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Alaqeel SI, Arumugam N, Viswanathan V, Almansour AI, Kumar RS, Padmanaban R, Yeswanthkumar S, Premnath D, Ponmurugan K, Al-Dhabi NA, Perumal K. Synthesis, computational studies and antibacterial assessment of dispirooxindolopyrrolidine integrated indandione hybrids. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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2
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Nagaraju S, Sathish K, Kashinath D. Applications of 3,5‐Dialkyl‐4‐nitroisoxazoles and Their Derivatives in Organic Synthesis
#. ChemistrySelect 2021. [DOI: 10.1002/slct.202101719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sakkani Nagaraju
- Department of Chemistry National Institute of Technology Warangal-506 004 India 2677
| | - Kota Sathish
- Department of Chemistry National Institute of Technology Warangal-506 004 India 2677
| | - Dhurke Kashinath
- Department of Chemistry National Institute of Technology Warangal-506 004 India 2677
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3
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A Multidimensional Group Testing Approach for the Reagent Optimisation of a Suzuki C–C Coupling Reaction. Catal Letters 2021. [DOI: 10.1007/s10562-021-03670-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Kumar RS, M. Al-thamili D, Almansour AI, Arumugam N, Mohammad F. A One-Pot Three-Component Synthesis and Investigation of the In Vitro Mechanistic Anticancer Activity of Highly Functionalized Spirooxindole-Pyrrolidine Heterocyclic Hybrids. Molecules 2020; 25:molecules25235581. [PMID: 33261115 PMCID: PMC7730040 DOI: 10.3390/molecules25235581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 01/07/2023] Open
Abstract
With an aim to develop more effective and affordable anticancer agents possessing a unique mechanism of action, we designed and synthesized derivatives of spirooxindole-pyrrolidine heterocyclic hybrids in good yields through a one-pot three-component (3+2) cycloaddition strategy. The synthesized compounds were characterized thoroughly for the physicochemical properties by making use of FT-IR, NMR spectroscopy, and mass spectrometry. Further, these compounds have been evaluated for the influence of anticancer activity against HepG2 cells up to 200 µg/mL concentration. The highly active molecular scaffold was tested for the in-depth mechanistic studies, and it was found that the major pathway of cell death is apoptosis which occurs through the induction of reactive oxygen species followed by the involvement of caspases.
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In Vitro Molecular Biology Studies of Spirooxindole Heterocyclic Hybrids. Processes (Basel) 2020. [DOI: 10.3390/pr8111473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the present report, we provide the results of the molecular biology studies of spiroheterocyclic hybrids, where the derivatives are found to possess potential anticancer activity towards cancer cells. A series of spiroxindole–pyrrolidine heterocyclic hybrids were evaluated for cell viability and proliferation against HepG2 cancer cells at concentrations in the range of 12.5–200 µg/mL over two different time periods of 24 and 48 h. In addition, the highly active compounds were also verified for their behavior towards noncancer cells (L929 cells), and it was found that the tested derivatives were not aggressive due to the observation of only limited cell loss, as compared to the cancer cells. Further analysis of the observed toxicity mechanism showed the apoptotic pathway was mediated by oxidative stress, with the involvement of caspases.
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Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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Yang J, Liu XW, Wang DD, Tian MY, Han SN, Feng TT, Liu XL, Mei RQ, Zhou Y. Diversity-oriented one-pot multicomponent synthesis of spirooxindole derivatives and their biological evaluation for anticancer activities. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.10.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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Pulaganti M, C M A, Kumar CS. Design, synthesis, and evaluation of pyrazolo-pyrazole derivatives on Methylisocitratelyase of Pseudomonas aeruginosa: in silico and in vitro study. J Biomol Struct Dyn 2016; 35:2509-2529. [PMID: 27686121 DOI: 10.1080/07391102.2016.1223754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic micro-organism causing diseases both in animals and humans. In case of human pathology, the role of P. aeruginosa is one of the major concerns in intensive care septicemia. Presently, the drug resistance strains of P. aeruginosa are arising mainly by developing multiple mechanisms due to its natural and acquired resistance to many of the antimicrobial agents commonly used in clinical practice. As a result, there is a direct need to invent new drugs so that they may restrict the outbreak of multidrug resistant strains. Virtual high-throughput insilico screening, which helps to identify the chemical ligands that bind to the enzymes, is an important tool in drug discovery and the drugs discovered in this way are clinically tested. In this study, Methylisocitratelyase (MICL), which is essential for the survival of the bacterium and which doesn't show any similarity with the humans, was selected to evaluate the functions of high-affinity inhibitors (PPI-analogs) that are identified using the virtual screening approach. By adopting the computational analysis tools, structural, functional, and inhibitor interactions of MICL against P. aeruginosa were identified. The PPIA-32 is found to be the best binding interactions with MICL. PPIA-32 reduces the binding affinity for substrate to residues required for MICL enzyme activity and also Root Mean Square Deviation simulations show the most stable nature of PPA32-MICL(complex) than that of MICL alone, thereby effectively inhibiting the growth of virulent P. aeruginosa. To our surprise, the same phenomenon is also identified with other gram-negative bacteria like Escherichia coli, Klebsiella pneumoniae, and Salmonella typhi.
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Affiliation(s)
- Madhusudana Pulaganti
- a BIF, Department of Biochemistry , Sri Krishnadevaraya University , Anantapur 515 003 , India.,b Department of Biotechnology , Acharya Nagarjuna University , Guntur 522 510 , India
| | - Anuradha C M
- c Department of Biotechnology , Sri Krishnadevaraya University , Anantapur 515 003 , India
| | - Chitta Suresh Kumar
- a BIF, Department of Biochemistry , Sri Krishnadevaraya University , Anantapur 515 003 , India
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9
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Liu XL, Feng TT, Wang DD, Liu HH, Yang C, Li XN, Lin B, Zhao Z, Zhou Y. Synthesis and in vitro evaluation of pyrimidine-fused 3-alkenyloxindoles as potential anticancer agents. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.07.100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Liu XL, Feng TT, Jiang WD, Yang C, Tian MY, Jiang Y, Lin B, Zhao Z, Zhou Y. Molecular hybridization-guided 1,3-dipolar cycloaddition reaction enabled pyrimidine-fused spiropyrrolidine oxindoles synthesis as potential anticancer agents. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.08.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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1,3-Dipolar cycloaddition enabled isoxazole-fused spiropyrrolidine oxindoles syntheses from 3-methyl-4-nitro-5-alkenyl-isoxazoles and azomethine ylides. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.01.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Liu XL, Yang C, Zhang WH, Zhou G, Ma XT, Lin B, Zhang M, Zhou Y, Feng TT. Construction of turmerone motif-fused spiropyrrolidine oxindoles and their biological evaluation for anticancer activities. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.02.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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A facile and efficient synthesis of polycyclic spiropyrrolidine oxindoles bearing mesityl oxide unit via a three-component 1,3-dipolar cycloaddition reaction. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.08.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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14
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Morin MST, Arndtsen BA. Chiral Phosphorus-Based 1,3-Dipoles: A Modular Approach to Enantioselective 1,3-Dipolar Cycloaddition and Polycyclic 2-Pyrroline Synthesis. Org Lett 2014; 16:1056-9. [PMID: 24502319 DOI: 10.1021/ol4035512] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie S. T. Morin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8, Canada
| | - Bruce A. Arndtsen
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8, Canada
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15
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Liu J, Sun H, Liu X, Ouyang L, Kang T, Xie Y, Wang X. Direct construction of novel exo′-selective spiropyrrolidine bisoxindoles via a three-component 1,3-dipolar cycloaddition reaction. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.02.099] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Breistein P, Johansson J, Ibrahem I, Lin S, Deiana L, Sun J, Cordova A. One-Step Catalytic Enantioselective α-Quaternary 5-Hydroxyproline Synthesis: An Asymmetric Entry to Highly Functionalized α-Quaternary Proline Derivatives. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100911] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Galloway WRJD, Spring DR. PNA to DNA to microarray decoding facilitates ligand discovery. ACTA ACUST UNITED AC 2012; 18:1209-10. [PMID: 22035789 DOI: 10.1016/j.chembiol.2011.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The development of a method for the amplification of PNA tags (Svensen et al., in this issue of Chemistry & Biology) should expand the range of biological targets amenable to screening using PNA-encoded combinatorial libraries and thus facilitate the discovery of new biologically useful agents.
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Lin S, Deiana L, Zhao GL, Sun J, Córdova A. Dynamic One-Pot Three-Component Catalytic Asymmetric Transformation by Combination of Hydrogen-Bond-Donating and Amine Catalysts. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101966] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Lin S, Deiana L, Zhao GL, Sun J, Córdova A. Dynamic One-Pot Three-Component Catalytic Asymmetric Transformation by Combination of Hydrogen-Bond-Donating and Amine Catalysts. Angew Chem Int Ed Engl 2011; 50:7624-30. [DOI: 10.1002/anie.201101966] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Indexed: 11/09/2022]
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Chen X, Tan PH, Zhang Y, Pei D. On-bead screening of combinatorial libraries: reduction of nonspecific binding by decreasing surface ligand density. ACTA ACUST UNITED AC 2010; 11:604-11. [PMID: 19397369 DOI: 10.1021/cc9000168] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries provides a powerful method for the rapid identification of active compounds against molecular or cellular targets. However, on-bead screening is susceptible to interference from nonspecific binding, which results in biased screening data and false positives. In this work, we have found that a major source of nonspecific binding is derived from the high ligand loading on the library beads, which permits a macromolecular target (e.g., a protein) to simultaneously interact with multiple ligands on the bead surface. To circumvent this problem, we have synthesized a phosphotyrosyl (pY)-containing peptide library on spatially segregated TentaGel microbeads, which feature a 10-fold reduced peptide loading on the bead surface but a normal peptide loading in the bead interior. The library was screened against a panel of 10 Src homology 2 (SH2) domains including those of Csk and Fyn kinases and adaptor protein SLAP, and the specific recognition motif(s) was successfully identified for each of the domains. In contrast, when the SH2 domains were screened against a control library that contained unaltered (high) ligand loading at the bead surface, six of them exhibited varying degrees of sequence biases, ranging from minor perturbation in the relative abundance of different sequences to the exclusive selection of false positive sequences that have no measurable affinity to the target protein. These results indicate that reduction of the ligand loading on the bead surface represents a simple, effective strategy to largely eliminate the interference from nonspecific binding, while preserving sufficient amounts of materials in the bead interior for compound identification. This finding should further expand the utility of OBOC libraries in biomedical research.
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Affiliation(s)
- Xianwen Chen
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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Ibrahem I, Rios R, Vesely J, Córdova A. Organocatalytic asymmetric multi-component [C+NC+CC] synthesis of highly functionalized pyrrolidine derivatives. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.07.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bräse S, Gil C, Knepper K, Zimmermann V. Organic azides: an exploding diversity of a unique class of compounds. Angew Chem Int Ed Engl 2006; 44:5188-240. [PMID: 16100733 DOI: 10.1002/anie.200400657] [Citation(s) in RCA: 1614] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Since the discovery of organic azides by Peter Griess more than 140 years ago, numerous syntheses of these energy-rich molecules have been developed. In more recent times in particular, completely new perspectives have been developed for their use in peptide chemistry, combinatorial chemistry, and heterocyclic synthesis. Organic azides have assumed an important position at the interface between chemistry, biology, medicine, and materials science. In this Review, the fundamental characteristics of azide chemistry and current developments are presented. The focus will be placed on cycloadditions (Huisgen reaction), aza ylide chemistry, and the synthesis of heterocycles. Further reactions such as the aza-Wittig reaction, the Sundberg rearrangement, the Staudinger ligation, the Boyer and Boyer-Aubé rearrangements, the Curtius rearrangement, the Schmidt rearrangement, and the Hemetsberger rearrangement bear witness to the versatility of modern azide chemistry.
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Affiliation(s)
- Stefan Bräse
- Institut für Organische Chemie, Universität Karlsruhe TH, Germany.
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25
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Fenniri H, Terreau O, Chun S, Oh SJ, Finney WF, Morris MD. Classification of spectroscopically encoded resins by Raman mapping and infrared hyperspectral imaging. ACTA ACUST UNITED AC 2006; 8:192-8. [PMID: 16529514 DOI: 10.1021/cc050128i] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Barcoded resins (BCRs) were recently introduced as a potential platform for pre-encoded multiplexed synthesis, screening, and biomedical diagnostics. A key step toward the development of this strategy is the ability to rapidly interrogate and classify the BCRs in a high-throughput, noninvasive manner. Here, we describe a one-step strategy based on Raman mapping and Fourier transform infrared imaging to classify and spatially resolve randomly distributed BCRs. To illustrate this methodology, mixtures of up to 25 different BCRs were imaged and classified with 100% confidence. This strategy can be readily extended to a larger pool of resins, provided each BCR features a unique vibrational fingerprint (spectroscopic barcode). We have also established that reliable single-bead Raman spectra can be recorded in 10 ms, thus confirming that Raman mapping, in particular, could be a very fast method to classify the BCRs.
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Affiliation(s)
- Hicham Fenniri
- National Institute of Nanotechnology, National Research Council (NINT-NRC) and Department of Chemistry, University of Alberta, ECERF: 9107-116 Street, Edmonton, Alberta T6G 2V4, Canada.
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26
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Du WB, Fang Q, Fang ZL. Microfluidic Sequential Injection Analysis in a Short Capillary. Anal Chem 2006; 78:6404-10. [PMID: 16970315 DOI: 10.1021/ac060714d] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An automated microfluidic sequential injection analysis system that efficiently manipulates sample and reagent solutions in the nanoliter range in approximately 10 s per analytical cycle is described. The system consisted of a 6-cm-long, typically 75-microm i.d., fused-silica capillary (which functioned as a sampling probe and reactor as well as a flow-through detection cell), a horizontally oriented waste reservoir that provided liquid level differences for inducing gravity-driven flows, an autosampling device holding samples and reagents with horizontally fixed slotted microvials, and a laser-induced fluorescence detection system. Sample and reagent zones were sequentially introduced via gravity-driven flow by scanning the capillary tip (functioning as the sampling probe) through the vial slots, while vials containing sample, reagent, and carrier were sequentially rotated to the probe by programmed movement of the vial holders. Sequentially injected nanoliter zones were rapidly mixed by convection and diffusion within the carrier flow, demonstrating a behavior that conformed well to the Taylor dispersion model, and zone penetration effects were characterized and optimized under Taylor's dispersion theory guidelines. For the determination of fluorescein, a high throughput of 400 h(-1) was achieved, rapidly producing calibration curves (five points) within 45 s. Owing to its adaptability to the Taylor's dispersion model, the system was used also for measuring diffusion coefficients of fluorescent species. Potentials for using the system in enzyme inhibition assays were demonstrated by a reaction involving the conversion of fluorescein digalactoside to fluorescent hydrolysates via beta-galactosidase and the inhibition of beta-galactosidase by diethylenetriaminepentaacetic acid.
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Affiliation(s)
- Wen-Bin Du
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, China
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Garner P, Kaniskan HU, Hu J, Youngs WJ, Panzner M. Asymmetric Multicomponent [C+NC+CC] Synthesis of Highly Functionalized Pyrrolidines Catalyzed by Silver(I). Org Lett 2006; 8:3647-50. [PMID: 16898782 DOI: 10.1021/ol061113b] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Highly functionalized pyrrolidines are obtained in a single chemical step via a mild, efficient, and selective Ag(I)-catalyzed asymmetric [C+NC+CC] coupling process. Oppolzer's camphorsultam enables the desired reaction cascade and provides a reliable means to control the developing stereochemistry and purify the products. This three-component reaction provides unprecedented access to structurally diverse pyrrolidines for both target- and diversity-oriented syntheses.
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Affiliation(s)
- Philip Garner
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, USA.
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Chun S, Xu J, Cheng J, Ding L, Winograd N, Fenniri H. Spectroscopically encoded resins for high throughput imaging time-of-flight secondary ion mass spectrometry. ACTA ACUST UNITED AC 2006; 8:18-25. [PMID: 16398549 DOI: 10.1021/cc050086y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spectroscopic barcoding was recently introduced as a new pre-encoding strategy wherein the resin beads are not just carriers for solid phase synthesis, but are, in addition, the repository of the synthetic scheme to which they were subjected. To expand the repertoire of spectroscopically barcoded resins (BCRs), here we introduce a new family of halogenated polystyrene-based polymers designed for high-throughput combinatorial analysis using not only infrared and Raman spectroscopy but also imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS). In particular, we have established that (a) the halogen content of these new resins can be used as an encoding element in quantitative imaging ToF-SIMS and (b) the number of styrene monomers used to generate unique vibrational fingerprints can be significantly reduced by using monomers in different molar ratios. The combination of quantitative imaging ToF-SIMS and vibrational spectroscopy is anticipated to dramatically increase the repertoire of possible BCRs from a few hundreds to several thousands.
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Affiliation(s)
- Sangki Chun
- LG Chem Research Park, 104-1 Moonji-Dong, Yuseong-Gu, Daejeon 305-380, Korea
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Portnoy M, Ben-Aroya Bar-Nir B. Solid-Phase Pyrrolidine Synthesis via 1,3- Dipolar Cycloaddition of Azomethine Ylides Generated by the Decarboxylative Route. HETEROCYCLES 2006. [DOI: 10.3987/com-05-s(t)47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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30
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Bräse S, Gil C, Knepper K, Zimmermann V. Organische Azide - explodierende Vielfalt bei einer einzigartigen Substanzklasse. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200400657] [Citation(s) in RCA: 346] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Maclean D, Holden F, Davis AM, Scheuerman RA, Yanofsky S, Holmes CP, Fitch WL, Tsutsui K, Barrett RW, Gallop MA. Agonists of the Follicle Stimulating Hormone Receptor from an Encoded Thiazolidinone Library. ACTA ACUST UNITED AC 2003; 6:196-206. [PMID: 15002967 DOI: 10.1021/cc0300154] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design, synthesis, characterization, and screening of a large, encoded thiazolidinone library are described. Three sets of 35 building blocks were combined by encoded split-pool synthesis to give a library containing more than 42 000 members. Building block selection was based in part on a novel small molecule follicle stimulating hormone receptor agonist hit and in part for diversity. HPLC/MS techniques were applied at the single-bead level to build confidence in the reliability of library construction. Application of two distinct screening strategies resulted in the identification of compounds with significantly improved potency over the initial hit. This work demonstrates the versatility of encoded libraries for preparing a large number of analogues of a given hit while simultaneously generating a large collection of compounds for screening against other targets.
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Affiliation(s)
- Derek Maclean
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, CA 94304, USA.
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32
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Fenniri H, Chun S, Ding L, Zyrianov Y, Hallenga K. Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly(ethylene glycol) graft copolymers. J Am Chem Soc 2003; 125:10546-60. [PMID: 12940737 DOI: 10.1021/ja035665q] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we describe the preparation of 25 beaded polystyrene-poly(ethylene glycol) graft copolymers from six spectroscopically active styrene monomers: styrene, 2,5-dimethylstyrene, 4-methylstyrene, 2,4-dimethylstyrene, 4-tert-butylstyrene, and 3-methylstyrene. These polymers were thoroughly characterized by Raman, infrared, and (1)H/(13)C NMR spectroscopies, and differential scanning calorimetry. Determination of the swelling properties, peptide synthesis, and on-bead streptavidin-alkaline phosphatase (SAP) binding assay further established that their physical and chemical properties where not significantly altered by the diversity of their encoded polystyrene core. Each of the 25 resins displayed a unique Raman and infrared vibrational fingerprint, which was converted into a "spectroscopic barcode". The position of each bar matches the peak wavenumber in the corresponding spectrum but is independent of its intensity. From this simplified representation similarity maps comparing 35 000 resin pairs were generated to establish the spectroscopic barcoding as a reliable encoding methodology. In effect, in 99% of the cases, the highest similarity coefficients were obtained for resin pairs prepared from the same styrene derivatives even after SAP binding assay. We have also shown that a small but unique combination of a resin's vibrations (30-40%) is sufficient for its identification. However, in rare cases where a resin's vibrational signature has been severely compromised, both the Raman and infrared barcodes were synergistically and reliably utilized to unequivocally identify its chemical make up.
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Affiliation(s)
- Hicham Fenniri
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA.
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Hackbarth CJ, Chen DZ, Lewis JG, Clark K, Mangold JB, Cramer JA, Margolis PS, Wang W, Koehn J, Wu C, Lopez S, Withers G, Gu H, Dunn E, Kulathila R, Pan SH, Porter WL, Jacobs J, Trias J, Patel DV, Weidmann B, White RJ, Yuan Z. N-alkyl urea hydroxamic acids as a new class of peptide deformylase inhibitors with antibacterial activity. Antimicrob Agents Chemother 2002; 46:2752-64. [PMID: 12183225 PMCID: PMC127453 DOI: 10.1128/aac.46.9.2752-2764.2002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Revised: 03/16/2002] [Accepted: 06/05/2002] [Indexed: 11/20/2022] Open
Abstract
Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth and is a new target for the development of antibacterial agents. All previously reported PDF inhibitors with sufficient antibacterial activity share the structural feature of a 2-substituted alkanoyl at the P(1)' site. Using a combination of iterative parallel synthesis and traditional medicinal chemistry, we have identified a new class of PDF inhibitors with N-alkyl urea at the P(1)' site. Compounds with MICs of 200 micro M for matrilysin and other mammalian metalloproteases. Structure-activity relationship analysis identified preferred substitutions resulting in improved potency and decreased cytotoxity. One of the compounds (VRC4307) was cocrystallized with PDF, and the enzyme-inhibitor structure was determined at a resolution of 1.7 A. This structural information indicated that the urea compounds adopt a binding position similar to that previously determined for succinate hydroxamates. Two compounds, VRC4232 and VRC4307, displayed in vivo efficacy in a mouse protection assay, with 50% protective doses of 30.8 and 17.9 mg/kg of body weight, respectively. These N-alkyl urea hydroxamic acids provide a starting point for identifying new PDF inhibitors that can serve as antimicrobial agents.
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35
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Seneci P. Encoding techniques for pool libraries of small organic molecules. J Recept Signal Transduct Res 2001; 21:409-45. [PMID: 11789691 DOI: 10.1081/rrs-100107925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- P Seneci
- GlaxoWellcome Medicines Research Centre, Verona, Italy
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36
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Pyrrolidine synthesis on polystyrene supports: development of a ‘one-pot’ dipolar cycloaddition strategy. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01061-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Liu X, Takahashi LH, Fitch WL, Rozing G, Bayle C, Couderc F. Capillary electrochromatography-laser-induced fluorescence method for separation and detection of dansylated dialkylamine tags in encoded combinatorial libraries. J Chromatogr A 2001; 924:323-9. [PMID: 11521881 DOI: 10.1016/s0021-9673(01)00939-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LC-fluorescence and LC-MS methods have been previously reported for use in decoding bead-based combinatorial libraries. We present the use of capillary electrochromatography (CEC) for highly selective decoding in combination with laser-induced fluorescence (LIF) detection for high sensitivity. The results are compared to prior data obtained using HPLC with fluorescence detection. The use of CEC shows promise for miniaturization and multiplexing for future applications, and the use of LIF detection can allow for detection at sub-pmol amounts.
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Affiliation(s)
- X Liu
- Affymax Research Institute, Santa Clara, CA, 95051, USA
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38
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Floyd CD, Leblanc C, Whittaker M. Combinatorial chemistry as a tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2000; 36:91-168. [PMID: 10818672 DOI: 10.1016/s0079-6468(08)70046-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.
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Affiliation(s)
- C D Floyd
- British Biotech Pharmaceuticals Limited, Oxford, U.K
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39
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Hanessian S, Bayrakdarian M. Pyrrolidine as a cogwheel-like scaffold for the deployment of diverse functionality through cycloaddition reactions of metallo-1,3-dipoles in aqueous media. Bioorg Med Chem Lett 2000; 10:427-31. [PMID: 10743941 DOI: 10.1016/s0960-894x(00)00020-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of glycinatocopper complexes with cinnamaldehydes under mildy basic aqueous conditions, affords polysubstituted prolines, which can be systematically modified in a number of chemoselective transformations.
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Affiliation(s)
- S Hanessian
- Department of Chemistry, Université de Montréal, Station Centre-ville, QC, Canada.
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40
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Tan DS, Foley MA, Stockwell BR, Shair MD, Schreiber SL. Synthesis and Preliminary Evaluation of a Library of Polycyclic Small Molecules for Use in Chemical Genetic Assays. J Am Chem Soc 1999. [DOI: 10.1021/ja992144n] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Derek S. Tan
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Harvard Institute of Chemistry and Cell Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
| | - Michael A. Foley
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Harvard Institute of Chemistry and Cell Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
| | - Brent R. Stockwell
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Harvard Institute of Chemistry and Cell Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
| | - Matthew D. Shair
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Harvard Institute of Chemistry and Cell Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
| | - Stuart L. Schreiber
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Harvard Institute of Chemistry and Cell Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
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41
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Abstract
Strategies for the parallel synthesis of small molecule arrays are reviewed with an emphasis on those approaches that integrate the sciences of organic synthesis and product purification. The use of phase-trafficking reagents (PTRs) and phase-switching strategies are highlighted, which allow the rapid, parallel synthesis of small molecule arrays with built-in purification determinants.
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Affiliation(s)
- D L Flynn
- Amgen, INC, One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA
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Schwarz MK, Tumelty D, Gallop MA. Solid-Phase Synthesis of 3,5-Disubstituted 2,3-Dihydro-1,5-benzothiazepin-4(5H)-ones. J Org Chem 1999. [DOI: 10.1021/jo981567p] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthias K. Schwarz
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, California 94304
| | - David Tumelty
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, California 94304
| | - Mark A. Gallop
- Affymax Research Institute, 4001 Miranda Avenue, Palo Alto, California 94304
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43
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Dolle RE. Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997. ACTA ACUST UNITED AC 1999. [DOI: 10.1007/978-94-017-0735-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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Chapter 27. Application of Combinatorial and Parallel Synthesis to Medicinal Chemistry. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1999. [DOI: 10.1016/s0065-7743(08)60589-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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45
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Dolle RE. Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997. Mol Divers 1998; 3:199-233. [PMID: 9850519 DOI: 10.1023/a:1009699413828] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This review is a historical accounting of chemical libraries from which biologically active agents have been obtained. The comprehensive tabulation includes citations as early as 1992, when the first descriptions of biologically active libraries were disclosed, and continues through 1997. Four tables are provided listing libraries screened against (1) proteolytic enzymes, (2) non-proteolytic enzymes, (3) G-protein coupled receptors (GPCRs), and (4) other targets not classified in the first three tables (e.g. non-GPCRs, integrins, antiinfectives). A name, generic structure, and size is provided for each library citation, accompanied by the molecular screen and the structure and potency of the most active library member. In total, 86 libraries are presented with 60% of the contributions reported from pharmaceutical and biotechnology companies. Approximately 70% of the libraries have used alpha-amino acid synthons in their construction and 85% of the libraries include one or more amide bonds.
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Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia, Inc., Princeton, NJ 08540, USA.
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46
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Boussie TR, Coutard C, Turner H, Murphy V, Powers TS. Festphasensynthese und Kodierung von Katalysatorbibliotheken für Olefinpolymerisationen. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19981204)110:23<3472::aid-ange3472>3.0.co;2-d] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Holtzapple CK, Stanker LH. Affinity Selection of Compounds in a Fluoroquinolone Chemical Library by On-Line Immunoaffinity Deletion Coupled to Column HPLC. Anal Chem 1998. [DOI: 10.1021/ac9807417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carol K. Holtzapple
- Food Animal Protection Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, 2881 F & B Road, College Station, Texas 77845
| | - Larry H. Stanker
- Food Animal Protection Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, 2881 F & B Road, College Station, Texas 77845
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49
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Abstract
There continues to be considerable effort towards the construction of compound libraries targeted for the inhibition of protease enzymes. New tag-encoding methods for library deconvolution have been applied to this problem and there has been particular interest in novel solid-phase linkers for the introduction of key pharmacophore groups required for protease inhibition. Recent reports have tended to focus on nonpeptidic libraries, and, notably, structure-based design methods are now being applied to direct library design.
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Affiliation(s)
- M Whittaker
- British Biotech Pharmaceuticals Ltd, Oxford, UK.
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50
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Fecik RA, Frank KE, Gentry EJ, Menon SR, Mitscher LA, Telikepalli H. The search for orally active medications through combinatorial chemistry. Med Res Rev 1998; 18:149-85. [PMID: 9578985 DOI: 10.1002/(sici)1098-1128(199805)18:3<149::aid-med2>3.0.co;2-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The literature of combinatorial chemistry is reviewed with particular attention paid to considerations of absorption, distribution, metabolism and excretion in the design and evaluation of libraries containing drug-like molecules. Published libraries are evaluated in particular for the likelihood that the products would possess oral bioavailability.
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Affiliation(s)
- R A Fecik
- Department of Medicinal Chemistry, Kansas University, Lawrence 66045-2506, USA
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