpensive and practical apparatus for solid-phase chemistry and parallel synthesis is described. This new apparatus fills an important void in the availability of portable tools for the synthesis of libraries of compounds in multi-milligram amounts. Individual reaction tube capacities range in size from 4 mL to 500 mL of operating liquid volume. Reaction blocks of 36 tubes x 4 mL or 24 tubes x 150 mL allow flexibility of operation. Insert tubes with frit ends function as filter sticks for resin wash and for maintenance of inert atmosphere. An electronic controller device connects to the reaction tubes for programmable entry of pulses of inert gas for resin mixing or vacuum for resin wash. The utility of this apparatus is illustrated by the synthesis of libraries based on 4-methaneamine imidazoles.

Strategies for discovering drugs from previously unexplored natural products

Natural products are the most consistently successful source of drug leads. Despite this, their use in drug discovery has fallen out of favour. Natural products continue to provide greater structural diversity than standard combinatorial chemistry and so they offer major opportunities for finding novel low molecular weight lead structures that are active against a wide range of assay targets. As less than 10% of the world's biodiversity has been tested for biological activity, many more useful natural lead compounds are awaiting discovery. The challenge is how to access this natural chemical diversity.

Combinatorial chemistry as a tool for drug discovery

The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.

Integrated bacterial genomics for the discovery of novel antimicrobials

Sequencing of bacterial genomes has been progressing with breathtaking speed. Currently, the genomes of 23 bacterial species are sequenced, with approximately 40 more sequencing projects in progress. Industrial research is now facing the challenge of translating this information efficiently into drug discovery. This review will summarize the impact of bacterial genomics, bioinformatics and second-generation genomic technologies on target identification, assay development, lead optimization and compound characterization.

Pharmacological applications of inorganic complexes

Inorganic complexes have long been utilized for many therapeutic purposes. They were used or tried, perhaps because of the general notion that inorganic compounds (e.g., metal complexes) are toxic and a controlled use of such a compound may suppress some biological process. In this review, we briefly outline the properties of several selected groups of inorganic complexes and how they can affect biological systems and contribute to human pathologies.

Physico-chemical and biological analysis of true combinatorial libraries

Combinatorial libraries offer new sources of compounds for the research of pharmacological agents such as receptor ligands, enzyme inhibitors or substrates and antibody-binding epitopes. The present review stresses the main roles played by both physico-chemical analysis, particularly when complex mixture of compounds are synthesized as libraries, and biological analysis from which active compounds are identified. After a brief discussion of semantic problems related to the designation of the product mixtures, the physico-chemical analysis of mixtures is reviewed with special emphasis on mass spectrometric techniques. These methods are able both to give a representative view of a library composition and to identify single critical compounds in large libraries. Then the biological screening of such combinatorial libraries is critically discussed with respect to the power and limitations of the methods used for the identification of the active components. Special attention is given to the complex process of library deconvolution. It is pointed out that while combinatorial techniques have evolved towards sophisticated high-tech methods, simple and robust biochemical tests should be used to deconvolute. From a large panel of published examples, a set of trends are identified which should help investigators to choose the most appropriate assay for the discovery of new entities.

Genomes and proteomes: towards a multidimensional view of biology

The third Siena proteomics conference held August 31-September 4, 1998, heralded a change in emphasis from technology development to using proteomics to assist in resolving biological questions. In this review, proteomics is placed in context with other major influences in the way discovery research is conducted in biology. The current status of genomics is examined in its broadest sense, including how such studies may influence the development of proteomics. It is suggested that we are entering a new phase in biology where information is no longer limiting and integration of different technologies is required to attack the big problems of biology. While much of the focus of funding bodies, both in the public and private sector, is on practical outcomes (new drugs, etc.), the new technologies are equally amenable to attacking long-standing fundamental challenges, such as cell division, cell patterning and morphogenesis.

Chance favors the prepared mind--from serendipity to rational drug design

Accidental discoveries always played an important role in science, especially in the search for new drugs. Several examples of serendipitous findings, leading to therapeutically useful drugs, are presented and discussed. Captopril, an antihypertensive Angiotensin-converting enzyme inhibitor, was the first drug that could be derived from a structural model of a protein. Dorzolamide, a Carboanhydrase inhibitor for the treatment of glaucoma, and the HIV protease inhibitors Saquinavir, Indinavir, Ritonavir, and Nelfinavir are further examples of therapeutically used drugs from structure-based design. More enzyme inhibitors, e.g. the anti-influenza drugs Zanamivir and GS 4104, are in clinical development. In the absence of a protein 3D structure, the 3D structures of certain ligands may be used for rational design. This approach is exemplified by the design of specifically acting integrin receptor antagonists. In the last years, combinatorial and computational approaches became important methods for rational drug design. SAR by NMR searches for low-affinity ligands that bind to proximal subsites of an enzyme; linkage with an appropriate tether produces nanomolar inhibitors. The de novo design program LUDI and the docking program FlexX are tools for the computer-aided design of protein ligands. Work is in progress to combine such approaches to strategies for combinatorial drug design.