Methodologies for Generating Solution-Phase Combinatorial Libraries

Microtiter plate based chemistry and in situ screening: a useful approach for rapid inhibitor discovery

The use of libraries extracted from nature or constructed by combinatorial chemistry, have been widely appreciated in the drug discovery area. In this perspective, we present our contribution to the field of enzyme inhibitor discovery using a useful approach that allows diversification of a common core in a microtiter plate followed by in situ screening. Our method relies on an organic reaction that is highly selective, high yielding, amenable to the microscale and preferably can be performed in water. The core can be a designed molecule based on the structural and mechanistic information of the target, a compound with a weak binding affinity, or a natural product. Several reactions were found useful for this approach and were applied to the rapid discovery of potent inhibitors of representative enzymes.

Combinatorial Synthesis and Antibacterial Evaluation of an Indexed Chalcone Library

A 120-membered chalcone library has been designed and prepared from six differently substituted acetophenones (A1-A6) and 20 benzaldehydes (B1-B20). The library was subjected to biological studies targeted against six bacterial strains. For the identification of the most-active member(s) of the library, the so-called indexed or positional-scanning method was applied. Six out of 26 sub-libraries, i.e., AL1-AL6, were synthesized by keeping the acetophenone moiety A fixed and using equimolar quantities of the 20 different benzaldehydes. The remaining 20 sub-libraries BL1-BL20 were prepared by keeping the benzaldehyde B component fixed and varying the six acetophenones (Table 1). The bactericidal activities of the resulting sub-libraries were tested and used as indices to the rows or columns of a two-dimensional matrix. Finally, parallel synthesis of 24 specific members with the highest-expected antibacterial activities, present in two sub-libraries, was carried out. These chalcones were screened again, and the results were exploited for establishing the structure-activity relationship (SAR) and the identification of the lead compound, which turned out to be 1,3-bis(2-hydroxyphenyl)prop-2-en-1-one (A2B2) in terms of activity towards Staphylococcus aureus and Bacillus subtilis (Tables 5-7).

Asymmetric Synthesis of Multifunctionalized Pyrrolines by a Ruthenium Porphyrin-Catalyzed Three-Component Coupling Reaction

[reaction: see text] Chiral multifunctionalized pyrrolines have been synthesized by a ruthenium porphyrin catalyzed three-component coupling reaction. In a one-pot reaction, ruthenium porphyrins catalyzed in situ generation of chiral azomethine ylides from chiral diazo esters and imines. Asymmetric 1,3-dipolar cycloaddition reactions of the chiral azomethine ylides with dipolarophiles afforded the corresponding pyrrolines in good yields and high diastereoselectivity (up to 92% de).

Flash chemistry using electrochemical method and microsystems

This feature article provides a brief outline of the concept of flash chemistry for conducting extremely fast reactions in organic synthesis using electrochemically generated highly reactive species and microsystems.

Combinatorial synthesis of benztropine libraries and their evaluation as monoamine transporter inhibitors

A combinatorial synthesis of benztropine analogues is presented. Radical azidonation of 3-benzyloxy-8-azabicyclo[3.2.1]octane-8-carboxylic acid tert-butyl ester 3 to 3-(1-azidobenzyloxy)-8-azabicyclo[3.2.1]octane-8-carboxylic acid tert-butyl ester 4 was used as a key step in the synthesis. This step was optimized by adding 10% DMF to the reaction. Reaction of 4 with phenyl magnesium bromide followed by Boc removal and N-methylation gave benztropine 1. Reaction of five-component Grignard reagents with 4 was used to create a two-dimensional library of 25 N-normethylbenztropine analogues. Further reaction of this library with five alkyl bromides was carried out to create a three-dimensional library containing 125 compounds. Screening of the libraries towards binding and inhibition of uptake of the human dopamine (hDAT), serotonin (hSERT) and norepinephrine transporters (hNET) was carried out. None of the synthesized compounds were found to be stronger than benztropine, and none were selective for inhibition of binding over monoamine uptake.

Stereoisomer libraries: total synthesis of all 16 stereoisomers of the pine sawfly sex pheromone by a fluorous mixture-synthesis approach

All 16 stereoisomers of the sex pheromone of pine sawfly (3,7,11-trimethylundecanol propanoate ester) have been synthesized on a 10- to 20-mg scale by a split-parallel fluorous mixture-synthesis approach. Spectral data obtained for all 32 compounds (16 alcohols and the corresponding propionates) matched well with published data, thereby validating the fluorous-tag encoding of diastereoisomers. This fluorous-tag encoding method is recommended for the efficient synthesis of multiple stereoisomers for spectroscopic studies, biological tests, or other structure-function relationships.

Chiral recognition: design and preparation of chiral stationary phases using selectors derived from ugi multicomponent condensation reactions and a combinatorial approach

Combinatorial approaches together with high-throughput screening have been used to develop highly selective stationary phases for chiral recognition. Libraries of potential chiral selectors have been prepared by the Ugi multicomponent condensation reactions and screened for their enantioselectivity using the reciprocal approach involving a chiral stationary phase with immobilized model target compound N-(3,5-dinitrobenzoyl)-alpha-l-leucine. The best candidates were identified from the library of phenyl amides of 2-oxo-azetidineacetic acid derivatives. This screening also enabled specification of the functionalities of the selector desired to achieve the highest level of chiral recognition. The substituents of the phenyl ring adjacent to the chiral center of the selector candidates exhibited the most profound effect on the chiral recognition. The best candidate was then synthesized on a larger scale, resolved into single enantiomers using preparative enantioselective HPLC, and attached to porous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) beads via an ester linkage to afford the desired stationary phase. Selectivities alpha as high as 3.2 were found for the separation of a variety of amino acid derivatives.

Preparation of potential inhibitors of the mur-pathway enzymes on solid support using an acetal linker

Here, we report a novel strategy for the combinatorial or parallel solid-phase synthesis of potential inhibitors of the mur-pathway enzymes. The strategy involves the efficient use of p-alkoxybenzylidene acetal linker for reversible immobilization of sugar scaffolds to solid phase. This methodology was used to synthesize several glycopeptides on solid phase in good yields.

The combined solid/solution-phase synthesis of nitrosamines: the evolution of the "libraries from libraries" concept

The generation of diverse chemical libraries using the "libraries from libraries" concept by combining solid-phase and solution-phase methods is described. The central features of the approaches presented are the use of solid-phase synthesis methods for the generation of a combinatorial polyamine library. Following cleavage from the resin with HF, the polyamine library was reacted with ethyl nitrite in the solution phase to yield the desired nitrosamine library in good yield and purity. The approaches described enable the efficient syntheses of individual nitrosamines as well as mixture-based nitrosamine libraries.

Glass microchip with three-dimensional microchannel network for 2 x 2 parallel synthesis

An integrated multireactor system for 2 x 2 parallel organic synthesis has been developed on a single glass microchip. Three-dimensional channel circuits in the chip were fabricated by laminating three glass plate layers. The fabrication method is a straightforward extension of the conventional one, and topological equivalence for any three-dimensional circuits can be constructed easily with it. 2 x 2 phase-transfer amide formation reactions, which constitute a simple model for combinatorial synthesis, were successfully carried out on the microchip, and the integrity of the three-dimensional circuits was confirmed. Combinatorial chemistry with multi-microreactors, in conjunction with a high-throughput screening method based on micro-TAS technologies, is expected to provide an efficient tool for drug discovery.

Solution-phase preparation of a 560-compound library of individual pure mappicine analogues by fluorous mixture synthesis

Solution-phase mixture synthesis has efficiency advantages and favorable reaction kinetics. Applications of this technique, however, have been discouraged by the difficulty in obtaining individual, pure final products by using conventional separation and identification processes. Introduced here is a new strategy for mixture synthesis that addresses the separation and identification problems. Members of a series of organic substrates are paired with a series of fluorous tags of different chain lengths. The tagged starting materials are then mixed and taken through a multistep reaction process. Fluorous chromatography is used to demix the tagged product mixtures on the basis of the fluorine content of the tags to provide the individual pure components of the mixture, which are detagged to release the final products. The utility of fluorous mixture synthesis is demonstrated by the preparation of a 560-membered library of analogues of the natural product mappicine. A seven-component mixture is carried through a four-step mixture synthesis (two one-pot and two parallel steps) to incorporate two additional points of diversity onto the tetracyclic core. Methods for analysis and purification of the intermediates are established for the quality control of the mixture synthesis.

New tools and concepts for modern organic synthesis

The increasing need to efficiently assemble small molecules as potential modulators of therapeutic targets that are emerging from genomics and proteomics is driving the development of novel technologies for small-molecule synthesis. Here, we describe some of the general applications and approaches to synthesis using one such technology--solid-supported reagents--that has been shown to significantly improve productivity in the generation of combinatorial libraries and complex target molecules.

Toward the combinatorial synthesis of polyketide libraries: asymmetric aldol reactions with alpha-chiral aldehydes on solid support

[reaction: see text] The viability of performing stereocontrolled aldol additions with alpha-chiral aldehydes attached by a silyl linker to a hydroxymethylpolystyrene resin is demonstrated for boron and titanium enolates. Subsequent ketone reduction and manipulation on the solid support leads to elaborate stereopentad sequences, as occur in 6-deoxyerythronolide B and discodermolide.

Simultaneous preparation of four truncated analogues of discodermolide by fluorous mixture synthesis

[structure: see text] Four truncated analogues of the natural product discodermolide were synthesized in a single synthetic sequence. Precursors bearing four different groups at C22, each with a unique fluorous p-methoxybenzyl substituent on the C17 hydroxy group, were mixed and taken through an nine-step sequence. Demixing by fluorous chromatography followed by deprotection and purification provided the individual analogues in 3-7% overall yields and with a savings of 24 synthetic steps. Fluorous mixture synthesis is recommended as a new technique to make multiple natural product analogues in a single multistep synthesis.

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.

Work-up strategies for high-throughput solution synthesis

The key bottleneck in parallel synthesis has, in truth, always been the isolation and purification of the reaction products, rather than carrying out the reactions themselves. Solution-phase chemistry for parallel synthesis has recently been re-emphasized and has stimulated the development of a wide-range of practical tools for efficient high-throughput work-up, which are gaining increasing acceptance in medicinal chemistry groups.

Click Chemistry: Diverse Chemical Function from a Few Good Reactions

Examination of nature's favorite molecules reveals a striking preference for making carbon-heteroatom bonds over carbon-carbon bonds-surely no surprise given that carbon dioxide is nature's starting material and that most reactions are performed in water. Nucleic acids, proteins, and polysaccharides are condensation polymers of small subunits stitched together by carbon-heteroatom bonds. Even the 35 or so building blocks from which these crucial molecules are made each contain, at most, six contiguous C-C bonds, except for the three aromatic amino acids. Taking our cue from nature's approach, we address here the development of a set of powerful, highly reliable, and selective reactions for the rapid synthesis of useful new compounds and combinatorial libraries through heteroatom links (C-X-C), an approach we call "click chemistry". Click chemistry is at once defined, enabled, and constrained by a handful of nearly perfect "spring-loaded" reactions. The stringent criteria for a process to earn click chemistry status are described along with examples of the molecular frameworks that are easily made using this spartan, but powerful, synthetic strategy.

Fluorous mixture synthesis: a fluorous-tagging strategy for the synthesis and separation of mixtures of organic compounds

The solution-phase synthesis of organic compounds as mixtures rather than in individual pure form offers efficiency advantages that are negated by the difficulty in separating and identifying the components of the final mixture. Here, a strategy for mixture synthesis that addresses these separation and identification problems is presented. A series of organic substrates was tagged with a series of fluorous tags of increasing fluorine content. The compounds were then mixed, and multistep reactions were conducted to make enantiomers or analogs of the natural product mappicine. The resulting tagged products were then demixed by fluorous chromatography (eluting in order of increasing fluorine content) to provide the individual pure components of the mixture, which were detagged to release the final products.