Methodologies for Generating Solution-Phase Combinatorial Libraries

Ultrasound-Promoted Scavenging: A Rapid Parallel Purification for Solution Phase Combinatorial Synthesis

Ultrasound irradiation enhances the mass transfer and reaction rate in scavenging, avoiding the trouble of time-consuming purification procedure in solution-phase parallel synthesis. An application of this technique is demonstrated in the scavenging of excess isothiocyanates from reaction mixtures.

Magnetically Retrievable Nanocomposite Based on Thiosemicarbazide-Formaldehyde Resin as a Versatile Nucleophilic Scavenger

A magnetically retrievable nanocomposite was prepared by in situ polycondensation and entrapment of iron oxide nanoparticles. This material was found to be efficient in trapping excess electrophilic reagents such as carbonyl compounds, acid chlorides and isothiocyanates. Advantages of the new scavenger include facile preparation, high loading capacity, low cost, satisfactory swelling properties in polar solvents, and convenient magnetic recovery.

Ultrasound-Assisted Solvent-Free Parallel Synthesis of 3-Arylcoumarins Using N-Acylbenzotriazoles

An ultrasound-assisted one-pot acylation/cyclization reaction between N-acylbenzotriazoles and 2-hydroxybenzaldehydes has been developed for the synthesis of substituted 3-arylcoumarins. Using ultrasound not only allows rapid and clean conversion but also simplifies experimental setup and parallel workup leading to rapid generation of 3-arylcoumarin libraries under mild, solvent-free, and chromatography-free conditions.

N,N-Dicarboxymethyl hydrazine: an old but neglected reagent for chemoselective derivatization of carbonyl compounds

N,N-Dicarboxymethyl hydrazine was found to be a chemoselective derivatization reagent of carbonyl compounds with potential applications in organic synthesis and isolation processes.

Parallel and combinatorial liquid-phase synthesis of alkylbiphenyls using pentaerythritol support

Unfunctionalized alkylbiphenyls were fabricated by a parallel and combinatorial synthesis using pentaerythritol as a tetrapodal soluble support for a sulfonate-based traceless multifunctional linker system. Nickel N-heterocyclic carbene-catalyzed reactions of pentaerythritol tetrakis(biphenylsulfonate)s with primary alkylmagnesium bromides generated the alkylbiphenyl derivatives by desulfitative cleavage/cross-coupling of the C-S bond without any "memory" of the attachment on the support. Though the reactions were completed with sufficient yields in 12 h at room temperature, even with only 1.5 equiv of nucleophiles, they still retained the benefits of facile isolation observed in polymer-supported reactions.

Assembly of four diverse heterocyclic libraries enabled by Prins cyclization, Au-catalyzed enyne cycloisomerization, and automated amide synthesis

We describe a unified synthetic strategy for efficient assembly of four new heterocyclic libraries. The synthesis began by creating a range of structurally diverse pyrrolidinones or piperidinones. Such compounds were obtained in a simple one-flask operation starting with readily available amines, ketoesters, and unsaturated anhydrides. The use of tetrahydropyran-containing ketoesters, which were rapidly assembled by our Prins cyclization protocol, enabled efficient fusion of pyran and piperidinone cores. A newly developed Au(I)-catalyzed cycloisomerization of alkyne-containing enamides further expanded heterocyclic diversity by providing rapid entry into a wide range of bicyclic and tricyclic dienamides. The final stage of the process entailed diversification of each of the initially produced carboxylic acids using a fully automated platform for amide synthesis, which delivered 1872 compounds in high diastereomeric and chemical purity.

Aryl nitrile oxide cycloaddition reactions in the presence of pinacol boronic acid ester

An aryl substrate with dual functionality consisting of a nitrile oxide and a pinacolyl boronate ester was prepared by mild hypervalent iodine oxidation (diacetoxyiodobenzene) of the corresponding aldoxime, without decomposition of the boronate functionality. The nitrile oxide was trapped in situ with a variety of dipolarophiles to yield aryl isoxazolines with the boronate ester function intact and available for subsequent reaction.

Microfluidic platform for combinatorial synthesis in picolitre droplets

This paper presents a droplet-based microfluidic platform for miniaturized combinatorial synthesis. As a proof of concept, a library of small molecules for early stage drug screening was produced. We present an efficient strategy for producing a 7 × 3 library of potential thrombin inhibitors that can be utilized for other combinatorial synthesis applications. Picolitre droplets containing the first type of reagent (reagents A(1), A(2), …, A(m)) were formed individually in identical microfluidic chips and then stored off chip with the aid of stabilizing surfactants. These droplets were then mixed to form a library of droplets containing reagents A(1-m), each individually compartmentalized, which was reinjected into a second microfluidic chip and combinatorially fused with picolitre droplets containing the second reagent (reagents B(1), B(2), …, B(n)) that were formed on chip. The concept was demonstrated with a three-component Ugi-type reaction involving an amine (reagents A(1-3)), an aldehyde (reagents B(1-7)), and an isocyanide (held constant), to synthesize a library of small molecules with potential thrombin inhibitory activity. Our technique produced 10(6) droplets of each reaction at a rate of 2.3 kHz. Each droplet had a reaction volume of 3.1 pL, at least six orders of magnitude lower than conventional techniques. The droplets can then be divided into aliquots for different downstream screening applications. In addition to medicinal chemistry applications, this combinatorial droplet-based approach holds great potential for other applications that involve sampling large areas of chemical parameter space with minimal reagent consumption; such an approach could be beneficial when optimizing reaction conditions or performing combinatorial reactions aimed at producing novel materials.

Solution-phase parallel synthesis of a diverse library of 1,2-dihydroisoquinolines

Synthesis of a 105 membered library of 1,2-dihydroisoquinolines is described. The 1,2-dihydroisoquinoline compounds have been prepared in good yields using a Lewis acid and organocatalyst-cocatalyzed multicomponent reaction of 2-(1-alkynyl)benzaldehydes, amines, and ketones. Various indoles have also been employed as pronucleophiles, furnishing 1-(3-indolyl)-1,2-dihydroisoquinolines. The halogen functionality present in some of the synthesized compounds allows for further diversification by palladium-catalyzed Suzuki−Miyaura and Sonogashira cross-couplings to give more diversified 1,2-dihydroisoquinoline derivatives.

Estimation of affinities of ligands in mixtures via magnetic recovery of target-ligand complexes and chromatographic analyses: chemometrics and an experimental model

Abstract

Conclusions

This new method is robust and effective for each mixture possessing a limited number of candidate ligands whose molar quantities have moderate differences, and its integration with PCS has promise to routinely practice the mixture-based library strategy.

A Facile Approach to the Synthesis of 3,4-Disubstituted-2-Aminothiazolium Derivatives through the Use of A "Volatilizable" Support

A facile solid-phase synthetic approach to the synthesis of 3,4-disubstituted-2-aminothiazolium derivatives was reported. Functionalized aminomethylphenyl silica gel was used as a "volatilizable" support. The products were cleaved with 10% HF and were obtained in high yields and purities.

Synthesis of tetrahydro-beta-carbolines and tetrahydroisoquinolines fused to pyrrolidines and solution-phase parallel acylation

A structurally diverse library of potentially pharmacologically important compounds employing classical synthesis methods is described. These compounds are synthesized from beta-aryl pyrrolidines, providing products with the 2-arylethyl amine moiety, a structural feature often encountered in compounds active in the central nervous system. Tri- and tetracyclic scaffolds were obtained using the Pictet-Spengler reaction, resulting in hexahydropyrrolo[3,4-c]isoquinolines 1-3, an octahydropyrrolo[3',4':5,6]pyrido[3,4-b]indole 4, and a hexahydrofuro[2,3-d]pyrrolo[3,4-b]pyridine 5. These scaffolds were further derivatized in parallel fashion to make a 32-membered amide library with yields from 62 to 100% (90% average) and purities from 63 to 100% (93% average).

Structure-activity relationships of carbocyclic 6-benzylthioinosine analogues as subversive substrates of Toxoplasma gondii adenosine kinase

Carbocyclic 6-benzylthioinosine analogues were synthesized and evaluated for their binding affinity against Toxoplasma gondii adenosine kinase [EC.2.7.1.20]. Various substituents on the aromatic ring of the 6-benzylthio group resulted in increased binding affinity to the enzyme as compared to the unsubstituted compound. Carbocyclic 6-(p-methylbenzylthio)inosine 9n exhibited the most potent binding affinity. Docking simulations were performed to position compound 9n into the T. gondii adenosine kinase active site to determine the probable binding mode. Experimental investigations and theoretical calculations further support that an oxygen atom of the sugar is not critical for the ligand-binding. In agreement with its binding affinity, carbocyclic 6-(p-methylbenzylthio)inosine 9n demonstrated significant anti-toxoplasma activity (IC(50)=11.9microM) in cell culture without any apparent host-toxicity.

Solution-phase parallel synthesis of a multi-substituted benzo[b]thiophene library

Generation of a library using parallel syntheses of multi-substituted benzo[b]thiophenes is described. The requisite 3-iodobenzo[b]thiophenes are readily prepared in excellent yields from various alkynes bearing electron-rich aromatic rings by electrophilic cyclization using I(2) in CH(2)Cl(2). The heteroaromatic carbon-iodine bonds allow further diversification by palladium-catalyzed Suzuki-Miyaura, Sonogashira, Heck, and carboalkoxylation chemistry to give multi-substituted benzo[b]thiophene derivatives.

Palladium-catalyzed coupling of ammonia with aryl chlorides, bromides, iodides, and sulfonates: a general method for the preparation of primary arylamines

We report that the complex generated from Pd[P(o-tol)(3)](2) and the alkylbisphosphine CyPF-t-Bu is a highly active and selective catalyst for the coupling of ammonia with aryl chlorides, bromides, iodides, and sulfonates. The couplings of ammonia with this catalyst conducted with a solution of ammonia in dioxane form primary arylamines from a variety of aryl electrophiles in high yields. Catalyst loadings as low as 0.1 mol % were sufficient for reactions of many aryl chlorides and bromides. In the presence of this catalyst, aryl sulfonates also coupled with ammonia for the first time in high yields. A comparison of reactions in the presence of this catalyst versus those in the presence of existing copper and palladium systems revealed a complementary, if not broader, substrate scope. The utility of this method to generate amides, imides, and carbamates is illustrated by a one-pot synthesis of a small library of these carbonyl compounds from aryl bromides and chlorides, ammonia, and acid chlorides or anhydrides. Mechanistic studies show that reactions conducted with the combination of Pd[P(o-tol)(3)](2) and CyPF-t-Bu as catalyst occur with faster rates and higher yields than those conducted with CyPF-t-Bu and palladiun(II) as catalyst precursors because of the low concentration of active catalyst that is generated from the combination of palladium(II), ammonia, and base.

Flash chemistry: fast chemical synthesis by using microreactors

This concept article provides a brief outline of the concept of flash chemistry for carrying out extremely fast reactions in organic synthesis by using microreactors. Generation of highly reactive species is one of the key elements of flash chemistry. Another important element of flash chemistry is the control of extremely fast reactions to obtain the desired products selectively. Fast reactions are usually highly exothermic, and heat removal is an important factor in controlling such reactions. Heat transfer occurs very rapidly in microreactors by virtue of a large surface area per unit volume, making precise temperature control possible. Fast reactions often involve highly unstable intermediates, which decompose very quickly, making reaction control difficult. The residence time can be greatly reduced in microreactors, and this feature is quite effective in controlling such reactions. For extremely fast reactions, kinetics often cannot be used because of the lack of homogeneity of the reaction environment when they are conducted in conventional reactors such as flasks. Fast mixing using micromixers solves such problems. The concept of flash chemistry has been successfully applied to various organic reactions including a) highly exothermic reactions that are difficult to control in conventional reactors, b) reactions in which a reactive intermediate easily decomposes in conventional reactors, c) reactions in which undesired byproducts are produced in the subsequent reactions in conventional reactors, and d) reactions whose products easily decompose in conventional reactors. The concept of flash chemistry can be also applied to polymer synthesis. Cationic polymerization can be conducted with an excellent level of molecular-weight control and molecular-weight distribution control.

Studies towards the synthesis of methionine aminopeptidase inhibitors: diversification utilizing a ROMP-derived coupling reagent

Efforts to synthesize potential methionine aminopeptidase inhibitors is described. Preliminary SAR and docking studies served as a guide to design the compound libraries. "Chromatography-free" synthesis of various heterocyclic amides was realized by using a high-load, soluble coupling reagent derived via ring-opening metathesis polymerization (ROMP). Subsequent microwave-assisted Suzuki reactions with ortho-substituted arylboronic acids, followed by chromatographic purification afforded a 55-member library in high yields and purities. While the biological testing was not satisfactory, concurrent X-ray crystallography studies revealed key structural features essential for inhibition of methionine aminopeptidase, which directed fruitful results reported in the accompanying manuscript. In addition, in silico Lipinksi profiles and ADME properties of the library are also reported.

meso-Tetra(pentafluorophenyl)porphyrin as an efficient platform for combinatorial synthesis and the selection of new photodynamic therapeutics using a cancer cell line

The four para fluoro groups on 5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin (TPPF20) are known to react with a variety of nucleophiles, but the reaction conditions for this substitution reaction depend on the nature of the nucleophiles, e.g. primary amines versus thiols. Glycosylated derivatives of this core porphyrin have been shown to be effective photodynamic agents in the induction of necrosis or apoptosis in several cancer cell lines. The present report demonstrates that TPPF20 can be used as a core platform to efficiently generate a variety of solution-phase combinatorial libraries. The focused combinatorial libraries have substituents that are chosen from a set of motifs known to bind biopolymers such as DNA, be taken up by cancer cells, or to render the compounds amphipathic. Incubation of a breast cancer cell line with these solution-phase libraries, followed by cell lyses and extraction, affords a selection assay. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the extracts allows identification of the molecules taken up by the cells. Cell binding assays of the winning compounds synthesized directly indicate that both glycosylation and amphipathicity are key properties since neither tetraglycosylated porphyrins nor those with four polar groups are selected to the same extent. In addition, photodynamic efficacy was evaluated.

Traceless Liquid-Phase Synthesis of Biphenyls and Terphenyls Using Pentaerythritol as a Tetrapodal Soluble Support

Application of a novel sulfonate-based traceless multifunctional linker system using pentaerythritol as a tetrapodal soluble support was demonstrated using liquid-phase parallel and combinatorial preparation of biphenyl and terphenyl compounds. Nickel-catalyzed reactions of pentaerythritol tetrakis(arenesulfonate)s with arylmagnesium bromides generated the desired products in sufficient yields through reductive cleavage/cross-coupling of the C-S bond. Homogeneous pentaerythritol-supported reactions could be accomplished using less nucleophile with shorter reaction periods than could the corresponding heterogeneous polymer-supported reactions. This liquid-phase approach using a small polyfunctionalized support combines advantages of solution-phase and solid-phase syntheses by allowing high reactivity, high atom economy, simple isolation, and real-time monitoring of the reaction progress.

Parallel Solution-Phase Synthesis of 2-Alkylthio-5-arylidene-3,5-dihydro-4H-imidazol-4-one by One-Pot Three-Component Domino Reaction

A practical protocol for the preparation of a parallel solution-phase library of 5-arylidene imidazolone is reported. Target compounds were obtained in good yield, stereoselectively, and purity by one-pot domino reaction from various thiohydantoines, arylaldimines, and halogenoalkanes. Purification of the final products by recrystallization with a mixture of pentane/ethanol allowed simple isolation of the 17 components of the array.

Synthesis, biological evaluation and molecular modeling studies of N6-benzyladenosine analogues as potential anti-toxoplasma agents

Toxoplasma gondii is an opportunistic pathogen responsible for toxoplasmosis. T. gondii is a purine auxotroph incapable of de novo purine biosynthesis and depends on salvage pathways for its purine requirements. Adenosine kinase (EC.2.7.1.20) is the major enzyme in the salvage of purines in these parasites. 6-Benzylthioinosine and analogues were established as "subversive substrates" for the T. gondii, but not for the human adenosine kinase. Therefore, these compounds act as selective anti-toxoplasma agents. In the present study, a series of N(6)-benzyladenosine analogues were synthesized from 6-chloropurine riboside with substituted benzylamines via solution phase parallel synthesis. These N(6)-benzyladenosine analogues were evaluated for their binding affinity to purified T. gondii adenosine kinase. Furthermore, the anti-toxoplasma efficacy and host toxicity of these compounds were tested in cell culture. Certain substituents on the aromatic ring improved binding affinity to T. gondii adenosine kinase when compared to the unsubstituted N(6)-benzyladenosine. Similarly, varying the type and position of the substituents on the aromatic ring led to different degrees of potency and selectivity as anti-toxoplasma agents. Among the synthesized analogues, N(6)-(2,4-dimethoxybenzyl)adenosine exhibited the most favorable anti-toxoplasma activity without host toxicity. The binding mode of the synthesized N(6)-benzyladenosine analogues were characterized to illustrate the role of additional hydrophobic effect and van der Waals interaction within an active site of T. gondii adenosine kinase by induced fit molecular modeling.

Diversity-Oriented Asymmetric Synthesis of Hapalosin: Construction of Three Small C9/C4/C3-Modified Hapalosin Analogue Libraries

A flexible approach to the beta-hydroxy gamma-amino acid residue (fragment C) of hapalosin has been developed on the basis of the the regio- and diastereoselective Grignard reaction. The method allows the introduction of different side chains at the C9 of hapalosin. Asymmetric syntheses of hapalosin (1a), 9-homohapalosin (1b), 9-i-butyl-hapalosin (1c), 8-epi-hapalosin (epi-1a), and three small libraries diversified at C9 (3-member, 1L3), C9/ C4 (9-member, 1L9), or C9/C4/C3 (27-member, 1L27) have been produced using this method.

Solution-phase parallel synthesis of a library of delta(2)-pyrazolines

A parallel synthesis of a library (80 members) of 2-pyrazolines in solution phase is described. The 2-pyrazoline core was accessed through the [3 + 2] cycloaddition of nitrilimines with enoyl oxazolidinones. The cycloaddition provided two regioisomers, the major product being the C regioisomer. The oxazolidinone moiety was further reduced to the primary alcohol, producing another library of 5-hydroxymethyl-2-pyrazolines. The Lipinski profiles and calculated ADME properties of the compounds are also reported.

Advances in Microwave-Assisted Combinatorial Chemistry Without Polymer-Supported Reagents

Combinatorial methodologies have dramatically changed the chemical research and discovery process, offering an unlimited source of new molecule entities to be screened for activity. The application of microwave irradiation in Combinatorial Chemistry and high-throughput synthesis has become increasingly popular. By taking advantage of this energy source, compound libraries for lead generation can be assembled in a fraction of time required by conventional thermal heating. This review focuses on the advances in developing synthetic methodologies in microwave without polymer-supported reagents suitable for combinatorial chemistry, including the advances in microwave-assisted fluorous synthesis technology.

Platform Synthesis: A Useful Strategy for Rapid and Systematic Generation of Molecular Diversity

Emergence of library-based approaches have changed the way of developing new functional molecules in materials science and pharmaceutical science. Therefore, reliable methods for rapid and systematic generation of functional molecules are highly called for in this field. We herein describe our concept of "platform synthesis" as a useful strategy for generating molecular diversity. This simple yet powerful strategy realizes the synthesis of a number of interesting multifunctional molecules, such as multisubstituted olefins, in a programmable and diversity-oriented format. As well as applications to the synthesis of pharmaceutically important molecules, such as tamoxifen and CDP840, applications to materials science, which have led to the discovery of interesting fluorescent materials and properties, are also described.