Synthesis Of Combinatorial Libraries Research Articles

Encoding Combinatorial Libraries: A Novel Application of Fluorescent Silica Colloids

A major challenge associated with using large chemical libraries synthesized on microscopic solid support beads is the rapid discrimination of individual compounds in these libraries. This challenge can be overcome by encoding the beads with 1 μm silica colloidal particles (“reporters”) that contain specific and identifiable combinations of fluorescent dyes. The colored bar code generated on support beads during combinatorial library synthesis can be easily, rapidly, and inexpensively decoded through the use of fluorescence microscopy. All reporters are precoated with polyelectrolytes [poly(acrylic acid), PAA, poly(sodium 4-styrenesulfonate), PSSS, polyethylenimine, PEI, and/or poly(diallyldimethylammonium chloride), PDADMAC] with the aim of enhancing surface charge, promoting electrostatic attraction to the bead, and facilitating polymer bridging between the bead and reporter for permanent adhesion. As shown in this article, reporters coated with polyelectrolytes clearly outperform uncoated reporters with regard to quantity of attached reporters per bead (54 ± 23 in 2500 μm2 area for PEI/PAA coated and 11 ± 6 for uncoated reporters) and minimization of cross-contamination (1 red reporter in 2500 μm2 area of green-labeled bead for PEI/PAA coated and 26 ± 15 red reporters on green-labeled beads for uncoated reporters after 10 days). Examination of various polyelectrolyte systems shows that the magnitude of the ξ-potential of polyelectrolyte-coated reporters (−64 mV for PDADMAC/PSSS and −42 mV for PEI/PAA-coated reporters) has no correlation with the number of reporters that adhere to the solid support beads (21 ± 16 in 2500 μm2 area for PDADMAC/PSSS and 54 ± 23 for PEI/PAA-coated reporters). The contribution of polymer bridging to the adhesion has a far greater influence than electrostatic attraction and is demonstrated by modification of the polyelectrolyte multilayers using γ irradiation of precoated reporters either in aqueous solution or in polyelectrolyte solution.

Synthesis and Biological Evaluation of a Focused Mixture Library of Analogues of the Antimitotic Marine Natural Product Curacin A

The marine natural product curacin A served as the lead compound for the combinatorial synthesis of 6-compound mixture libraries. Fluorous trapping with a vinyl ether tag was used to streamline purification of the heterogeneous multicomponent reaction products and provide chemically clearly defined mixtures. The screening profile of one mixture library, 17mix, was attractive enough to warrant the re-synthesis of the individual compounds, and an evaluation of their biological effects validated the composite data previously obtained on the product mixture. The most active of these compounds inhibited tubulin polymerization with an IC50 of ca. 1 μM, showed an average growth inhibition activity GI50 of ca. 250 nM, inhibited [3H]colchicine binding to tubulin, and blocked mitotic progression at nanomolar concentrations. These compounds represent some of the most potent synthetic curacin A analogues identified to date but have simplified structures, greater water solubility, and increased chemical stability.

Comprehensive survey of combinatorial library synthesis: 1999.

ADVERTISEMENT RETURN TO ISSUEReviewNEXTComprehensive Survey of Combinatorial Library Synthesis: 1999Roland E. DolleView Author Information Department of Chemistry, Pharmacopeia, Inc., P.O. Box 5350, Princeton, New Jersey 08543-5350 Cite this: J. Comb. Chem. 2000, 2, 5, 383–433Publication Date (Web):September 12, 2000Publication History Received30 June 2000Published online12 September 2000Published inissue 1 September 2000https://doi.org/10.1021/cc000055xCopyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1024Altmetric-Citations134LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (2 MB) SUBJECTS:Inhibitors,Optimization,Organic polymers,Peptides and proteins,Receptors Get e-Alerts

Non-Amide-Based Combinatorial Libraries Derived fromN-Boc-Iminodiacetic Acid: Solution-Phase Synthesis of Piperazinone Libraries with Activity Against LEF-1/β-Catenin-Mediated Transcription

The development of a solution-phase approach to the rapid, parallel synthesis of highly functionalized piperazinones in only four steps starting from N-Boc-iminodiacetic acid is detailed. The efforts represent the extension of the solution-phase synthesis of combinatorial libraries from N-Boc-iminodiacetic acid to non-amide-based libraries where simple liquid-liquid extractions are employed to purify all reaction products. This methodology was applied to the synthesis of a diverse 150-member library with substituents in three positions of the piperazinone core. Screening results from a luciferase reporter assay indicate that a number of library members are novel repressors of LEF-1/β-catenin-mediated transcription, and may be effective agents against colorectal tumors. Two secondary libraries (100 members each) designed from these lead structures were synthesized and screened, providing additional active agents and insight into key structure-activity relationships in the series. These compounds represent only the second class of small molecules which repress transcription of reporter genes containing LEF-1 responsive elements, and the first group not based on DNA minor-groove-binding agents.

A Modular Approach to Structurally Diverse Bidentate Chelate Ligands for Transition Metal Catalysis

A modular approach to a new class of structurally diverse bidentate P/N, P/P, P/S, and P/Se chelate ligands has been developed. Starting from hydroquinone, various ligands were synthesized in a divergent manner via orthogonally bis-protected bromohydroquinones as the central building block. The first donor functionality (L1) is introduced to the aromatic (hydroquinone) ligand backbone either by Pd-catalyzed cross-coupling (Suzuki coupling) with hetero-aryl bromides, by Pd-catalyzed amination, or by lithiation and subsequent treatment with electrophiles (e.g., chlorophosphanes, disulfides, diselenides, or carbamoyl chlorides). After selective deprotection, the second ligand tooth (L2) is attached by reaction of the phenolic OH functionality with a chlorophosphane, a chlorophosphite, or a related reagent. Some of the resulting chelate ligands were converted into the respective PdX2 complexes (X=Cl, I), two of which were characterized by X-ray crystallography. The methodology developed opens an access to a broad variety of new chiral and achiral transition metal complexes and is generally suited for the solid-phase synthesis of combinatorial libraries, as will be reported separately.

A modular approach to structurally diverse bidentate chelate ligands for transition metal catalysis

A modular approach to a new class of structurally diverse bidentate P/N, P/P, P/S, and P/Se chelate ligands has been developed. Starting from hydroquinone, various ligands were synthesized in a divergent manner via orthogonally bis-protected bromohydroquinones as the central building block. The first donor functionality (L1) is introduced to the aromatic (hydroquinone) ligand backbone either by Pd-catalyzed cross-coupling (Suzuki coupling) with hetero-aryl bromides, by Pd-catalyzed amination, or by lithiation and subsequent treatment with electrophiles (e.g., chlorophosphanes, disulfides, diselenides, or carbamoyl chlorides). After selective deprotection, the second ligand tooth (L2) is attached by reaction of the phenolic OH functionality with a chlorophosphane, a chlorophosphite, or a related reagent. Some of the resulting chelate ligands were converted into the respective PdX2 complexes (X = Cl, I), two of which were characterized by X-ray crystallography. The methodology developed opens an access to a broad variety of new chiral and achiral transition metal complexes and is generally suited for the solid-phase synthesis of combinatorial libraries, as will be reported separately.

Euclidean shape-encoded combinatorial chemical libraries.

A method for the encoding of split/mix combinatorial chemical libraries based on Euclidean shapes is described. The shapes are fashioned from a polymeric matrix designed to swell in common organic solvents while retaining their unique forms, and exhibit good mechanical strength. The lightly crosslinked gel-type polymer was processed into an array of Euclidean forms that serve as encoding elements in the synthesis of combinatorial chemical libraries by using the split/pool methodology. To assess the viability of this approach, a library of compounds based on a urea scaffold was prepared. The validity of this methodology was demonstrated through correct deconvolution of the library mixture by shape discrimination. Furthermore, because the shapes used have a large surface area to volume ratio, each monolith can act as an independent chemical reactor. This simplifies the analytical identification process because each compound can be prepared in significant quantities and isolated as single entities. Given the high loading capacity of the monoliths and the conceptually simple encoding strategy, it is envisioned that these Euclidean forms will find significant application in combinatorial and high-throughput synthetic chemistry.

A solid-phase synthetic route to substituted 7-azabenzimidazoles suitable for combinatorial library synthesis

A novel route for the solid-phase synthesis of 1,2,5-substituted 7-azabenzimidazole derivatives has been developed. Primary amines are attached to an aldehyde resin then coupled to 6-chloro-5-nitro-nicotinyl chloride. Subsequent alkylation with amines, reduction of the nitro group and cyclisation with aldehydes gives 1,2,5-substituted 7-azabenzimidazole derivatives.

Design of an organic sequence suitable for the solid phase combinatorial synthesis of libraries of macro-heterocycles

The solid as well as solution phase synthesis of two 14-membered macro-heterocycles is reported. The macrocycles are built out of four or three major building blocks and contain serine, a trans alkene and the malonate unit inside the framework. The macrocyclization was an SN2 reaction between a nucleophilic malonate anion and an allylic chloride leaving group. The first macrocycle, an ether, was obtained with an overall yield of 8% for the eleven steps on solid support similar to the 11% yield in solution. The overall yield for the second target macrolactone was 45% on solid phase for the six steps and was higher than in solution (35%). The stability of the DHP linker to various reagents and reactions conditions is noteworthy.

A new polymer-bound N-hydroxysuccinimidyl active ester linker

Synthesis of a new N-hydroxysuccinimidyl resin is described and the N-acylation with this resin provides amide products in high yields and excellent purities. This new linker is suitable for combinatorial library synthesis.

Mass spectrometry in combinatorial chemistry

In the fast expanding field of combinatorial chemistry, profiling libraries has always been a matter of concern—as illustrated by the buoyant literature over the past seven years. Spectroscopic methods, including especially mass spectrometry and to a lesser extent IR and NMR, have been applied at different levels of combinatorial library synthesis: in the rehearsal phase to optimize the chemistry prior to library generation, to confirm library composition, and to characterize after screening each structure that exhibits positive response. Most of the efforts have been concentrated on library composition assessment. The difficulties of such analyses have evolved from the infancy of the combinatorial concept, where large mixtures were prepared, to the recent parallel syntheses of collections of discrete compounds. Whereas the complexity of the analyses has diminished, an increased degree of automation was simultaneously required to achieve efficient library component identification and quantification. In this respect, mass spectrometry has been found to be the method of choice, providing rapid, sensitive, and informative analyses, especially when coupled to chromatographic separation. Fully automated workstations able to cope with several hundreds of compounds per day have been designed. After a brief introduction to describe the combinatorial approach, library characterization will be discussed in detail, considering first the solution-based methodologies and secondly the support-bound material analyses. © 2000 John Wiley & Sons, Inc., Mass Spec Rev 19: 139–161, 2000

ChemInform Abstract: Total Synthesis of Sarcodictyins A and B Solid‐ and Solution‐phase Synthesis and Biological Evaluation of Combinatorial Sarcodictyin Libraries

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Combinatorial ion synthesis and ion beam analyses of materials libraries on thermally grown SiO 2

We first report a method combining ion implantation and physical masking to generate material libraries of various ion-implanted samples. This approach offers rapid synthesis of samples with potential new compounds formed in the matrix, which may have specific luminescent properties. The depth-resolved cathodoluminescence (CL) measurements, accompanied with Rutherford backscattering spectrometry (RBS) and proton elastic scattering (PES) revealed some specific optical properties in the samples correlated with implanted ion distributions. These measurements are capable of nondestructively and rapidly characterizing the composition and the inhomogeneity of the combinatorial film libraries, which may determine their physical properties.

Toward Larger Chemical Libraries: Encoding with Fluorescent Colloids in Combinatorial Chemistry

Chemical library technology plays a central role in research areas such as drug discovery and gene screening.1 The most powerful combinatorial library synthesis method is the iterative “split and mix” synthesis on insoluble microscopic beads.2 This technique is an efficient method for accessing all combinations of chosen monomers such as nucleic acids, amino acids, or sugars in a small number of reactions. Compound identification from such large pools of compounds, be it bound to resin (one compound per bead) or in solution, is achieved through covalent attachment of molecular tags to the beads3 or through iterative deconvolution technologies.4 Herein we introduce an encoding method that involves physically attaching fluorescent colloidal particles (“reporters”) to the surface of solid support beads during split and mix syntheses, to produce an information-rich, colored barcode that can be easily, rapidly, and inexpensively decoded using fluorescence microscopy. This “colloidal barcoding” technique eliminates the need for compatible tagging chemistry in conventional molecular tagging3 or optical encoding5 procedures and permits unambiguous identification of compounds in libraries of any size and type.

Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin.

We have developed a strategy for the synthesis of positional-scanning synthetic combinatorial libraries (PS-SCL) that does not depend on the identity of the P1 substituent. To demonstrate the strategy, we synthesized a tetrapeptide positional library in which the P1 amino acid is held constant as a lysine and the P4-P3-P2 positions are positionally randomized. The 6,859 members of the library were synthesized on solid support with an alkane sulfonamide linker, and then displaced from the solid support by condensation with a fluorogenic 7-amino-4-methylcoumarin-derivatized lysine. This library was used to determine the extended substrate specificities of two trypsin-like enzymes, plasmin and thrombin, which are involved in the blood coagulation pathway. The optimal P4 to P2 substrate specificity for plasmin was P4-Lys/Nle (norleucine)/Val/Ile/Phe, P3-Xaa, and P2-Tyr/Phe/Trp. This cleavage sequence has recently been identified in some of plasmin's physiological substrates. The optimal P4 to P2 extended substrate sequence determined for thrombin was P4-Nle/Leu/Ile/Phe/Val, P3-Xaa, and P2-Pro, a sequence found in many of the physiological substrates of thrombin. Single-substrate kinetic analysis of plasmin and thrombin was used to validate the substrate preferences resulting from the PS-SCL. By three-dimensional structural modeling of the substrates into the active sites of plasmin and thrombin, we identified potential determinants of the defined substrate specificity. This method is amenable to the incorporation of diverse substituents at the P1 position for exploring molecular recognition elements in proteolytic enzymes.

Solid phase synthesis of 1-substituted pyroglutamates

Starting from a dipeptide containing the t Bu ester of glutamic acid, disubstituted 2-pyrrolidinones were prepared in good yield and high purity. Cyclization takes place using DPPA as activating reagent. Diversity was achieved through reductive alkylation of the starting dipeptide and N-alkylation following the cyclization step. This approach has been used for the synthesis of both individual compounds and mixture-based combinatorial libraries.

The Sulfamate Functional Group as a New Anchor for Solid-Phase Organic Synthesis

[reaction: see text] Sulfamate derivatives were loaded on trityl chloride resin, and two variants of cleavage were developed for this sulfamate anchor: an acid treatment to easily restore the free sulfamate and a nucleophilic treatment to generate the corresponding phenol. In addition to loading/cleavage assays and stability experiments, a model sequence of reactions was performed with the new sulfamate anchor to show its applicability in further combinatorial solid-phase synthesis of libraries of biologically relevant sulfamate derivatives.

Mass spectrometry in combinatorial chemistry.

In the fast expanding field of combinatorial chemistry, profiling libraries has always been a matter of concern--as illustrated by the buoyant literature over the past seven years. Spectroscopic methods, including especially mass spectrometry and to a lesser extent IR and NMR, have been applied at different levels of combinatorial library synthesis: in the rehearsal phase to optimize the chemistry prior to library generation, to confirm library composition, and to characterize after screening each structure that exhibits positive response. Most of the efforts have been concentrated on library composition assessment. The difficulties of such analyses have evolved from the infancy of the combinatorial concept, where large mixtures were prepared, to the recent parallel syntheses of collections of discrete compounds. Whereas the complexity of the analyses has diminished, an increased degree of automation was simultaneously required to achieve efficient library component identification and quantification. In this respect, mass spectrometry has been found to be the method of choice, providing rapid, sensitive, and informative analyses, especially when coupled to chromatographic separation. Fully automated workstations able to cope with several hundreds of compounds per day have been designed. After a brief introduction to describe the combinatorial approach, library characterization will be discussed in detail, considering first the solution-based methodologies and secondly the support-bound material analyses.

Solid-phase synthesis of phenolic steroids: from optimization studies to a convenient procedure for combinatorial synthesis of biologically relevant estradiol derivatives.

During the course of our studies on therapeutic agents for the treatment of breast cancer, we became interested in the solid-phase combinatorial synthesis of estradiol derivatives that contain a functionalized side chain at either position 16 beta or 7 alpha. Both types of compounds have already demonstrated inhibitory activity toward both biosynthesis and action of estradiol. As a first step, two versatile precursors bearing an azidoalkyl side chain at either position 16 beta or 7 alpha of estradiol were synthesized using standard solution-phase methods. Afterward, the effectiveness of five linkers to attach the phenolic function of these estradiol derivatives to a polystyrene resin was investigated; they were benzylic ether (Merrifield), 4-alkoxy-benzylic ethers (Wang, Sheppard), tetrahydropyranyl ether (Ellman), benzoic ester, and o-nitrobenzyl ether. To test the linker in a synthetic context, a short sequence of reactions, including reduction of the azide and acylation of the corresponding amine, was performed on the polymer-bound estradiol derivative. While all of the tested linkers proved effective in attaching the phenol functionality of the precursor, only the o-nitrobenzyl ether photolabile linker enabled the release of the final products in acceptable purities. Consequently, this linker was used to perform successfully the solid-phase synthesis of four different classes of estradiol derivatives in acceptable yields and excellent purities. This study was preliminary to the combinatorial synthesis of larger libraries of biologically relevant estradiol derivatives.

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.