Formats for combinatorial synthesis: solid-phase,liquid-phase and surface

Methods for combinatorial and parallel synthesis continue to evolve in order to meet the demands of modern synthetic organic chemistry. The nature of the support, while typically overlooked, is a key consideration for successful combinatorial organic synthesis. Developments in combinatorial synthesis technologies such as the 'lab-on-a-chip' concept and 96-well-plate-compatible resin plugs have been reported, which should contribute to meeting the increasing challenges of this field.     

Automated synthesis and combinatorial chemistry

The advent of combinatorial chemistry for the high-throughput synthesis of compounds has driven the advancement of new and emerging technologies for synthetic chemistry laboratories. Automated methods for reaction design, information management, chemical synthesis, compound analysis, and biological testing are necessary to realize the full potential of combinatorial chemistry efforts.     

The chemical-biological interface: developments in automated and miniaturised screening technology

The rapidly changing developments in genomics and combinatorial chemistry, generating new drug targets and large numbers of compounds, have caused a revolution in high-throughput screening technologies. Key to this revolution has been the introduction of robotics and automation, together with new biological assay technologies (e.g., homogeneous time resolved fluorescence). With ever increasing workloads, together with economic and logistical constraints, miniaturisation is rapidly becoming essential for the future of high-throughput screening and combinatorial chemistry. This is evident from the introduction of high-density microtitre plates, small volume liquid handling robots and associated detection technology.     

Tools for genome-wide strain design and construction

Advances in DNA sequencing and synthesis technologies concurrent with the development of new recombinant DNA approaches have enabled the extension of directed evolution algorithms to the genome-scale. It is now possible to simultaneously map the effect of mutation(s) in each and every gene in the genome onto almost any screenable or selectable phenotype in less than a week. Such maps can be used to direct the design and construction of libraries containing billions of rationally designed combinatorial mutations. Such combinatorial libraries can now also be created and evaluated in less than a week. The review presents and discusses these new technologies within the context of directed evolution and inverse metabolic engineering.     

Innovative approaches to novel antibacterial drug discovery

Increasing antibiotic resistance in microorganisms and new emerging pathogens have become a major problem in our society. Rising to satisfy this urgent medical need is a recent confluence of powerful new drug discovery technologies: combinatorial chemistry; sequence and functional genomic analysis; and novel methods of high-throughput screening. The combination of these technologies will bring to bear untapped power in the search for new antimicrobials.     

Combinatorial chemistry,automation and molecular diversity: new trends in the pharmaceutical industry

Combinatorial chemistry has emerged as a set of novel strategies for the synthesis of large sets of compounds (combinatorial libraries) for biological evaluation. Within a few years combinatorial chemistry has undergone a series of changes in trends, which are closely related to two important factors in libraries: numbers and quality. While the number of compounds in a library may be easily expressed, it is a lot more difficult to indicate the degree of quality of a library. This degree of quality can be split into two aspects : purity and diversity. The changing trends in combinatorial chemistry with respect to the strategies, the technologies, the libraries themselves (numbers and purity aspects) and the molecular diversity are outlined in this paper.     

Novel miniaturized systems in high-throughput screening

High-throughput screening (HTS) using high-density microplates is the primary method for the discovery of novel lead candidate molecules. However, new strategies that eschew 2D microplate technology, including technologies that enable mass screening of targets against large combinatorial libraries, have the potential to greatly increase throughput and decrease unit cost. This review presents an overview of state-of-the-art microplate-based HTS technology and includes a discussion of emerging miniaturized systems for HTS. We focus on new methods of encoding combinatorial libraries that promise throughputs of as many as 100,000 compounds per second.     

Exploring the possibilities presented by protein engineering

A combination of classical and powerful new combinatorial genetic techniques allows the redesign of enzyme activities and creation of proteins that are tailored to have specific properties. These technologies have far-reaching consequences for the future design of crop plants and the storage compounds within them.     

Combinatorial search for advanced luminescence materials.

Phosphors are key materials in fluorescent lighting, displays, x-ray scintillation, etc. The rapid development of modern photonic technologies, e.g., mercury-free lamps, flat panel displays, CT-detector array, etc., demands timely discovery of advanced phosphors. To this end, a combinatorial approach has been developed and applied to accelerated experimental search of advanced phosphors and scintillators. Phosphor libraries can be made in both thin film and powder form, using masking strategies and liquid dispensing systems, respectively. High-density libraries with 100 to 1000 discrete phosphor compositions on a 1"-square substrate can be made routinely. Both compositions and synthesis temperatures can be screened in a high-throughput mode. In this article, details on the existing methods of combinatorial synthesis and screening of phosphors will be reported with examples. These methods are generic tools for application of combinatorial chemistry in the discovery of other solid state materials. A few highly efficient phosphors discovered with combinatorial methods have been reproduced in bulk form and their luminescent properties measured.     

Techniques for analysis and purification in high-throughput chemistry

The success of combinatorial chemistry, and the increased emphasis on single well-characterised compounds of high purity, has had a significant impact on analytical and purification technologies. The requirement for ever-increasing throughput has led to the automation and parallelisation of these techniques. Advances have also been made in developing faster methods to augment throughput further.     

Histone modifications: from genome-wide maps to functional insights

A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases. Integration of datasets and improved technologies will provide the way forward.     

Microchip-based high-throughput screening analysis of combinatorial libraries

In recent years, there have been significant advances in biochemical assay miniturization and integration of microchip-based technologies with combinatorial library screening for high-throughput and large-scale applications. Small-molecule microarrays, protein arrays and cell-based arrays and conventional DNA arrays as well as microfluidic approaches in HTS are discussed in this review.     

Chemical synthesis in nanosized cavities

This account briefly discusses methods of in-cavity synthesis with the main focus on molecularly imprinted polymers and self-assembled capsules. Discussed are examples that highlight recent progress and outline key challenges for the further development of in-cavity synthesis. Emphasis is intentionally placed at potential applications in drug discovery and combinatorial technologies.     

Computational Chemistry in Lead Identification,Library Design and Lead Optimisation

Abstract

We describe a variety of the computational techniques which we use in the drug discovery and design process. Some of these computational methods are designed to support the new experimental technologies of high-throughput screening and combinatorial chemistry. We also consider some new approaches to problems of long-standing interest such as protein-ligand docking and the prediction of free energies of binding.     

Natural products and combinatorial chemistry: back to the future

The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.     

Inkjet dispensing technology: applications in drug discovery

The past year has seen significant advances in the reduction to practice of inkjet dispensing technology in drug discovery applications. Although much of the work in this area has been done by relatively few ‘early innovators’, broader acceptance of the feasibility of the use of inkjet dispensing is on the rise. Of the three main areas of drug discovery — genomics, high-throughput screening, and combinatorial chemistry — high-throughput screening has had the most applications to date. The burgeoning field of genomics has seen rapid incorporation of technologies that enable miniaturization of gene expression experiments. Inkjet dispensing has a clear role in this effort. Finally, as the miniaturization needs of combinatorial chemistry become more clear, inkjet dispensing technology will potentially play a role.     

Combinatorial vector fields and the valley structure of fitness landscapes

Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis, however. Here we develop a framework that interprets adaptive walks as deterministic trajectories in combinatorial vector fields and in return associate these combinatorial vector fields with weights that measure their steepness across the landscape. We show that the combinatorial vector fields and their weights have a product structure that is governed by the neutrality of the landscape. This product structure makes practical computations feasible. The framework presented here also provides an alternative, and mathematically more convenient, way of defining notions of valleys, saddle points, and barriers in landscape. As an application, we propose a refined approximation for transition rates between macrostates that are associated with the valleys of the landscape.     

Transition Dependency: A Gene-Gene Interaction Measure for Times Series Microarray Data

Gene-Gene dependency plays a very important role in system biology as it pertains to the crucial understanding of different biological mechanisms. Time-course microarray data provides a new platform useful to reveal the dynamic mechanism of gene-gene dependencies. Existing interaction measures are mostly based on association measures, such as Pearson or Spearman correlations. However, it is well known that such interaction measures can only capture linear or monotonic dependency relationships but not for nonlinear combinatorial dependency relationships. With the invocation of hidden Markov models, we propose a new measure of pairwise dependency based on transition probabilities. The new dynamic interaction measure checks whether or not the joint transition kernel of the bivariate state variables is the product of two marginal transition kernels. This new measure enables us not only to evaluate the strength, but also to infer the details of gene dependencies. It reveals nonlinear combinatorial dependency structure in two aspects: between two genes and across adjacent time points. We conduct a bootstrap-based test for presence/absence of the dependency between every pair of genes. Simulation studies and real biological data analysis demonstrate the application of the proposed method. The software package is available under request.     

Quarterly U.S. patent review: first quarter, 1999.

The following are among the U.S. patents, issued in the first quarter of 1999, directed to combinatorial chemistry and related technologies. Patent issuances in the field are growing in number. Additionally, patents claiming libraries themselves, as opposed to synthetic methodologies, are becoming more common. It is impossible to be comprehensive. The author would be pleased to recognize additional patents and invites the use of his e-mail address for this purpose.