'One bead two compound libraries' for detecting chemical and biochemical conversions

When combinatorial chemistry was introduced 13 years ago, the expectations were high for the delivery of results, particularly in the pharmaceutical industry. However, combinatorial chemistry was implemented independently of the application for which the products were going to be used. Resins developed only for efficient solid-phase synthesis were used and products were employed in existing assays developed for traditional solution studies. There was almost no assay or technology development and the use of real combinatorial methods soon had to give way to high-throughput synthesis and traditional screening. However, during recent years more sophisticated resins and assay techniques have been developed that may result in a second and more successful implementation of real integrated combinatorial chemistry. The first in this line of new developments is the 'one bead two compound' assay, in which the resin bead in addition to a combinatorial library member contains a reporter compound that can act as a beacon to monitor the activity of the library member. This powerful concept can be generally applied in all fields of combinatorial chemistry including drug, catalysts and material development.     

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.     

Solution-phase combinatorial synthesis and evaluation of piperazine-2,5-dione derivatives

An efficient one-pot synthesis of a 61-membered combinatorial chemistry library of piperazine-2,5-diones was accomplished. Results of combinatorial synthesis, purification, analysis, and biological evaluation are described.     

Solid-phase synthesis: a paradigm shift.

A personal review by the first graduate student of Professor R. Bruce Merrifield of the evolution of solid-phase synthesis and its acceptance by various subsets of the chemistry community. Solid-phase synthesis, as currently practised in the synthesis of biopolymers, combinatorial solid-phase organic chemistry, synthesis of natural products, catalyst selection, chemical ligation and materials development, has proven a paradigm shift for the chemistry community.     

Combinatorial solid phase peptide synthesis and bioassays

Solid phase peptide synthesis method, which was introduced by Merrifield in 1963, has spawned the concept of combinatorial chemistry. In this review, we summarize the present technologies of solid phase peptide synthesis (SPPS) that are related to combinatorial chemistry. The conventional methods of peptide library synthesis on polymer support are parallel synthesis, split and mix synthesis and reagent mixture synthesis. Combining surface chemistry with the recent technology of microelectronic semiconductor fabrication system, the peptide microarray synthesis methods on a planar solid support are developed, which leads to spatially addressable peptide library. There are two kinds of peptide microarray synthesis methodologies: pre-synthesized peptide immobilization onto a glass or membrane substrate and in situ peptide synthesis by a photolithography or the SPOT method. This review also discusses the application of peptide libraries for high-throughput bioassays, for example, peptide ligand screening for antibody or cell signaling, enzyme substrate and inhibitor screening as well as other applications.     

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.     

Combinatorial carbohydrate chemistry

The application of combinatorial chemistry to the synthesis of carbohydrate-based compound collections has received increased attention in recent years. New strategies for the solution-phase synthesis of oligosaccharide libraries have been reported, and the use of monosaccharides as scaffolds in the generation of combinatorial libraries has been described. Novel approaches to the assembly of carbohydrate-based antibiotics, such as aminoglycoside analogs and vancomycin derivatives, have also been disclosed.     

Recent developments and applications of liquid-phase strategies in organic synthesis.

Chemistry on soluble polymer supports, termed liquid-phase organic synthesis, is developing into an increasingly viable alternative or adjunct to the classical solid-phase approach across the broad spectrum of polymer-supported organic chemistry. Recent advances in the field include the use of soluble polymers in the combinatorial synthesis of peptide and small-molecule libraries, as catalyst and reagent supports, and as functionalized polymer-quench reagents for purifying solution-phase combinatorial libraries.     

Natural products as a hunting ground for combinatorial chemistry

Natural products have a long history of success as biologically active leads for therapeutic agents. The ability to prepare analogues and to discover structure-activity relationships is necessary to truly harness the potential of natural products. Recently, combinatorial chemistry has risen to this challenge, and even fairly complex natural products can be targeted for parallel synthesis. Academic and industrial efforts have employed natural products from the peptide, alkaloid, polyketide, and terpenoid and steroid classes in combinatorial chemistry approaches for the production of medicinally important compounds.     

At the crossroads of chemistry and biology

The life sciences are molecular and the harnessing of information gleaned from genomics and proteomics will require interdisciplinary research integrating chemistry and biology. This approach is illustrated by the synthesis and biological evaluation of lipidated peptides and proteins and the delineation of a concept arguing for natural product guided combinatorial chemistry.     

Parallel and combinatorial approaches for synthesis of ligands

Although new detection screening methods must still be developed, the actual main limitation in combinatorial chemistry seems to be the diversity of ligands that can be generated in terms of real structural and chemical diversity. Thus, there is a strong interest for the development of different strategies for the parallel or combinatorial synthesis of ligands. We report here a selection of recent attempts proposing 'open' approaches able to increase the diversity of molecular architecture truly accessible via parallel or combinatorial processes.     

Combinatorial biochemistry in plants: the case of O-methyltransferases

Combinatorial chemistry is common place today in chemical synthesis. Virtually thousands of derivatives of a molecule can be achieved by automated systems. The use of biological systems to exploit combinatorial chemistry (combinatorial biochemistry) now has multiple examples in the polyketide field. The modular functional domain structure of polyketide synthases have been recombined through genetic engineering into unnatural constellations in heterologous hosts in order to produce polyketide structures not yet discovered in nature. We present herein an example for a potential type of combinatorial biochemistry in alkaloidal systems using various combinations of Thalictrum tuberosum (meadow rue) O-methyltransferase subunits that result in heterodimeric enzymes with substrate specificities that differ from those of the homodimeric native enzymes.     

Immobilized catalysts in combinatorial chemistry

As a new methodology for library synthesis in combinatorial chemistry, the use of immobilized catalysts and multi-component reactions is focused. In the past two years, many advances have been made in this emerging field, leading to the efficient library synthesis of, for example, quinolines, amino ketones and amino esters.     

Beyond Rf tagging

The split-pool diversity orientated synthesis method, which requires some form of encoding to track the synthesis of discrete compounds, has been the lynchpin of most combinatorial synthesis efforts. The use of encoding methods in combinatorial chemistry has matured, and depending on their level of resources, chemists now have a diverse choice of encoding methods available. New methods of encoding have been developed that are inexpensive, simple to incorporate into any laboratory, and utilize analytical equipment such as MS, FTIR and NMR that are readily available to most organic chemists.     

Synthesis of encoded modified oligonucleotide libraries. Part 1: orthogonal chemistry

The basis for further development of combinatorial libraries of modified oligonucleotides tagged by a codifying sequence is discussed. The chemistry involved in the orthogonal synthesis of both strands and some representative examples of building blocks are presented.     

Combinatorial syntheses of sugar derivatives

There has been an exponential growth in interest of the functional roles of carbohydrates and cell surface glycoconjugates in the past 10 years. The importance of glycoconjugates as mediators of biosignals has stimulated investigation into simple and versatile methods for their synthesis. The synthesis of carbohydrates and glycoconjugates by combinatorial chemistry has gained considerable interest.     

Facile Synthesis of Orthogonally Protected Optically Pure Keto- and Diketopiperazine Building Blocks for Combinatorial Chemistry

A simple and convenient synthesis of orthogonally protected multi-tethered, optically pure 2-ketopiperazine and 2,5-diketopiperazine scaffolds for Fmoc and Boc combinatorial chemistry was achieved, starting from accessible chiral amino acid precursors, by sequentially utilizing reductive alkylation, dipeptide coupling and ketopiperazine ring formation as key steps. These scaffolds can introduce valuable drug-like properties in three independent directions to any medicinally relevant piperazine-based motif by “around the scaffold” drug optimization. In addition, these building blocks have a wide application scope in managing fast and efficient multi-cyclic optimization processes in the combinatorial chemistry and drug design fields.     

High-speed combinatorial synthesis utilizing microwave irradiation

Recent advances in microwave-assisted combinatorial chemistry include high-speed solid-phase and polymer-supported organic synthesis, rapid parallel synthesis of compound libraries, and library generation by automated sequential microwave irradiation. In addition, new instrumentation for high-throughput microwave-assisted synthesis continues to be developed at a steady pace. The impressive speed combined with the unmatched control over reaction parameters justifies the growing interest in this application of microwave heating.     

Mesofluidic devices for DNA-programmed combinatorial chemistry

Hybrid combinatorial chemistry strategies that use DNA as an information-carrying medium are proving to be powerful tools for molecular discovery. In order to extend these efforts, we present a highly parallel format for DNA-programmed chemical library synthesis. The new format uses a standard microwell plate footprint and is compatible with commercially available automation technology. It can accommodate a wide variety of combinatorial synthetic schemes with up to 384 different building blocks per chemical step. We demonstrate that fluidic routing of DNA populations in the highly parallel format occurs with excellent specificity, and that chemistry on DNA arrayed into 384 well plates proceeds robustly, two requirements for the high-fidelity translation and efficient in vitro evolution of small molecules.     

A solid-phase synthesis for beta-turn mimetics of sialyl Lewis X

A solid-phase synthesis of heterocyclic beta-turn mimetics of sialyl Lewis X, which is a natural carbohydrate ligand of selectins, was established. This synthetic method could be very useful for drug discovery of selectin antagonists using combinatorial chemistry techniques.