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Pradhan S, Tyagi R, Sharma S. Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges. J Appl Microbiol 2022; 133:2742-2759. [PMID: 36039728 DOI: 10.1111/jam.15799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022]
Abstract
Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.
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Affiliation(s)
- Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Rashi Tyagi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
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2
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Peptide Affinity Chromatography Applied to Therapeutic Antibodies Purification. Int J Pept Res Ther 2021; 27:2905-2921. [PMID: 34690622 PMCID: PMC8525457 DOI: 10.1007/s10989-021-10299-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
The interest in therapeutic monoclonal antibodies (mAbs) has significantly grown in the pharmaceutical industry, exceeding 100 FDA mAbs approved. Although the upstream processing of their industrial production has been significantly improved in the last years, the downstream processing still depends on immobilized protein A affinity chromatography. The high cost, low capacity and short half-life of immobilized protein A chromatography matrices, encouraged the design of alternative short-peptide ligands for mAb purification. Most of these peptides have been obtained by screening combinatorial peptide libraries. These low-cost ligands can be easily produced by solid-phase peptide synthesis and can be immobilized on chromatographic supports, thus obtaining matrices with high capacity and selectivity. Furthermore, matrices with immobilized peptide ligands have longer half-life than those with protein A due to the higher stability of the peptides. In this review the design and synthesis of peptide ligands, their immobilization on chromatographic supports and the evaluation of the affinity supports for their application in mAb purification is described.
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3
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Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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4
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New approach for screening anti-tumor compounds. Sci Bull (Beijing) 2013. [DOI: 10.1007/bf03325643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Armishaw CJ, Banerjee J, Ganno ML, Reilley KJ, Eans SO, Mizrachi E, Gyanda R, Hoot MR, Houghten RA, McLaughlin JP. Discovery of novel antinociceptive α-conotoxin analogues from the direct in vivo screening of a synthetic mixture-based combinatorial library. ACS COMBINATORIAL SCIENCE 2013; 15:153-61. [PMID: 23414173 DOI: 10.1021/co300152x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Marine cone snail venoms consist of large, naturally occurring combinatorial libraries of disulfide-constrained peptide neurotoxins known as conotoxins, which have profound potential in the development of analgesics. In this study, we report a synthetic combinatorial strategy that probes the hypervariable regions of conotoxin frameworks to discover novel analgesic agents by utilizing high diversity mixture-based positional-scanning synthetic combinatorial libraries (PS-SCLs). We hypothesized that the direct in vivo testing of these mixture-based combinatorial library samples during the discovery phase would facilitate the identification of novel individual compounds with desirable antinociceptive profiles while simultaneously eliminating many compounds with poor activity or liabilities of locomotion and respiration. A PS-SCL was designed based on the α-conotoxin RgIA-ΔR n-loop region and consisted of 10,648 compounds systematically arranged into 66 mixture samples. Mixtures were directly screened in vivo using the mouse 55 °C warm-water tail-withdrawal assay, which allowed deconvolution of amino acid residues at each position that confer antinociceptive activity. A second generation library of 36 individual α-conotoxin analogues was synthesized using systematic combinations of amino acids identified from PS-SCL deconvolution and further screened for antinociceptive activity. Six individual analogues exhibited comparable antinociceptive activity to that of the recognized analgesic α-conotoxin RgIA-ΔR, and were selected for further examination of antinociceptive, respiratory, and locomotor effects. Three lead compounds were identified that produced dose-dependent antinociception without significant respiratory depression or decreased locomotor activity. Our results represent a unique approach for rapidly developing novel lead α-conotoxin analogues as low-liability analgesics with promising therapeutic potential.
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Affiliation(s)
- Christopher J. Armishaw
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Jayati Banerjee
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Michelle L. Ganno
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Kate J. Reilley
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Shainnel O. Eans
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Elisa Mizrachi
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Reena Gyanda
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Michelle R. Hoot
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Jay P. McLaughlin
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
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6
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Tan X, Hu L, Luquette LJ, Gao G, Liu Y, Qu H, Xi R, Lu ZJ, Park PJ, Elledge SJ. Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol 2012; 30:1125-30. [PMID: 23064238 PMCID: PMC3494743 DOI: 10.1038/nbt.2391] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 09/12/2012] [Indexed: 11/25/2022]
Abstract
The systematic identification of effective drug combinations has been hindered by the unavailability of methods that can explore the large combinatorial search space of drug interactions. Here we present a multiplex screening method named MuSIC (Multiplex Screening for Interacting Compounds), which expedites the comprehensive assessment of pair-wise compound interactions. We examined ~500,000 drug pairs from 1000 FDA-approved or clinically tested drugs and identified drugs that synergize to inhibit HIV replication. Our analysis reveals an enrichment of anti-inflammatory drugs in drug combinations that synergize against HIV, indicating HIV benefits from inflammation that accompanies its infection. Multiple drug pairs identified in this study, including glucocorticoid and nitazoxanide, synergize by targeting different steps of the HIV life cycle. As inflammation accompanies HIV infection, our findings indicate that inhibiting inflammation could curb HIV propagation. MuSIC can be applied to a wide variety of disease-relevant screens to facilitate efficient identification of compound combinations.
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Affiliation(s)
- Xu Tan
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
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7
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Abstract
High-throughput screening (HTS) is a key process used in drug discovery to identify hits from compound libraries that may become leads for medicinal chemistry optimization. This updated overview discusses the utilization of compound libraries, compounds derived from combinatorial and parallel synthesis campaigns and natural product sources; creation of mother and daughter plates; and compound storage, handling, and bar coding in HTS. The unit also presents an overview of established and emerging assay technologies (i.e., time-resolved fluorescence, fluorescence polarization, fluorescence-correlation spectroscopy, functional whole cell assays, and high-content assays) and their integration in automation hardware and IT systems. This revised unit provides updated descriptions of state-of-the-art instrumentation and technologies in this rapidly changing environment. The section on assay methodologies now also covers enzyme complementation assays and methods for high-throughput screening of ion channel activities. Finally, a section on criteria for assay robustness is included discussing the Z'-factor, which is now a widely accepted criterion for evaluation and validation of high throughput screening assays.
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Affiliation(s)
- Michael Entzeroth
- Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), Singapore
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8
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Khan MOF, Deimling MJ, Philip A. Medicinal chemistry and the pharmacy curriculum. AMERICAN JOURNAL OF PHARMACEUTICAL EDUCATION 2011; 75:161. [PMID: 22102751 PMCID: PMC3220342 DOI: 10.5688/ajpe758161] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/18/2011] [Indexed: 05/27/2023]
Abstract
The origins and advancements of pharmacy, medicinal chemistry, and drug discovery are interwoven in nature. Medicinal chemistry provides pharmacy students with a thorough understanding of drug mechanisms of action, structure-activity relationships (SAR), acid-base and physicochemical properties, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles. A comprehensive understanding of the chemical basis of drug action equips pharmacy students with the ability to answer rationally the "why" and "how" questions related to drug action and it sets the pharmacist apart as the chemical expert among health care professionals. By imparting an exclusive knowledge base, medicinal chemistry plays a vital role in providing critical thinking and evidence-based problem-solving skills to pharmacy students, enabling them to make optimal patient-specific therapeutic decisions. This review highlights the parallel nature of the history of pharmacy and medicinal chemistry, as well as the key elements of medicinal chemistry and drug discovery that make it an indispensable component of the pharmacy curriculum.
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Affiliation(s)
- M O Faruk Khan
- College of Pharmacy, Southwestern Oklahoma State University, Weatherford, 73096, USA.
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9
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10
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Dam HH, Beijleveld H, Reinhoudt DN, Verboom W. In the Pursuit for Better Actinide Ligands: An Efficient Strategy for their Discovery. J Am Chem Soc 2008; 130:5542-51. [DOI: 10.1021/ja800222a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henk H. Dam
- Laboratories of Supramolecular Chemistry and Technology and Molecular Nanofabrication, Mesa+ Research Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Hans Beijleveld
- Laboratories of Supramolecular Chemistry and Technology and Molecular Nanofabrication, Mesa+ Research Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - David N. Reinhoudt
- Laboratories of Supramolecular Chemistry and Technology and Molecular Nanofabrication, Mesa+ Research Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Willem Verboom
- Laboratories of Supramolecular Chemistry and Technology and Molecular Nanofabrication, Mesa+ Research Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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11
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Houghten RA, Dooley CT, Appel JR. In vitro and direct in vivo testing of mixture-based combinatorial libraries for the identification of highly active and specific opiate ligands. AAPS JOURNAL 2006; 8:E371-82. [PMID: 16796388 PMCID: PMC3231577 DOI: 10.1007/bf02854908] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The use of combinatorial libraries for the identification of novel opiate and related ligands in opioid receptor assays is reviewed. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids is reviewed. New opioid compounds have also been identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (eg, polyamine, urea) and heterocyclic (eg, bicyclic guanidine) libraries are reviewed.
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Affiliation(s)
- Richard A Houghten
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, CA 92121, USA.
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12
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Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem 2006; 49:2151-4. [PMID: 16570910 PMCID: PMC1540993 DOI: 10.1021/jm060029z] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Screening in mixtures is a common approach for increasing the efficiency of high-throughput screening. Here we investigate how the "compound load" of mixtures influences promiscuous aggregate-based inhibition. We screened 764 molecules individually and in mixtures of 10 at 5 miccroM each, comparing the observed inhibition of the mixtures to that predicted from single-compound results. Synergistic effects on aggregation predominated, although antagonism was also observed. These results suggest that screening mixtures can increase aggregation-based inhibition in a nonadditive manner.
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Affiliation(s)
- Brian Y Feng
- Department of Pharmaceutical Chemistry and Graduate Group in Chemistry and Chemical Biology, University of California- San Francisco, 1700 4th Street, California 94143-2550, USA
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13
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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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14
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Nefzi A, Ostresh JM, Houghten RA. Combinatorial chemistry: mixture-based combinatorial libraries of acyclic and heterocyclic compounds from amino acids and short peptides. EXS 2003:109-23. [PMID: 12613174 DOI: 10.1007/978-3-0348-7997-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- Adel Nefzi
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, CA 92121, USA
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15
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Madder A, Li L, De Muynck H, Farcy N, Van Haver D, Fant F, Vanhoenacker G, Sandra P, Davis AP, De Clercq PJ. Evaluation of a two-stage screening procedure in the combinatorial search for serine protease-like activity. JOURNAL OF COMBINATORIAL CHEMISTRY 2002; 4:552-62. [PMID: 12425599 DOI: 10.1021/cc020016g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of peptidosteroid derivatives containing two independent peptide chains in which Ser and His are incorporated were synthesized by solid-phase peptide synthesis. The activity of the different compounds in the hydrolysis of the activated substrate NF31 was assessed in a stepwise fashion. First, the different resin-bound derivatives 6a-l and 6x-z were individually assayed for serine esterification in the absence of water. The use of a colored substrate allowed for a visual identification of the most active compounds. Through the inclusion of control substances, the involvement of histidine in the mechanism for serine acylation was shown. Second, the hydrolysis and methanolysis of the different acylated derivatives 8a-l and 8x were evaluated using UV spectroscopy, again indicating the involvement of histidine. The feasibility of applying the above procedures in a combinatorial context was proven via the screening of artificial libraries, created by mixing the different resin-bound peptidosteroid compounds. In this respect, the use of a photocleavable linker allowed for the unambiguous structural characterization of the selected members via application of single-bead electrospray tandem mass spectrometry.
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Affiliation(s)
- Annemieke Madder
- Laboratory of Organic Synthesis, Department of Organic Chemistry, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium
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16
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Chan ECY, Wang AW, Jia WP, Dollinger GD. An automated LC method for the small-scale purification of organic molecules derived from combinatorial libraries. J Pharm Biomed Anal 2002; 29:139-46. [PMID: 12062672 DOI: 10.1016/s0731-7085(02)00044-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This paper presented the development of an automated HPLC small-scale purification method for single bead compounds derived from combinatorial libraries. The method was found to produce higher and more consistent recoveries of purified compounds as compared to conventional manual HPLC purification. Using the manual method, the average percentage recovery of one synthetic compound was determined to be 24% and the coefficients of variation (C.V.%) of recovery were found to be greater than 38%. Using the automated system, the average percentages recovery of a standard compound at 600 and 1000 micromol l(-1) were determined to be 72.63+/-10.17% and 81.34+/-4.39%, respectively. This represented an approximate 3-folds increase in percentage recovery compared to that of the manual small-scale purification process. It was also found that the C.V.% of recovery were less than 15% at both concentration levels. The development of this automated method was found to be straightforward. The importance and implications of this study were discussed.
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Affiliation(s)
- Eric C Y Chan
- Analytical Chemistry, Chemistry Discovery, S*B10 Pte Ltd, 1 Science Park Road, #05-09, The Capricon, Singapore Science Park II, Singapore 117528, Singapore.
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17
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Bräse S, Neuß B. Glossar von Begriffen der Kombinatorischen Chemie. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3757(20020301)114:5<893::aid-ange893>3.0.co;2-s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Seneci P. Direct deconvolution techniques for pool libraries of small organic molecules. J Recept Signal Transduct Res 2001; 21:377-408. [PMID: 11789690 DOI: 10.1081/rrs-100107924] [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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19
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Hwang S, Tamilarasu N, Rana TM. Selection of HIV replication inhibitors: chemistry and biology. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 49:167-97. [PMID: 11013764 DOI: 10.1016/s1054-3589(00)49027-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- S Hwang
- Department of Pharmacology, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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20
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Computer Aided Analysis of Split and Mix Combinatorial Libraries. JOURNAL OF COMBINATORIAL CHEMISTRY 2001; 3:20-27. [PMID: 11148060 DOI: 10.1021/cc000045w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Combinatorial chemistry using split and pool synthesis involves making and testing mixtures of compounds in pools which are subsets of the larger compound collection. These subsets are created during the synthesis of the collection through a resin splitting and mixing method. Tests are conducted on each of the final pools of mixtures and the individual compounds within a mixture of interest are then identified through some deconvolution scheme, originally involving selective re-synthesis. It is possible that different schemes for splitting and mixing will have different consequences on the overall effort necessary to deconvolute interesting mixtures. The evaluation of different protocols of splitting and mixing involves consideration of more possibilities than can be exhaustively or optimally determined manually in a realistic time frame for most compound collections. We present herein a computational scheme to aid in this analysis. The approach exhaustively examines possible splitting and mixing strategies for the interrelated values of total library size, number of combinatorial steps, number of reaction vessels, and number of compounds per final pool. Weighting factors may be introduced into the various steps. The resulting complete list of splitting and mixing options is scored based on a variable weighting strategy for the total effort of synthesis and deconvolution. The results indicate the splitting/mixing strategy used has an impact on overall efficiency and should be considered in the design of compound libraries.
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21
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Houghten RA. Parallel array and mixture-based synthetic combinatorial chemistry: tools for the next millennium. Annu Rev Pharmacol Toxicol 2000; 40:273-82. [PMID: 10836136 DOI: 10.1146/annurev.pharmtox.40.1.273] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Technological advances continue to be a central driving force in the acceleration of the drug discovery process. Combinatorial chemistry methods, developed over the past 15 years, represent a paradigm shift in drug discovery. Initially viewed as a curiosity by the pharmaceutical industry, combinatorial chemistry is now recognized as an essential tool that decreases the time of discovery and increases the throughput of chemical screening by as much as 1000-fold. The use of parallel array synthesis approaches and mixture-based combinatorial libraries for drug discovery is reviewed.
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Affiliation(s)
- R A Houghten
- Torrey Pines Institute for Molecular Studies, San Diego, California 92121, USA.
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22
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Drug discovery and vaccine development using mixture-based synthetic combinatorial libraries. Drug Discov Today 2000; 5:276-285. [PMID: 10856909 DOI: 10.1016/s1359-6446(00)01513-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The approaches and concepts that encompass combinatorial chemistry represent a paradigm shift in drug discovery and basic research. Viewed initially as a curiosity by the pharmaceutical industry, combinatorial chemistry approaches are now recognized as essential drug discovery tools that decrease the time taken for discovery and increase the throughput of chemical screening by as much as 1000-fold. Although the use of mixture-based synthetic combinatorial libraries was one of the first approaches presented, its inherent strengths are only recently being recognized. Numerous mixture-based libraries of peptides, peptidomimetics and heterocycles have been synthesized and deconvoluted using the positional scanning approach. Mixture-based library approaches for drug discovery and vaccine development will be reviewed herein.
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Abstract
Here we review the use of combinatorial libraries in opioid receptor assays. Following a brief description of the history of the combinatorial field, methods for the generation of synthetic libraries and the deconvolution of mixture-based libraries are presented. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides from combinatorial libraries is reviewed. The peptides found are composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids, and range from tetrapeptides to decapeptides. Likewise, new opioid compounds identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (e.g., polyamine, urea) and heterocyclic (e.g., bicyclic guanidine) libraries, are reviewed.
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Affiliation(s)
- C T Dooley
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, USA
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24
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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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25
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De Muynck H, Madder A, Farcy N, De Clercq PJ, Pérez-Payán MN, Öhberg LM, Davis AP. Application of Combinatorial Procedures in the Search for Serine-Protease-Like Activity with Focus on the Acyl Transfer Step. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000103)112:1<149::aid-ange149>3.0.co;2-n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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26
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Boutin JA, Lahaye C, Pegurier C, Nicolas JP, Fauchere JL, Langlois M, Renard P, Delagrange P, Canet E. Screening of ligand binding on melatonin receptor using non-peptide combinatorial libraries. J Recept Signal Transduct Res 2000; 20:105-18. [PMID: 10711500 DOI: 10.3109/10799890009150040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The screening of combinatorial libraries requires a deconvolution procedure to obtain, in fine, the most active compound of the starting library. The standard screening assays used in regular molecular pharmacology, have been poorly assessed when transposed to combinatorial chemistry-related experiments, particularly those involving large numbers of chemicals in a single assay. One key issue is the effect of the inactive analogs on the identification of the active ligand in mixtures. We chose melatonin receptors to measure the apparent affinity of a single ligand when tested alone or in mixtures of non-peptide low molecular weight compounds. Using ligands with IC50 from the micro- to the picomolar range, mixed with increasingly complex mixtures of 5 to 20 or 25 inactive compounds, we analyzed the displacements from the mt1 and MT2 melatonin receptor subtypes of the radioligand 2-iodomelatonin (KD= 25 pmol/l and 200 pmol/l, respectively) . The behavior of equimolar mixtures in displacement curves led to the conclusion that the observed binding affinity reflects the dilution effect of mixing the active component with inactive compounds but does not reveal noticeable interactions which would interfere with the binding process. From the practical point of view, the concentrations of the active species in the binding assay should be large enough to displace significantly the radioligand, a requirement which may be limited by the solubility of the ligand mixtures. In contrast, previous observations with peptide libraries report that the dilution effect is often compensated by additive or synergic action of structurally related analogs, thus making possible the deconvolution of very large (typically up to 10(7) compounds) peptide libraries.
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Affiliation(s)
- J A Boutin
- Division de Pharmacologie Moléculaire et Cellulaire, Institut de Recherches SERVIER, Croissy-sur-Seine, France
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Houghten RA, Pinilla C, Appel JR, Blondelle SE, Dooley CT, Eichler J, Nefzi A, Ostresh JM. Mixture-based synthetic combinatorial libraries. J Med Chem 1999; 42:3743-78. [PMID: 10508425 DOI: 10.1021/jm990174v] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R A Houghten
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121, USA
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28
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Appel JR, Johnson J, Narayanan VL, Houghten RA. Identification of novel antitumor agents from mixture-based synthetic combinatorial libraries using cell-based assays. Mol Divers 1999; 4:91-102. [PMID: 10425632 DOI: 10.1023/a:1026441400053] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new strategy is presented here which integrates combinatorial library technology with the antitumor in vitro screening system at the National Cancer Institute in the search for novel antitumor agents. Mixture-based synthetic combinatorial libraries (SCLs) representing hundreds of thousands to millions of individual compounds were screened against the cell-based assay, which evaluates compounds for their ability to inhibit the growth of 60 different human tumor cell lines. Five different SCLs, composed of peptides, peptidomimetics, polyamines or small molecules were first tested against three cell lines to identify the most active SCLs. Two SCLs, namely the N-perbenzylated pentamine and the N-acylated permethylated triamine, were deconvoluted to yield individual compounds having significant activities against the 60 tumor cell lines. Active compounds were tested in mice to determine the maximum tolerated dose, followed by in vivo testing in a hollow fiber assay. Using this strategy, three different compounds identified directly from SCLs are currently being evaluated in human tumor xenografts. This study demonstrates for the first time the use of in vitro cell-based assays to identify antitumor lead compounds from mixture-based combinatorial libraries.
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Affiliation(s)
- J R Appel
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, USA.
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29
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Abstract
The combination of high-performance liquid chromatography and mass spectrometry (LC/MS) has had a significant impact on drug development over the past decade. Continual improvements in LC/MS interface technologies combined with powerful features for structure analysis, qualitative and quantitative, have resulted in a widened scope of application. These improvements coincided with breakthroughs in combinatorial chemistry, molecular biology, and an overall industry trend of accelerated development. New technologies have created a situation where the rate of sample generation far exceeds the rate of sample analysis. As a result, new paradigms for the analysis of drugs and related substances have been developed. The growth in LC/MS applications has been extensive, with retention time and molecular weight emerging as essential analytical features from drug target to product. LC/MS-based methodologies that involve automation, predictive or surrogate models, and open access systems have become a permanent fixture in the drug development landscape. An iterative cycle of "what is it?" and "how much is there?" continues to fuel the tremendous growth of LC/MS in the pharmaceutical industry. During this time, LC/MS has become widely accepted as an integral part of the drug development process. This review describes the utility of LC/MS techniques for accelerated drug development and provides a perspective on the significant changes in strategies for pharmaceutical analysis. Future applications of LC/MS technologies for accelerated drug development and emerging industry trends are also discussed.
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Affiliation(s)
- M S Lee
- Milestone Development Services, Pennington, New Jersey 08534-0813, USA
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30
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Boutin JA, Lambert PH, Bertin S, Volland JP, Fauchère JL. Physico-chemical and biological analysis of true combinatorial libraries. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 725:17-37. [PMID: 10226875 DOI: 10.1016/s0378-4347(98)00569-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Combinatorial libraries offer new sources of compounds for the research of pharmacological agents such as receptor ligands, enzyme inhibitors or substrates and antibody-binding epitopes. The present review stresses the main roles played by both physico-chemical analysis, particularly when complex mixture of compounds are synthesized as libraries, and biological analysis from which active compounds are identified. After a brief discussion of semantic problems related to the designation of the product mixtures, the physico-chemical analysis of mixtures is reviewed with special emphasis on mass spectrometric techniques. These methods are able both to give a representative view of a library composition and to identify single critical compounds in large libraries. Then the biological screening of such combinatorial libraries is critically discussed with respect to the power and limitations of the methods used for the identification of the active components. Special attention is given to the complex process of library deconvolution. It is pointed out that while combinatorial techniques have evolved towards sophisticated high-tech methods, simple and robust biochemical tests should be used to deconvolute. From a large panel of published examples, a set of trends are identified which should help investigators to choose the most appropriate assay for the discovery of new entities.
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Affiliation(s)
- J A Boutin
- Department of Molecular and Cellular Pharmacology, Institut de Recherches SERVIER, Croissy-sur-Seine, France
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31
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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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32
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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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33
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Eliseev AV, Nelen MI. Use of Molecular Recognition To Drive Chemical Evolution: Mechanisms of an Automated Genetic Algorithm Implementation. Chemistry 1998. [DOI: 10.1002/(sici)1521-3765(19980515)4:5<825::aid-chem825>3.0.co;2-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Boutin JA, Gesson I, Henlin JM, Bertin S, Lambert PH, Volland JP, Fauchère JL. Limitations of the coupling of amino acid mixtures for the preparation of equimolar peptide libraries. Mol Divers 1998; 3:43-60. [PMID: 9527476 DOI: 10.1023/a:1009602707067] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The standard method of peptide library synthesis involves coupling steps in which a single amino acid is reacted with a mixture of resin-bound amino acids. The more recently described positional scanning strategy (in which each position in the peptide sequence is occupied in turn by a single residue) is different since it involves the coupling of mixtures of amino acids to mixtures of resin-bound amino acids. In the present study, we analyze the compounds produced under these conditions measuring coupling rates and amounts of formed products, using mainly UV, HPLC, LC/MS and MS/MS techniques. Our data do not permit to conclude that the resulting libraries are complete. Indeed, our analytical data indicate that a large part of the di-, tri- and tetrapeptides synthesized with this method are not present in the final mixture. Although chemical compensation (in which poor coupling kinetics is compensated by a larger excess of the incoming amino acid) has been thought to counterbalance these biases, our experiments show that the compensation method does not take into account the crucial influence of the resin-bound amino acid and that even the dipeptide libraries obtained in this way are far from completeness. The present work provides strong evidence that the coupling of mixtures of amino acids to resin-bound residues, which is required by the positional scanning strategy, results in incomplete and/or non-equimolar libraries. It also clearly confirms that coupling rates in solid-phase peptide synthesis are dependent on the nature of both the incoming and the immobilized amino acid.
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Affiliation(s)
- J A Boutin
- Department of Peptide and Combinatorial Chemistry, Institut de Recherches SERVIER, Suresnes, France
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35
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An H, Haly BD, Cook PD. Discovery of novel pyridinopolyamines with potent antimicrobial activity: deconvolution of mixtures synthesized by solution-phase combinatorial chemistry. J Med Chem 1998; 41:706-16. [PMID: 9513599 DOI: 10.1021/jm970598u] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A 1638-member pyridinopolyamine library, consisting of 13 sublibraries of 126 members prepared by a solution-phase approach, was completely deconvoluted from orthogonally protected intermediates by a combination of iterative and positional scanning procedures. Antibacterial assays against Streptococcus pyogenes and Escherichia coli imp- and a Candida albicans yeast specificity assay were employed to follow the activity of sublibraries. Screening of the 13 sublibraries, which were prepared by a synthetic method that places the differentiating functionality in a selected position A (secondary amine), at the end of the synthesis (fix last), provided several first-round activities. Subsequently, six single pyridinopolyamines (2-7) were prepared where the first-round winner, a hydrogen atom, is in the first deconvoluted position and the remaining three positions contained the same functionalities. The range of antibacterial and yeast activities of these single compounds suggested that a more active and selective compound may be discovered by completely deconvoluting the first-round active sublibraries. Pyridinopolyamine positions B (secondary benzylamine) and C (primary benzylamine) were then sequentially positionally scanned with a set of six meta-substituted benzyl functionalities to generate two sets of second/third-round sublibraries, containing 21 or 36 compounds in each sublibrary, respectively. High-throughput screening yielded sublibraries 15, 18, and 21 with MICs of 1-5 microM against S. pyogenes and E. coli imp-. Using rounds 1 and 2/3 screening data, two sets of single compounds (22-27) and (28-32) with the combination of m-(trifluoromethyl)-benzyl group at position C and m-(trifluoromethyl)benzyl or m-methylbenzyl group at position B with position D (primary benzylamine) fixed were synthesized in the fourth round deconvolution. Subsequently, broader screening of deconvoluted compounds against a tier II panel of wild-type bacteria identified eight compounds (5, 7, 27, and 29-32) with approximately 100-fold greater selectivity for Gram-positive than Gram-negative bacteria. Thus, S. pyogenes, S. pyogenes (wild-type), Streptomyces aureus, and Enterococcus faecalis were inhibited at MICs of 1-12 microM, whereas MICs for E. coli, Klebsiella pneumoniae, Proteus vulgaris, and Pseudomonas aeruginosa were > 100 microM. These eight compounds were not active (> 100 microM) against fungus C. albicans.
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Affiliation(s)
- H An
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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36
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Oldenburg KR. Current and Future Trends in High Throughput Screening for Drug Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1998. [DOI: 10.1016/s0065-7743(08)61095-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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37
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Konings DA, Wyatt JR, Ecker DJ, Freier SM. Strategies for rapid deconvolution of combinational libraries: comparative evaluation using a model system. J Med Chem 1997; 40:4386-95. [PMID: 9435908 DOI: 10.1021/jm970503o] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Synthesis and testing of complex mixtures maximize the number of compounds that can be prepared and tested in a combinatorial library. When mixtures of compounds are screened, however, the identity of the compound(s) selected may depend on the deconvolution procedure employed. Previously, we developed a model system for evaluation of deconvolution procedures and used it to compare pooling strategies for iterative and noniterative deconvolution [Freier et al. J. Med. Chem. 1995, 38, 344-352]. We have now extended the model studies to include simulations of procedures with overlapping subsets such as subtractive pooling [Carell et al. Angew, Chem., Int. Ed. Engl. 1994, 33, 2061-2064], bogus coin pooling [Blake and Litzi-Davis. Bioconjugate Chem. 1992, 3, 510-513], and orthogonal pooling [D'Prez et al. J. Am. Chem. Soc. 1995, 117, 5405-5406]. These strategies required synthesis and testing of fewer subsets than did the more traditional nonoverlapping iterative strategies. The compounds identified using simulations of these strategies, however, were not the most active compounds in the library and were substantially less active than those identified by simulations of more traditional strategies.
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Affiliation(s)
- D A Konings
- ISIS Pharmaceuticals, Carlsbad, California 92008, USA
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38
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Ceulemans G, Van Aerschot A, Wroblowski B, Rozenski J, Hendrix C, Herdewijn P. Oligonucleotide Analogues with 4-Hydroxy-N-Acetylprolinol as Sugar Substitute. Chemistry 1997. [DOI: 10.1002/chem.19970031215] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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39
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Abstract
The past year has seen a maturation of molecular modeling, with an increasing number of comparative studies between established methods becoming possible, together with an explosion of new work especially in the areas of combinatorial chemistry and molecular diversity. Traditionally 'difficult' areas such as modeling oligosaccharides look set to join the mainstream in the next few years.
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Affiliation(s)
- H B Broughton
- Merck, Sharp & Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Eastwick Road, Harlow, Essex, CM20 2QR, UK.
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40
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Wieboldt R, Zweigenbaum J, Henion J. Immunoaffinity Ultrafiltration with Ion Spray HPLC/MS for Screening Small-Molecule Libraries. Anal Chem 1997; 69:1683-91. [DOI: 10.1021/ac9610265] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Nefzi A, Ostresh JM, Houghten RA. The Current Status of Heterocyclic Combinatorial Libraries. Chem Rev 1997; 97:449-472. [PMID: 11848878 DOI: 10.1021/cr960010b] [Citation(s) in RCA: 512] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adel Nefzi
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121
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Abstract
This review serves to highlight the recent examples of combinatoric methodology as applied to the discovery and optimization of enzyme inhibitors. Early research efforts focused on the identification of polypeptides from libraries as inhibitors of proteases. As solution- and solid-phase chemistries gain in sophistication, libraries containing less peptidic structural motifs have been created. A recurring design stratagem relies on the synthesis of libraries incorporating pharmacophores with known affinity for the target enzyme. Screening of these structure-based libraries has led to the discovery of small-molecule inhibitors of both proteolytic and non-proteolytic enzymes alike. Two tables are provided listing the enzyme targeted libraries through 1996. A name, generic structure and size is given for each library citation, accompanied by the enzyme screen and the structure and potency of the most active library member.
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Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia Inc., Princeton, NJ 08540, USA
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43
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Affiliation(s)
- H Maehr
- Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA.
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44
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Beutel BA. Chapter 26. Discovery and Identification of Lead Compounds from Combinatorial Mixtures. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1997. [DOI: 10.1016/s0065-7743(08)61484-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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46
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Felder ER, Poppinger D. Combinatorial compound libraries for enhanced drug discovery approaches. ADVANCES IN DRUG RESEARCH 1997. [DOI: 10.1016/s0065-2490(97)80006-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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47
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Balkenhohl F, von dem Bussche-Hünnefeld C, Lansky A, Zechel C. Kombinatorische Synthese niedermolekularer organischer Verbindungen. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961082004] [Citation(s) in RCA: 173] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Konings DA, Wyatt JR, Ecker DJ, Freier SM. Deconvolution of combinatorial libraries for Drug discovery: theoretical comparison of pooling strategies. J Med Chem 1996; 39:2710-9. [PMID: 8709101 DOI: 10.1021/jm960168o] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Synthesis and testing of mixtures of compounds in a combinatorial library allow much greater throughput than synthesis and testing of individual compounds. When mixtures of compounds are screened, however, the possibility exists that the most active compound will not be identified. The specific strategies employed for pooling and deconvolution will affect the likelihood of success. We have used a nucleic acid hybridization example to develop a theoretical model of library deconvolution for a library of more than 250,000 compounds. This model was used to compare various strategies for pooling and deconvolution. Simulations were performed in the absence and presence of experimental error. We found iterative deconvolution to be most reliable when active molecules were assigned to the same subset in early rounds. Reliability was reduced only slightly when active molecules were assigned randomly to all subsets. Iterative deconvolution with as many as 65,536 compounds per subset did not drastically reduce the reliability compared to one-at-a-time testing. Pooling strategies compared using this theoretical model are compared experimentally in an accompanying paper.
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Affiliation(s)
- D A Konings
- ISIS Pharmaceuticals, Carlsbad, California 92008, USA
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