Efficient split synthesis for targeted libraries

We propose a new approach for fabricating more sophisticated combinatorial chemistry libraries via split synthesis and evaluate its potential through extensive simulation. Our algorithmically intensive method promises to reduce the time and materials costs of synthesizing libraries which are (1) too large to synthesize economically by sequential or parallel synthesis, (2) too long or irregular for conventional split synthesis generation techniques, and (3) not used in sufficient quantity to justify the setup costs of array makers. It also encourages the design of more focused and interesting libraries than are typically constructed using split synthesis. Our algorithms automate the design of efficient synthesis procedures for motif-based libraries which are too complex to design by hand. Our software allows the user to select the most desirable tradeoff between minimizing the number of steps in the synthesis process and containing the combinatorial explosion of the number of compounds synthesized.     

Modern separation techniques for the efficient workup in organic synthesis

The shift of paradigm in combinatorial chemistry, from large compound libraries (of mixtures) on a small scale towards defined compound libraries where each compound is prepared in an individual well, has stimulated the search for alternative separation approaches. The key to a rapid and efficient synthesis is not only the parallel arrangement of reactions, but simple work-up procedures so as to circumvent time-consuming and laborious purification steps. During the initial development stages of combinatorial synthesis it was believed that rational synthesis of individual compounds could only be achieved by solid-phase strategies. However, there are a number of problems in solid-phase chemistry: most notably there is the need for a suitable linker unit, the limitation of the reaction conditions to certain solvents and reagents, and the heterogeneous reaction conditions. Further disadvantages are: the moderate loading capacities of the polymeric support and the limited stability of the solid support. In the last few years several new separation techniques have been developed. Depending on the chemical problem or the class of compounds to be prepared, one can choose from a whole array of different approaches. Most of these modern separation approaches rely on solution-phase chemistry, even though some of them use solid-phase resins as tools (for example, as scavengers). Several of these separation techniques are based on liquid-liquid phase separation, including ionic liquids, fluorous phases, and supercritical solvents. Besides being benign with respect to their environmental aspects, they also show a number of advantages with respect to the work-up procedures of organic reactions as well as simplicity in the isolation of products. Another set of separation strategies involves polymeric supports (for example, as scavengers or for cyclative cleavage), either as solid phases or as soluble polymeric supports. In contrast to solid-phase resins, soluble polymeric supports allow reactions to be performed under homogeneous conditions, which can be an important factor in catalysis. At the same time, a whole set of techniques has been developed for the separation of these soluble polymeric supports from small target molecules. Finally, miscellaneous separation techniques, such as phase-switchable tags for precipitation by chemical modification or magnetic beads, can accelerate the separation of compounds in a parallel format.     

Recent advances in liquid-phase combinatorial chemistry

In combination with high throughput screening, combinatorial organic synthesis of large numbers of pharmaceutically interesting compounds may revolutionize the drug discovery process. Although combinatorial organic synthesis on solid supports is a useful approach, several groups are focusing their research efforts on liquid-phase combinatorial synthesis by the use of soluble polymer supports to generate libraries. This macromolecular carrier, in contrast to an insoluble matrix, is soluble in most organic solvents and has a strong tendency for precipitation in particular solvents. Liquid-phase combinatorial synthesis is a unique approach since homogeneous reaction conditions can be applied, but product purification similar to the solid-phase method can be carried out by simple filtration and washing. This method combines the positive aspects of classical solution-phase chemistry and solid-phase synthesis. This review examines the recent applications (1995-1999) of soluble polymer supports in the synthesis of combinatorial libraries.     

Microwave-assisted reactions in heterocyclic compounds with applications in medicinal and supramolecular chemistry

Microwave irradiation has been successfully applied in organic chemistry. Spectacular accelerations, higher yields under milder reaction conditions and higher product purities have all been reported. Indeed, a number of authors have described success in reactions that do not occur under conventional heating and modifications in selectivity (chemo-, regio- and stereoselectivity) have even been reported. 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. In this review we highlight our recent advances in this area, with a particular emphasis on cycloaddition reactions of heterocyclic compounds both with and without supports, applications in supramolecular chemistry and the reproducibility and scalability of organic reactions involving the use of microwave irradiation techniques.     

Preparative high-performance liquid chromatography-mass spectrometry for the high-throughput purification of combinatorial libraries

Accurate results for the testing of combinatorial libraries necessitates high purity of the library members. Therefore, combinatorial libraries derived from a combinatorial solution or solid-phase synthesis often require the purification of compounds that do not achieve a certain purity threshold. This study describes that preparative high-performance liquid chromatography (HPLC)-mass spectrometry (MS) is the method of choice for the purification of large arrays of diverse compounds. The adoption of this technology to the workflow of a solution phase combinatorial chemistry laboratory producing more than 20,000 compounds per year is described. Furthermore, the setup and logistics are discussed as well as the purity achievable for large libraries. Efficiency, speed, quality, and universality of preparative HPLC-MS are presented in detail for a library of 140 compounds, including data logistics and downstream processes as well.     

Combinatorial chemistry: a tool for the discovery of new catalysts

The discovery of new reactions and catalysts has always presented an intriguing challenge to scientists. With the rise of combinatorial chemistry, a new method has emerged that holds considerable promise to facilitate the task since it allows for the simultaneous generation and testing of a large number of compounds. The crucial difficulty lies in establishing general technologies for rapid and reliable screening of libraries to determine the catalytic activity of their members. Several recent publications have addressed this question by using infrared thermography, colorimetric assays and fluorescence spectroscopy. These techniques have not only been applied successfully to the high-throughput screening of parallel compound arrays but also to the screening of one-bead-one-compound libraries. This demonstrates that combinatorial chemistry possesses indeed the potential to establish itself as a powerful tool for the discovery of new catalysts. This review describes the methodologies used so far for the detection of catalytic events and will place particular emphasis on the on-bead screening of one-bead-one-compound libraries.     

Total Synthesis of Vancomycin Aglycon—Part 2: Synthesis of Amino Acids 1–3 and Construction of the AB-COD-DOE Ring Skeleton

A triazene-based synthetic strategy for the construction of the complex biaryl ethers and a Suzuki coupling reaction were the key steps in the synthesis of precursor 1 of the aglycon of vancomycin, which already contains the complete skeleton of the target compound. The cleavage of the triazene unit from the D ring and the removal of the other protecting groups led to the aglycon of vancomycin. These strategies should be particularly valuable for the synthesis of other naturally occurring glycopeptide antibiotics and offer opportunities for the synthesis of combinatorial libraries of compounds of the vancomycin family for chemical biology studies.     

Total Synthesis of Vancomycin Aglycon—Part 1: Synthesis of Amino Acids 4–7 and Construction of the AB-COD Ring Skeleton

A triazene-based synthetic strategy for the construction of the complex biaryl ethers and a Suzuki coupling reaction were the key steps in the synthesis of precursor 1 of the aglycon of vancomycin, which already contains the complete skeleton of the target compound. The cleavage of the triazene unit from the D ring and the removal of the other protecting groups led to the aglycon of vancomycin. These strategies should be particularly valuable for the synthesis of other naturally occurring glycopeptide antibiotics and offer opportunities for the synthesis of combinatorial libraries of compounds of the vancomycin family for chemical biology studies.     

Total Synthesis of Vancomycin Aglycon—Part 3: Final Stages

A triazene-based synthetic strategy for the construction of the complex biaryl ethers and a Suzuki coupling reaction were the key steps in the synthesis of precursor 1 of the aglycon of vancomycin, which already contains the complete skeleton of the target compound. The cleavage of the triazene unit from the D ring and the removal of the other protecting groups led to the aglycon of vancomycin. These strategies should be particularly valuable for the synthesis of other naturally occurring glycopeptide antibiotics and offer opportunities for the synthesis of combinatorial libraries of compounds of the vancomycin family for chemical biology studies.     

Combinatorial chemistry: libraries from libraries, the art of the diversity-oriented transformation of resin-bound peptides and chiral polyamides to low molecular weight acyclic and heterocyclic compounds

Combinatorial chemistry has deeply impacted the drug discovery process by accelerating the synthesis and screening of large numbers of compounds having therapeutic and/or diagnostic potential. These techniques offer unique enhancement in the potential identification of new and/or therapeutic candidates. Our efforts over the past 10 years in the design and diversity-oriented synthesis of low molecular weight acyclic and heterocyclic combinatorial libraries derived from amino acids, peptides, and/or peptidomimetics are described. Employing a "toolbox" of various chemical transformations, including alkylation, oxidation, reduction, acylation, and the use of a variety of multifunctional reagents, the "libraries from libraries" concept has enabled the continued development of an ever-expanding, structurally varied series of organic chemical libraries.     

High Speed Development and Synthesis of Novel Small Molecule Libraries

Combinatorial chemistry has produced libraries of millions of compounds in the last decade. Screening of those compounds, unfortunately, has not yet yielded as many new drug candidates as initially expected. Among a number of possible reasons, one is that many libraries combinatorial chemistry produced in the early periods are of the nature of linear, flat, and flexible molecules such as peptides and oligonucleotides, which do not have the desired properties to selectively interact with their targets to yield high quality hits and leads. In order to increase the number of quality hits and leads, rigid, structural featurerich and drug-like compound libraries are highly desirable. Design and development of structural features-rich and natural product-like combinatorial libraries, as well as high speed library production using modern solution and solid phase synthesis techniques such as IRORI's Directed Sorting technology, will be discussed.     

Designing a multiroute synthesis scheme in combinatorial chemistry

Solid-phase mix-and-split combinatorial synthesis is often used to produce large arrays of compounds to be tested during the various stages of the drug development process. This method can be represented by a synthesis graph in which nodes correspond to grow operations and arcs to beads transferred among the different reaction vessels. In this work, we address the problem of designing such a graph which maximizes the number of produced target compounds (namely, compounds out of an input library of desired molecules), given constraints on the number of beads used for library synthesis and on the number of reaction vessels available for concurrent grow steps. We present a heuristic based on a discrete search for solving this problem, test our solution on several data sets, explore its behavior, and show that it achieves good performance.     

Combinatorial Chemistry—Challenge and Chance for the Development of New Catalysts and Materials

One should not underestimate the capability of the combinatorial method in solid-state chemistry; this is the opinion of the author. Combinatorial chemistry can provide a large number of new compounds, but once the components that are interesting for a certain application have been successfully selected, the techniques of conventional catalysis and materials research are required. The strengths of conventional chemistry lie in the optimization, systematic modification, and improvement of new lead structures. In contrast, discovery is the potential strength of combinatorial chemistry. Careful design is most important for the synthesis of useful libraries, since the diversity of the periodic table is much too large to be accessed comprehensively or systematically by such large libraries.     

Computer Aided Analysis of Split and Mix Combinatorial Libraries

Combinatorial chemistry using split and pool synthesis involves making and testing mixtures of compounds in pools which are subsets of the larger compound collection. These subsets are created during the synthesis of the collection through a resin splitting and mixing method. Tests are conducted on each of the final pools of mixtures and the individual compounds within a mixture of interest are then identified through some deconvolution scheme, originally involving selective re-synthesis. It is possible that different schemes for splitting and mixing will have different consequences on the overall effort necessary to deconvolute interesting mixtures. The evaluation of different protocols of splitting and mixing involves consideration of more possibilities than can be exhaustively or optimally determined manually in a realistic time frame for most compound collections. We present herein a computational scheme to aid in this analysis. The approach exhaustively examines possible splitting and mixing strategies for the interrelated values of total library size, number of combinatorial steps, number of reaction vessels, and number of compounds per final pool. Weighting factors may be introduced into the various steps. The resulting complete list of splitting and mixing options is scored based on a variable weighting strategy for the total effort of synthesis and deconvolution. The results indicate the splitting/mixing strategy used has an impact on overall efficiency and should be considered in the design of compound libraries.     

Solid-phase synthesis of heterocyclic aromates: applicability towards combinatorial chemistry; a review

Because of their biological activity, stability in vivo, the rigid spatial positioning of their substituents, and their synthetic challenges, heterocyclic aromates continue to be of interest to both academic and industrial medicinal chemists. Currently, many drug-like heterocyclic aromates are prepared via solid-phase organic chemistry methods. This review examines the applicability of those methods towards combinatorial chemistry with respect to the basic demands of such an approach: 1) synthesis, work-up and subsequent purification should be easily automated enabling the efficient simultaneous synthesis of large numbers of highly pure compounds in a minimum amount of time, 2) large diversity among the ligands to be synthesized, 3) high conversion rates of the individual reaction steps, and 4) the use of commercially available starting materials. Although many methods have been developed for the synthesis of heterocyclic aromates, very few of the available methods enable the synthesis of highly diverse heteroaromatic libraries.     

Simulated molecular evolution in a full combinatorial library

BACKGROUND: The Darwinian concept of 'survival of the fittest' has inspired the development of evolutionary optimization methods to find molecules with desired properties in iterative feedback cycles of synthesis and testing. These methods have recently been applied to the computer-guided heuristic selection of molecules that bind with high affinity to a given biological target. We describe the optimization behavior and performance of genetic algorithms (GAs) that select molecules from a combinatorial library of potential thrombin inhibitors in 'artificial molecular evolution' experiments, on the basis of biological screening results. RESULTS: A full combinatorial library of 15,360 members structurally biased towards the serine protease thrombin was synthesized, and all were tested for their ability to inhibit the protease activity of thrombin. Using the resulting large structure-activity landscape, we simulated the evolutionary selection of potent thrombin inhibitors from this library using GAs. Optimal parameter sets were found (encoding strategy, population size, mutation and cross-over rate) for this artificial molecular evolution. CONCLUSIONS: A GA-based evolutionary selection is a valuable combinatorial optimization strategy to discover compounds with desired properties without needing to synthesize and test all possible combinations (i.e. all molecules). GAs are especially powerful when dealing with very large combinatorial libraries for which synthesis and screening of all members is not possible and/or when only a small number of compounds compared with the library size can be synthesized or tested. The optimization gradient or 'learning' per individual increases when using smaller population sizes and decreases for higher mutation rates.     

Hypervalent iodine mediated intramolecular cyclization of thioformanilides: expeditious approach to 2-substituted benzothiazoles

A new, mild, and efficient method has been developed for the synthesis of 2-substituted benzothiazoles via the intramolecular cyclization of thioformanilides by using hypervalent iodine reagents in CH2Cl2 at ambient temperature. The reaction proceeds via a thiyl radical in high yields to give the novel compound oxybis benzothiazole and is also amenable to generating combinatorial libraries of heterocyclic compounds by solid-phase synthesis.     

A fast exchange algorithm for designing focused libraries in lead optimization

Combinatorial chemistry is widely used in drug discovery. Once a lead compound has been identified, a series of R-groups and reagents can be selected and combined to generate new potential drugs. The combinatorial nature of this problem leads to chemical libraries containing usually a very large number of virtual compounds, far too large to permit their chemical synthesis. Therefore, one often wants to select a subset of "good" reagents for each R-group of reagents and synthesize all their possible combinations. In this research, one encounters some difficulties. First, the selection of reagents has to be done such that the compounds of the resulting sublibrary simultaneously optimize a series of chemical properties. For each compound, a desirability index, a concept proposed by Harrington,(20) is used to summarize those properties in one fitness value. Then a loss function is used as objective criteria to globally quantify the quality of a sublibrary. Second, there are a huge number of possible sublibraries, and the solutions space has to be explored as fast as possible. The WEALD algorithm proposed in this paper starts with a random solution and iterates by applying exchanges, a simple method proposed by Fedorov(13) and often used in the generation of optimal designs. Those exchanges are guided by a weighting of the reagents adapted recursively as the solutions space is explored. The algorithm is applied on a real database and reveals to converge rapidly. It is compared to results given by two other algorithms presented in the combinatorial chemistry literature: the Ultrafast algorithm of D. Agrafiotis and V. Lobanov and the Piccolo algorithm of W. Zheng et al.     

Chemically stable films for combinatorial fluorosensor arrays

Sensor arrays are useful for many purposes. Our interests include quasi-distributed intrinsic fiber optic arrays, those distributed along the length of an optical fiber. We have demonstrated an optical time-of-flight approach to distinguishing the fluorescence output of such arrays, as well as a synthesis of combinatorial libraries that takes advantage of a support of linear morphology to make numerous compounds in a simple manner without information loss in the synthesis. To unite these research areas, we needed an optical fiber cladding material that meets demanding synthetic and optical requirements. We have chosen the Meldal SPOCC polymer support as the best candidate for such a material and report here our initial results with this material.