Showing papers in "Combinatorial Chemistry & High Throughput Screening in 1998"

Evaluation of the antioxidant potential of natural products.

Abstract: Since reactive oxygen radicals play an important role in carcinogenesis and other human disease states, antioxidants present in consumable fruits, vegetables, and beverages have received considerable attention as cancer chemopreventive agents Thus, in order to identify antioxidants in plant extracts, test materials were assessed for potential to scavenge stable 1,2-diphenyl-2-picrylhydrazyl (DPPH) free radicals, reduce TPA-induced free radical formation in cultured HL-60 human leukemia cells, and inhibit responses observed with a xanthine/xanthine oxidase assay system Approximately 700 plant extracts were evaluated, and 28 were found to be active in the DPPH free radical scavenging assay Based on secondary analyses performed to assess inhibition of 7,12-dimethylbenz(a)anthracene-induced preneoplastic lesion formation with a mouse mammary organ culture model, Chorizanthe diffusa Benth (Polygonaceae), Mezoneuron cucullatum Roxb (Leguminosae), Cerbera manghas L (Apocynaceae) and Daphniphyllum calycinum Benth (Daphniphyllaceae) were selected and subjected to bioassay-guided fractionation 5,7,3',5'-Tetrahydroxy-8,4'-dimethoxyflavonol, 5,8,4'-trihydroxy-7,3'-dimethoxyflavonol, 5,3',4'-trihydroxy-7-methoxyflavonol, and 6,3',4'-trihydroxy-7-methoxyflavonol were identified as active principles from C diffusa Piceatannol, trans-resveratrol, apigenin and scirpusin A were found as the active principles of M cucullatum, olivil, (-)-carinol, and (+)-cycloolivil were active principles from C manghas, and 5,6,7,4'-tetrahydroxyflavone 3-O-rutinoside and kaempferol 3-O-neohesperidoside were active principles from D calycinum Of these substances, the hydroxystilbenes piceatannol and transresveratrol have thus far been shown to inhibit carcinogen-induced preneoplastic lesion formation in the mouse mammary gland organ culture model

Isocyanide based multi component reactions in combinatorial chemistry.

Abstract: Although usually regarded as a recent development, the combinatorial approach to the synthesis of libraries of new drug candidates was first described as early as 1961 using the isocyanide-based one-pot multicomponent Ugi reaction. Isocyanide-based multi component reactions (MCR's) markedly differ from their usual two component counterparts. In the context of combinatorial chemistry, they offer more structural variations, more accessible compounds and more diversity than any other previously known reaction. This review examines the history of isocyanide based MCR's and their applicability in combinatorial chemistry.

Solution phase combinatorial chemistry.

Abstract: Combinatorial chemistry and parallel array synthesis techniques are now used extensively in the drug discovery process. Although published literature has been dominated by solid phase chemistry approaches, the use of solution phase techniques has also been widely explored. This review considers the advantages and disadvantages of choosing solution phase approaches in the various stages of drug discovery and optimisation, and assesses the practical issues related to these approaches. The uses of standard solution chemistry, the related liquid phase approach, and of supported materials to enhance solution phase chemistry are all illustrated by a comprehensive review of the published literature over the past three years.

Solid phase synthesis of heterocycles by cyclization/cleavage methodologies.

Abstract: For the solid phase preparation of various (pharmacologically important) heterocycles, cyclization/cleavage (C/C) or cyclorelease strategies proved to be superior. CC approaches take utmost advantage of the benefits of solid phase synthesis. Besides the practical benefits of solid phase reactions, cyclative release approaches are distinguished especially because of the generally found high purity of the final detached products, since only the anticipated structures cleave off the resin. Also cyclization/cleavage strategies are "traceless", as the obtained moiety after cyclization is part of the formed heterocycle. Over the last thirty years numerous approaches towards important heterocycle classes have been published. Among the successfully applied strategies are carbon-nitrogen (sulfur) bond, carbon-oxygen bond, sulfur-sulfur bond and carbon-carbon forming reactions in the final cyclorelease step.

Deconvolution approaches in screening compound mixtures.

Abstract: Combinatorial chemistry initiatives can be used to generate compound mixtures, and it has become a challenge to effectively screen these mixtures for activity against a specified target. Overall mixture activity can be readily measured, however it is not a straightforward matter to identify all those components giving rise to the total activity (a process referred to as deconvolution). This review discusses the attraction in preparing and screening mixtures, and also addresses the difficulties inherent in their screening. Attention is paid to the current approaches of achieving mixture deconvolution, including synthetic pooling, fractionation, affinity-based isolation, and techniques requiring no physical separation. Recent successes in mixture screening suggest a rekindled interest in this area.

New developments in automated PrepLCMS extends the robustness and utility of the method for compound library analysis and purification.

Abstract: New developments in the high throughput purification of combinatorial libraries by automated preparative LC-MS is presented. To facilitate high speed purifications at the multimilligram level, short columns operated at ultra high flow rates were incorporated. In order to match the linear velocity of the short analytical columns for high speed separations (operated at 4.0 mL/min), it was required to operate the preparative columns at flow rates in excess of 70 mL/min. For chromatographically well-behaved compounds, analytical LC-MS analyses and preparative LC-MS analyses could be achieved in as little as 5 min. For compounds exhibiting poor chromatographic peak shapes and/or for compound mixtures requiring higher resolution separations, slightly longer preparative LC-MS analysis times were required (8-10 min/sample).

Screening for inhibitors of dihydrofolate reductase using pulsed ultrafiltration mass spectrometry.

Abstract: A method of screening combinatorial libraries for inhibitors of eukaryotic dihydrofolate reductase has been developed using pulsed ultra-filtration electrospray mass spectrometry, which is a continuous-flow affinity separation system for extracting and identifying high affinity ligands in combinatorial libraries. In this application, pulsed ultrafiltration conditions were optimized for the isolation and identification of inhibitors of dihydrofolate reductase from a 22 compound library containing six known inhibitors of the enzyme including trimethoprim, aminopterin, methotrexate, pyrimethamine, folic acid, and folinic acid, and 16 compounds without known affinity. In order to optimize the screening method, sources of non-specific binding were identified and minimized. A significant source of non-specific binding for this set of library compounds was hydrophobic interaction with the surfaces of the ultrafiltration chamber. After affinity separation of bound (high affinity) versus free (low affinity) library compounds during pulsed ultrafiltration, receptor-bound ligands were released and eluted using either organic solvent or acidified mobile phase. Although 80% methanol easily disrupted the receptor-ligand complexes, organic solvent had the undesirable effect of releasing non-specifically bound compounds from the chamber and thereby increasing the background noise. Interference from non-specific binding was minimized by releasing bound ligands using a low pH mobile phase eluent instead of organic solvent. Under the conditions used, pulsed ultrafiltration mass spectrometry selectively identified the two library compounds with the highest affinity for dihydrofolate reductase, methotrexate and aminopterin.

Ratio encoding combinatorial libraries with stable isotopes and their utility in pharmaceutical research.

Abstract: Combinatorial libraries are an important tool for lead discovery in the pharmaceutical industry. Advances in high throughput screening coupled with combinatorial chemistry can significantly reduce the time to find lead compounds. A major difficulty in developing large combinatorial libraries is the ability to identify active compounds. This paper describes a rapid and sensitive encoding/decoding methodology that utilizes stable isotopes and mass spectrometry. The ability of mass spectrometry to precisely determine the intensity of isotopic abundances provides a unique encoding strategy employing synthetically generated ratios of stable isotopes in a compound as the code. The application of ratio encoding is demonstrated using peptoid and imidazole chemistries. Supporting data demonstrate that the incorporation of one or more stable isotopes using unique-predetermined ratios can encode chemical libraries. In addition, the presence of a unique isotopic pattern in a ligand can facilitate the pharmacokinetic analysis. Isotope incorporation into a compound and subsequently into its metabolites reliably distinguishes products from other molecules in the mass spectrum. This is illustrated by metabolic analyses of peptoid and imidazole compounds.

Homogeneous pharmacologic and cell-based screens provide diverse strategies in drug discovery: somatostatin antagonists as a case study.

Abstract: The development of high throughput, homogeneous pharmacologic and functional assays and their implementation in screening combinatorial libraries has increased the pace of stochastic drug discovery in recent years. New, noninvasive approaches involving radiometric proximity assays, an array of fluorescence-based technologies, and reporter gene constructs in mammalian and nonmammalian systems are providing more options for the selection of specific therapeutic targets. The increasing sophistication of homogeneous assay designs has also served as a springboard to better lead validation in drug discovery initiatives. This review examines these approaches in the context of new drug discovery strategies which combine a growing repertoire of high throughput screening techniques. The utility and importance of cell-based assays vis-a-vis pharmacologic (cell-free) assays is considered with specific reference given to yeast-based functional screens and homogeneous binding methodologies used to search for somatostatin antagonists and other potential growth hormone secretagogues. Also considered is the custom tailoring of specific chemical libraries which provide yet another level of target selectivity. The advantages and shortcomings of these various technologies are discussed in light of emerging trends toward higher throughput and nanoscale formats which are pushing the limits of measurable response at the cellular and molecular level.

Combinatorial libraries: studies in molecular recognition.

Abstract: In recent years, combinatorial libraries have become a major tool for drug discovery and drug development. Along the way, one potential use of combinatorial chemistry libraries almost been neglected: the basic study of intermolecular interactions. Especially "one-bead-one-structure" libraries can be a powerful means for the discovery of ligands to synthetic receptors and vice versa. Encoded combinatorial libraries have been used to disclose ligands for well designed macrocyclic host molecules and to elucidate their specificities for peptide sequences. These studies led via receptors with more flexibility to simple host molecules without elaborate design that are accessible to combinatorial synthesis. These findings open a realm of possibilities and applications. An intriguing one is the development of chemical sensors for analytes that are otherwise hard or only unspecifically detected. Furthermore, such libraries and the techniques that were developed to handle them have been used to find new catalysts and enzyme mimics. In this review we put the emphasis on studies involving "one-bead-one-structure" libraries. We will review the techniques to generate them, to encode and analyze them, and to assay them. We will describe their past usage and the intriguing results of these studies and point out interesting new applications of such libraries for the study of non-covalent intermolecular interactions.

Rapid characterization of combinatorial libraries using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Abstract: The relatively new field of combinatorial chemistry has enabled researchers to create large mixtures of compounds that can be screened for leads in developing potential drug candidates. The new synthetic method has also created a need for better procedures to analyze the complex mixtures that are generated. The immediate goal in most cases is to verify the synthetic procedure and to determine the purity and completeness of the library sample before binding studies are initiated. We report here a method to rapidly characterize small-molecule combinatorial libraries in solution. All combinatorial library samples were synthesized by combining a core molecule bearing two acid chloride functionalities with various amino acids to generate libraries of 36, 78 and 120 components. Using electrospray ionization fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) we were able to identify 70-80% of the library components. All samples were analyzed as mixtures by direct infusion without chromatographic separation. Furthermore, nominally isobaric components could be resolved and identified through exact mass assignments without tandem mass spectrometery. ESI-FTICR-MS is a rapid and convenient tool for the characterization of small-molecule libraries. The method is especially useful for the analysis of larger libraries that contain many nominally isobaric components and impurities.

The properties of resin supports and their effects on solid-phase organic synthesis.

Abstract: Solvated resin supports are important carriers for solid-phase organic synthesis in combinatorial chemistry and high-throughput parallel synthesis. The physical properties of resin, resin swelling and dynamic solvation, effects of solvated supports on synthesis, kinetics, site interaction, and product purity are reviewed. Selective solvation of resin alters the local reactivity and accessibility of the bound substrate and the mobility of the entrapped reagent. Resin solvation changes during the course of the reaction when the attached substrate changes its polarity or other physicochemical properties. Selective adsorption determines the reaction kinetics and the action of a phase-transfer catalyst further improves the reaction on resin. Sites interact with each other in 1% DVB polystyrene resins to varying degrees depending on solvent, resin, and reactivity of the pendant groups. Total site isolation seems only achievable by controlling several factors simultaneously such as lower loading and steric hindrance. Through the proper selection of resin and solvent, alternating solvents to accommodate dynamic solvation of the resin, optimization of kinetics when changing solid supports and a careful control of resin impurities, solid-phase organic synthesis can lead to high quality combinatorial libraries.

A simple, inexpensive apparatus for performance of preparative scale solution phase multiple parallel synthesis of drug analogs. II. Biological evaluation of a retrospective library of quinolone antiinfective agents.

Abstract: A simple inexpensive apparatus is described consisting of conveniently commercially available components which is suitable for the solution phase multiple parallel synthesis of 24-72 analogs of drug-like molecules. The use of the apparatus is illustrated by preparation of a retrospective library of over 100 analogs of antimicrobial fluoroquinolones prepared in 0% to quantitative yields. Each analog was prepared in up to 150 mg quantity and each was analyzed by NMR and mass spectrometric techniques to verify its purity and identity.

Encoded chemical synthesis coupled to screening: "Pot Assay".

Abstract: A variety of screening methodologies is available to identify lead compounds. Screening methods that would permit the direct use of libraries made via the Radiofrequency Encoded Combinatorial chemistry paradigm (each individual small molecule in the library is presented separately on an individual encoded support) have the potential to diminish burdensome steps in this process. Here we report on our studies leading to such a direct method, which we have termed a Pot Assay. Pot Assay is a multiplex assay, which simultaneously measures specific binding of a number of ligands to at least one target. Pot Assay uses specific radiofrequency signals to decode compounds that are high affinity binders. We validated this approach by evaluating the interaction of biotin and its analogs with labeled streptavidin. This report introduces Pot Assay as a rapid, simple, sensitive and accurate format for identifying active members of libraries synthesized on solid supports. The success of this study demonstrates the power of coupling Radiofrequency Encoded Combinatorial chemistry and screening. This assay format may be applied to a wide range of screens that are based on binding events: ligand/receptor, inhibitor/enzyme, antigen/antibody, protein/protein, DNA/protein, and RNA/DNA.

A combinatorial approach to new DNA minor groove binders.

Abstract: A combinatorial approach towards new DNA minor groove binders capable of recognizing GC base pairs is reported. From a partly AT--biased library of 5832 different octapeptides of the type Py-Py-X1-X2-X3-Py-Py-gamma Abu synthesized following the one bead one compound methodology, two compounds containing the central peptide sequences Val-beta Ala-Tyr and Pip-beta Ala-Tyr were selected by a fluorescence--double stranded DNA probing assay using the sequence 5'-TTTGTTT-3' as the probe. The two hits were independently synthesized and binding to a recombinant pUC-19 EcoRl/Pvull DNA restriction fragment containing the sequence 5'-TTTGTTT-3' demonstrated. Binding constants to eight targets in the DNA fragment were estimated from quantitative DNAse I footprinting.