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Sahrawat P, Kowalczyk P, Koszelewski D, Szymczak M, Kramkowski K, Wypych A, Ostaszewski R. Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains. Molecules 2022; 27:molecules27113633. [PMID: 35684570 PMCID: PMC9182016 DOI: 10.3390/molecules27113633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 12/25/2022] Open
Abstract
An efficient method for the synthesis of functionalized peptidomimetics via multicomponent Ugi reaction has been developed. The application of trifluoroethanol (TFE) as a reaction medium provided desired products with good yields. Further, using the developed cyclisation reaction, the obtained peptidomimetics were transformed into the cyclic analogues (diketopiperazines, DKPs). The goal of the performed studies was to revised and compare whether the structure of the obtained structurally flexible acyclic peptidomimetics and their rigid cycling analogue DKPs affect antimicrobial activity. We studied the potential of synthesized peptidomimetics, both cyclic and acyclic, as antimicrobial drugs on model E. coli bacteria strains (k12, R2–R4). The biological assays reveal that DKPs hold more potential as antimicrobial drugs compared to open chain Ugi peptidomimetics. We believe that it can be due to the rigid cyclic structure of DKPs which promotes the membrane penetration in the cell of studied pathogens. The obtained data clearly indicate the high antibiotic potential of synthesized diketopiperazine derivatives over tested antibiotics.
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Affiliation(s)
- Parul Sahrawat
- Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; (P.S.); (D.K.)
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jabłonna, Poland
- Correspondence: (P.K.); (R.O.)
| | - Dominik Koszelewski
- Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; (P.S.); (D.K.)
| | - Mateusz Szymczak
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
| | - Karol Kramkowski
- Department of Physical Chemistry, Medical University of Bialystok, Kilińskiego 1 Str., 15-089 Białystok, Poland;
| | - Aleksandra Wypych
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, ul. Wileńska 4, 87-100 Toruń, Poland;
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; (P.S.); (D.K.)
- Correspondence: (P.K.); (R.O.)
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2
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Muramatsu W, Yamamoto H. An economical approach for peptide synthesis via regioselective C-N bond cleavage of lactams. Chem Sci 2022; 13:6309-6315. [PMID: 35733900 PMCID: PMC9159104 DOI: 10.1039/d2sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/21/2022] [Indexed: 11/21/2022] Open
Abstract
An economical, solvent-free, and metal-free method for peptide synthesis via C-N bond cleavage using lactams has been developed. The method not only eliminates the need for condensation agents and their auxiliaries, which are essential for conventional peptide synthesis, but also exhibits high atom economy. The reaction is versatile because it can tolerate side chains bearing a range of functional groups, affording up to >99% yields of the corresponding peptides without racemisation or polymerisation. Moreover, the developed strategy enables peptide segment coupling, providing access to a hexapeptide that occurs as a repeat sequence in spider silk proteins.
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Affiliation(s)
- Wataru Muramatsu
- Peptide Research Center, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Hisashi Yamamoto
- Peptide Research Center, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
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3
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McConnell N, Xu Z, Kumarasamy V, Sun D, Frett B, Li HY. Synthesis of Constrained Heterocycles Employing Two Post-Ugi Cyclization Methods for Rapid Library Generation with In Cellulo Activity. ChemistrySelect 2017; 2:11821-11825. [PMID: 30140731 PMCID: PMC6103208 DOI: 10.1002/slct.201702179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/20/2017] [Indexed: 01/10/2024]
Abstract
Benzimidazoles and quinoxalinones are present in the core of many pharmacologically relevant compounds. Several combinatorial methods have been developed to attach ring systems to both scaffolds for derivatization at select positions. Herein, we describe the development of novel constrained heterocyclic compounds attached to the N1 position of both benzimidazole and quinoxalinone scaffolds. Utilizing robust post-Ugi cyclization methods, including the Ugi-deprotection-cyclization (UDC) methodology, allows for efficient access to a new area of chemical space. Additionally, molecular modeling and in cellulo screening was employed to therapeutically validate the compounds formed with this method.
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Affiliation(s)
- Nicholas McConnell
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85719 United States
| | - Zhigang Xu
- International Academy of Targeted Therapeutics and Innovation Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160 China
| | - Vishnu Kumarasamy
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85719 United States
| | - Daekyu Sun
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85719 United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
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Thakkar BS, Albrigtsen M, Svendsen JS, Andersen JH, Engh RA. Biofocussed chemoprospecting: An efficient approach for drug discovery. Chem Biol Drug Des 2017; 90:128-140. [DOI: 10.1111/cbdd.12934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 12/19/2022]
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5
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Xu Z, Martinez-Ariza G, Cappelli AP, Roberts SA, Hulme C. (Z)-Stereoselective Synthesis of Mono- and Bis-heterocyclic Benzimidazol-2-ones via Cascade Processes Coupled with the Ugi Multicomponent Reaction. J Org Chem 2015; 80:9007-15. [DOI: 10.1021/acs.joc.5b00955] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhigang Xu
- Biological
Sciences West Room 351, Department of Pharmacology and Toxicology,
College of Pharmacy, The University of Arizona, 1041, East Lowell Street, Tucson, Arizona 85721, United States
| | - Guillermo Martinez-Ariza
- Biological
Sciences West Room 351, Department of Pharmacology and Toxicology,
College of Pharmacy, The University of Arizona, 1041, East Lowell Street, Tucson, Arizona 85721, United States
| | - Alexandra P. Cappelli
- Biological
Sciences West Room 351, Department of Pharmacology and Toxicology,
College of Pharmacy, The University of Arizona, 1041, East Lowell Street, Tucson, Arizona 85721, United States
| | - Sue A. Roberts
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher Hulme
- Biological
Sciences West Room 351, Department of Pharmacology and Toxicology,
College of Pharmacy, The University of Arizona, 1041, East Lowell Street, Tucson, Arizona 85721, United States
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
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Zarganes-Tzitzikas T, Patil P, Khoury K, Herdtweck E, Dömling A. Concise Synthesis of Tetrazole-keto-piperazines by Two Consecutive Ugi Reactions. European J Org Chem 2015; 2015:51-55. [PMID: 26949370 PMCID: PMC4774864 DOI: 10.1002/ejoc.201403401] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Indexed: 01/09/2023]
Abstract
AbstractA concise route for the synthesis of the novel compound class tetrazole–diketopiperazines was developed. The approach involves the use of two multicomponent reactions: the Ugi tetrazole four‐component reaction (4CR) and the classical intramolecular Ugi 4CR. The tetrazole–diketopiperazines comprise analogs of and are bioisosteric to bioactive diketopiperazines, which thus draws attention for novel bioactive compound design. This scaffold was produced to fill the screening deck of the European lead factory.
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Affiliation(s)
- Tryfon Zarganes-Tzitzikas
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, Postbus 196, 9700 AD Groningen, Netherlands, Homepage: www.drugdesign.nl
| | - Pravin Patil
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, Postbus 196, 9700 AD Groningen, Netherlands, Homepage: www.drugdesign.nl
| | - Kareem Khoury
- Carmolex Inc., 2000 Technology Drive Suite 100, Pittsburgh, Pennsylvania 15219 United States, Homepage: www.carmolex.com
| | - Eberhardt Herdtweck
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching bei Munchen, Germany
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, Postbus 196, 9700 AD Groningen, Netherlands, Homepage: www.drugdesign.nl
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Minond D, Cudic M, Bionda N, Giulianotti M, Maida L, Houghten RA, Fields GB. Discovery of novel inhibitors of a disintegrin and metalloprotease 17 (ADAM17) using glycosylated and non-glycosylated substrates. J Biol Chem 2012; 287:36473-87. [PMID: 22927435 DOI: 10.1074/jbc.m112.389114] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A disintegrin and metalloprotease (ADAM) proteases are implicated in multiple diseases, but no drugs based on ADAM inhibition exist. Most of the ADAM inhibitors developed to date feature zinc-binding moieties that target the active site zinc, which leads to a lack of selectivity and off-target toxicity. We hypothesized that secondary binding site (exosite) inhibitors should provide a viable alternative to active site inhibitors. Potential exosites in ADAM structures have been reported, but no studies describing substrate features necessary for exosite interactions exist. Analysis of ADAM cognate substrates revealed that glycosylation is often present in the vicinity of the scissile bond. To study whether glycosylation plays a role in modulating ADAM activity, a tumor necrosis factor α (TNFα) substrate with and without a glycan moiety attached was synthesized and characterized. Glycosylation enhanced ADAM8 and -17 activities and decreased ADAM10 activity. Metalloprotease (MMP) activity was unaffected by TNFα substrate glycosylation. High throughput screening assays were developed using glycosylated and non-glycosylated substrate, and positional scanning was conducted. A novel chemotype of ADAM17-selective probes was discovered from the TPIMS library (Houghten, R. A., Pinilla, C., Giulianotti, M. A., Appel, J. R., Dooley, C. T., Nefzi, A., Ostresh, J. M., Yu, Y., Maggiora, G. M., Medina-Franco, J. L., Brunner, D., and Schneider, J. (2008) Strategies for the use of mixture-based synthetic combinatorial libraries. Scaffold ranking, direct testing in vivo, and enhanced deconvolution by computational methods. J. Comb. Chem. 10, 3-19; Pinilla, C., Appel, J. R., Borràs, E., and Houghten, R. A. (2003) Advances in the use of synthetic combinatorial chemistry. Mixture-based libraries. Nat. Med. 9, 118-122) that preferentially inhibited glycosylated substrate hydrolysis and spared ADAM10, MMP-8, and MMP-14. Kinetic studies revealed that ADAM17 inhibition occurred via a non-zinc-binding mechanism. Thus, modulation of proteolysis via glycosylation may be used for identifying novel, potentially exosite binding compounds. The newly described ADAM17 inhibitors represent research tools to investigate the role of ADAM17 in the progression of various diseases.
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Affiliation(s)
- Dmitriy Minond
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, USA.
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8
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Vainio MJ, Kogej T, Raubacher F. Automated recycling of chemistry for virtual screening and library design. J Chem Inf Model 2012; 52:1777-86. [PMID: 22657574 DOI: 10.1021/ci300157m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An early stage drug discovery project needs to identify a number of chemically diverse and attractive compounds. These hit compounds are typically found through high-throughput screening campaigns. The diversity of the chemical libraries used in screening is therefore important. In this study, we describe a virtual high-throughput screening system called Virtual Library. The system automatically "recycles" validated synthetic protocols and available starting materials to generate a large number of virtual compound libraries, and allows for fast searches in the generated libraries using a 2D fingerprint based screening method. Virtual Library links the returned virtual hit compounds back to experimental protocols to quickly assess the synthetic accessibility of the hits. The system can be used as an idea generator for library design to enrich the screening collection and to explore the structure-activity landscape around a specific active compound.
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Affiliation(s)
- Mikko J Vainio
- Discovery Sciences Computational Sciences, AstraZeneca R&D, Pepparedsleden 1, S-43183 Mölndal, Sweden
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9
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Borthwick AD. 2,5-Diketopiperazines: synthesis, reactions, medicinal chemistry, and bioactive natural products. Chem Rev 2012; 112:3641-716. [PMID: 22575049 DOI: 10.1021/cr200398y] [Citation(s) in RCA: 601] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Chen H, Engkvist O, Blomberg N. Combinatorial library design from reagent pharmacophore fingerprints. Methods Mol Biol 2011; 685:135-152. [PMID: 20981522 DOI: 10.1007/978-1-60761-931-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Combinatorial and parallel chemical synthesis technologies are powerful tools in early drug discovery projects. Over the past couple of years an increased emphasis on targeted lead generation libraries and focussed screening libraries in the pharmaceutical industry has driven a surge in computational methods to explore molecular frameworks to establish new chemical equity. In this chapter we describe a complementary technique in the library design process, termed ProSAR, to effectively cover the accessible pharmacophore space around a given scaffold. With this method reagents are selected such that each R-group on the scaffold has an optimal coverage of pharmacophoric features. This is achieved by optimising the Shannon entropy, i.e. the information content, of the topological pharmacophore distribution for the reagents. As this method enumerates compounds with a systematic variation of user-defined pharmacophores to the attachment point on the scaffold, the enumerated compounds may serve as a good starting point for deriving a structure-activity relationship (SAR).
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Affiliation(s)
- Hongming Chen
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Mölndal, Sweden.
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12
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13
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Campbell J, Blackwell HE. Efficient construction of diketopiperazine macroarrays through a cyclative-cleavage strategy and their evaluation as luminescence inhibitors in the bacterial symbiont Vibrio fischeri. ACTA ACUST UNITED AC 2010; 11:1094-9. [PMID: 19831384 DOI: 10.1021/cc900115x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diketopiperazines (DKPs) are a well-known class of heterocycles that have emerged as promising biologically active scaffolds. Solid-phase organic synthesis has become an important tool in the combinatorial exploration of these privileged structures, expediting the synthesis and, often, the discovery of active compounds. We recently identified several DKPs that are capable of inhibiting the luminescence response of the bacterial symbiont Vibrio fischeri, and we sought to further test the scope of this biological activity. Herein, we report the synthesis of DKP macroarrays using a SPOT-synthesis approach based on an Ugi/DeBoc/Cyclize strategy. Neither a spacer nor a linker was required for macroarray construction on cellulose support, and the cyclative cleavage produced high purity DKPs in good yields. Using this protocol, we prepared a library of 400 DKPs on cellulose support and evaluated its members as luminescence inhibitors in V. fischeri. We found six DKPs capable of inhibiting luminescence by at least 80% at 500 muM. Collectively, this work serves to further highlight the utility of the small molecule macroarray platform for the synthesis and evaluation of focused libraries.
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Affiliation(s)
- Jennifer Campbell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, USA
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14
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Banfi L, Basso A, Riva R. Synthesis of Heterocycles Through Classical Ugi and Passerini Reactions Followed by Secondary Transformations Involving One or Two Additional Functional Groups. SYNTHESIS OF HETEROCYCLES VIA MULTICOMPONENT REACTIONS I 2010. [DOI: 10.1007/7081_2009_23] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
A continuous assay method, such as the one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors and to aid in the design of MMP inhibitors, a variety of sequence specificity, phage display, and combinatorial chemistry studies have been performed. Results of these studies have been valuable for defining the differences in MMPs and for creating quenched fluorescent substrates that utilize fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET). FRET triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. The present chapter provides an overview of MMP and related FRET substrates and describes how to construct and utilize these substrates.
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16
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Rhoden CRB, Rivera DG, Kreye O, Bauer AK, Westermann B, Wessjohann LA. Rapid Access to N-Substituted Diketopiperazines by One-Pot Ugi-4CR/Deprotection+Activation/Cyclization (UDAC). ACTA ACUST UNITED AC 2009; 11:1078-82. [DOI: 10.1021/cc900106u] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristiano R. B. Rhoden
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany, and Institute of Chemistry, University of Halle, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Daniel G. Rivera
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany, and Institute of Chemistry, University of Halle, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Oliver Kreye
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany, and Institute of Chemistry, University of Halle, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Anne K. Bauer
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany, and Institute of Chemistry, University of Halle, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Bernhard Westermann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany, and Institute of Chemistry, University of Halle, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany, and Institute of Chemistry, University of Halle, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
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Chen H, Börjesson U, Engkvist O, Kogej T, Svensson MA, Blomberg N, Weigelt D, Burrows JN, Lange T. ProSAR: A New Methodology for Combinatorial Library Design. J Chem Inf Model 2009; 49:603-14. [DOI: 10.1021/ci800231d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongming Chen
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ulf Börjesson
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ola Engkvist
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Thierry Kogej
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Mats A. Svensson
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Niklas Blomberg
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Dirk Weigelt
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Jeremy N. Burrows
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Tim Lange
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
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Lauer-Fields JL, Minond D, Chase PS, Baillargeon PE, Saldanha SA, Stawikowska R, Hodder P, Fields GB. High throughput screening of potentially selective MMP-13 exosite inhibitors utilizing a triple-helical FRET substrate. Bioorg Med Chem 2009; 17:990-1005. [PMID: 18358729 PMCID: PMC3298815 DOI: 10.1016/j.bmc.2008.03.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2007] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 11/26/2022]
Abstract
The major components of the cartilage extracellular matrix are type II collagen and aggrecan. Matrix metalloproteinase 13 (MMP-13) has been implicated as the protease responsible for collagen degradation in cartilage during osteoarthritis (OA). In the present study, a triple-helical FRET substrate has been utilized for high throughput screening (HTS) of MMP-13 with the MLSCN compound library (n approximately 65,000). Thirty-four compounds from the HTS produced pharmacological dose-response curves. A secondary screen using RP-HPLC validated 25 compounds as MMP-13 inhibitors. Twelve of these compounds were selected for counter-screening with 6 representative MMP family members. Five compounds were found to be broad-spectrum MMP inhibitors, 3 inhibited MMP-13 and one other MMP, and 4 were selective for MMP-13. One of the selective inhibitors was more active against MMP-13 triple-helical peptidase activity compared with single-stranded peptidase activity. Since the THP FRET substrate has distinct conformational features that may interact with MMP secondary binding sites (exosites), novel non-active site-binding inhibitors may be identified via HTS protocols utilizing such assays.
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Affiliation(s)
- Janelle L. Lauer-Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Dmitriy Minond
- Lead Identification Department, The Scripps Research Institute Molecular Screening Center, Scripps Florida, 5353 Parkside Drive, RF-1, Jupiter, FL 33458
| | - Peter S. Chase
- Lead Identification Department, The Scripps Research Institute Molecular Screening Center, Scripps Florida, 5353 Parkside Drive, RF-1, Jupiter, FL 33458
| | - Pierre E. Baillargeon
- Lead Identification Department, The Scripps Research Institute Molecular Screening Center, Scripps Florida, 5353 Parkside Drive, RF-1, Jupiter, FL 33458
| | - S. Adrian Saldanha
- Lead Identification Department, The Scripps Research Institute Molecular Screening Center, Scripps Florida, 5353 Parkside Drive, RF-1, Jupiter, FL 33458
| | - Roma Stawikowska
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Peter Hodder
- Lead Identification Department, The Scripps Research Institute Molecular Screening Center, Scripps Florida, 5353 Parkside Drive, RF-1, Jupiter, FL 33458
| | - Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
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Specific targeting of metzincin family members with small-molecule inhibitors: Progress toward a multifarious challenge. Bioorg Med Chem 2008; 16:8781-94. [DOI: 10.1016/j.bmc.2008.08.058] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 08/22/2008] [Accepted: 08/26/2008] [Indexed: 12/20/2022]
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21
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A convergent synthesis of enantiopure bicyclic scaffolds through multicomponent Ugi reaction. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.10.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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O'Neill J, Blackwell HE. Solid-phase and microwave-assisted syntheses of 2,5-diketopiperazines: small molecules with great potential. Comb Chem High Throughput Screen 2007; 10:857-76. [PMID: 18288948 PMCID: PMC2585775 DOI: 10.2174/138620707783220365] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diketopiperazines (DKPs) are a well-known class of heterocycles that have recently emerged as a promising biologically active scaffold. Solid-phase organic synthesis has become an important tool in the combinatorial exploration of these privileged structures, expediting the synthesis and, therefore, the discovery of active compounds. To date, certain DKPs have shown potent activities against a range of diseases and biological phenomena, including bacterial infections, various cancers, asthma, infertility, premature labor, and HIV. Recent applications of solid-phase DKP synthesis, with a particular focus on cyclative cleavage and microwave-assisted reactions, are highlighted herein.
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Affiliation(s)
- J.C. O'Neill
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | - H. E. Blackwell
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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23
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Lauer-Fields JL, Spicer TP, Chase PS, Cudic M, Burstein GD, Nagase H, Hodder P, Fields GB. Screening of potential a disintegrin and metalloproteinase with thrombospondin motifs-4 inhibitors using a collagen model fluorescence resonance energy transfer substrate. Anal Biochem 2007; 373:43-51. [PMID: 17949675 DOI: 10.1016/j.ab.2007.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/29/2007] [Accepted: 09/03/2007] [Indexed: 01/07/2023]
Abstract
The major components of the cartilage extracellular matrix are type II collagen and aggrecan. Type II collagen provides cartilage with its tensile strength, whereas the water-binding capacity of aggrecan provides compressibility and elasticity. Aggrecan breakdown leads to an increase in proteolytic susceptibility of articular collagen; hence, aggrecan may also have a protective effect on type II collagen. Given their role in aggrecan degradation and differing substrate specificity profiles, the pursuit of inhibitors for both aggrecanase 1 (a disintegrin and metalloproteinase with thrombospondin motifs-4 [ADAMTS-4]) and aggrecanase 2 (ADAMTS-5) is desirable. We previously described collagen model fluorescence resonance energy transfer (FRET) substrates for aggrecan-degrading members of the ADAMTS family. These FRET substrate assays are also fully compatible with multiwell formats. In the current study, a collagen model FRET substrate was examined for inhibitor screening of ADAMTS-4. ADAMTS-4 was screened against a small compound library (n=960) with known pharmacological activity. Five compounds that inhibited ADAMTS-4>60% at a concentration of 1muM were identified. A secondary screen using reversed-phase high-performance liquid chromatography (RP-HPLC) was developed and performed for verification of the five potential inhibitors. Ultimately, piceatannol was confirmed as a novel inhibitor of ADAMTS-4, with an IC(50) value of 1muM. Because the collagen model FRET substrates have distinct conformational features that may interact with protease secondary substrate sites (exosites), nonactive site-binding inhibitors can be identified via this approach. Selective inhibitors for ADAMTS-4 would allow a more definitive evaluation of this protease in osteoarthritis and also represent a potential next generation in metalloproteinase therapeutics.
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Affiliation(s)
- Janelle L Lauer-Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
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24
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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25
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Verma RP, Hansch C. Matrix metalloproteinases (MMPs): chemical-biological functions and (Q)SARs. Bioorg Med Chem 2007; 15:2223-68. [PMID: 17275314 DOI: 10.1016/j.bmc.2007.01.011] [Citation(s) in RCA: 501] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 01/09/2007] [Accepted: 01/11/2007] [Indexed: 12/20/2022]
Abstract
Matrix metalloproteinases (MMPs) are a large family of calcium-dependent zinc-containing endopeptidases, which are responsible for the tissue remodeling and degradation of the extracellular matrix (ECM), including collagens, elastins, gelatin, matrix glycoproteins, and proteoglycan. They are regulated by hormones, growth factors, and cytokines, and are involved in ovarian functions. MMPs are excreted by a variety of connective tissue and pro-inflammatory cells including fibroblasts, osteoblasts, endothelial cells, macrophages, neutrophils, and lymphocytes. These enzymes are expressed as zymogens, which are subsequently processed by other proteolytic enzymes (such as serine proteases, furin, plasmin, and others) to generate the active forms. Matrix metalloproteinases are considered as promising targets for the treatment of cancer due to their strong involvement in malignant pathologies. Clinical/preclinical studies on MMP inhibition in tumor models brought positive results raising the idea that the development of strategies to inhibit MMPs may be proved to be a powerful tool to fight against cancer. However, the presence of an inherent flexibility in the MMP active-site limits dramatically the accurate modeling of MMP-inhibitor complexes. The interest in the application of quantitative structure-activity relationships (QSARs) has steadily increased in recent decades and we hope it may be useful in elucidating the mechanisms of chemical-biological interactions for this enzyme. In the present review, an attempt has been made to explore the in-depth knowledge from the classification of this enzyme to the clinical trials of their inhibitors. A total number of 92 QSAR models (44 published and 48 new formulated QSAR models) have also been presented to understand the chemical-biological interactions. QSAR results on the inhibition of various compound series against MMP-1, -2, -3, -7, -8, -9, -12, -13, and -14 reveal a number of interesting points. The most important of these are hydrophobicity and molar refractivity, which are the most important determinants of the activity.
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Affiliation(s)
- Rajeshwar P Verma
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, CA 91711, USA.
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26
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Tullberg M, Luthman K, Grøtli M. Microwave-assisted solid-phase synthesis of 2,5-diketopiperazines: solvent and resin dependence. ACTA ACUST UNITED AC 2007; 8:915-22. [PMID: 17096581 DOI: 10.1021/cc0600876] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-phase synthesis of diketopiperazines (DKPs) was preformed using various combinations of resins (polystyrene, TentaGel, ArgoGel, and PEGA) and solvents (toluene, tert-butyl alcohol, water, and toluene/2-butanol (1:4, v/v). The DKPs were synthesized from solid-phase bound dipeptides via intramolecular aminolysis. Both thermal and microwave-assisted solid-phase synthesis of DKPs gave high yields of products independently of resin and organic solvent used; however, only the PEGA resin resulted in high yields of DKPs in water independent of heating method. The short reaction times, high yields, and the possibility to run reactions in water when an appropriate resin is used makes the microwave-assisted solid-phase synthesis the method of choice. The method should be suitable for solid-phase synthesis of diketopiperazine-based libraries.
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Affiliation(s)
- Marcus Tullberg
- Department of Chemistry, Medicinal Chemistry, Göteborg University, SE-412 96 Göteborg, Sweden
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27
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Cain JP, Mayorov AV, Cai M, Wang H, Tan B, Chandler K, Lee Y, Petrov RR, Trivedi D, Hruby VJ. Design, synthesis, and biological evaluation of a new class of small molecule peptide mimetics targeting the melanocortin receptors. Bioorg Med Chem Lett 2006; 16:5462-7. [PMID: 16931008 PMCID: PMC1810397 DOI: 10.1016/j.bmcl.2006.07.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 06/23/2006] [Accepted: 07/05/2006] [Indexed: 10/24/2022]
Abstract
A new bicyclic template has been developed for the synthesis of peptide mimetics. Straightforward synthetic steps, starting from amino acids, allow the facile construction of a wide range of analogs. This system was designed to target the melanocortin receptors (MCRs), with functional group selection based on a known pharmacophore and guidance from molecular modeling to rationally identify positional and stereochemical isomers likely to be active. The functions of hMCRs are critical to myriad biological activities, including pigmentation, steroidogenesis, energy homeostasis, erectile activity, and inflammation. These G-protein-coupled receptors (GPCRs) are targets for drug discovery in a number of areas, including cancer, pain, and obesity therapeutics. All compounds from this series tested to date are antagonists which bind with high affinity. Importantly, many are highly selective for a particular MCR subtype, including some of the first completely hMC5R-selective antagonists reported.
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Affiliation(s)
- James P Cain
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA
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28
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Ramón DJ, Yus M. Asymmetric multicomponent reactions (AMCRs): the new frontier. Angew Chem Int Ed Engl 2006; 44:1602-34. [PMID: 15719349 DOI: 10.1002/anie.200460548] [Citation(s) in RCA: 1405] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Asymmetric multicomponent reactions involve the preparation of chiral compounds by the reaction of three or more reagents added simultaneously. This kind of addition and reaction has some advantages over classic divergent reaction strategies, such as lower costs, time, and energy, as well as environmentally friendlier aspects. All these advantages, together with the high level of stereoselectivity attained in some of these reactions, will force chemists in industry as in academia to adopt this new strategy of synthesis, or at least to consider it as a viable option. The positive aspects as well as the drawbacks of this strategy are discussed in this Review.
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Affiliation(s)
- Diego J Ramón
- Instituto de Síntesis Orgánica y Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Alicante, Apdo. 99, 03080-Alicante, Spain
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29
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Dömling A. Recent developments in isocyanide based multicomponent reactions in applied chemistry. Chem Rev 2006; 106:17-89. [PMID: 16402771 DOI: 10.1021/cr0505728] [Citation(s) in RCA: 3387] [Impact Index Per Article: 188.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Couladouros EA, Magos AD. Solid-phase total synthesis of (-)-Phenylhistine and (-)-Aurantiamine. Synthesis of a diverse dehydro-2,5-diketopiperazine library. Part II. Mol Divers 2005; 9:111-21. [PMID: 15789558 DOI: 10.1007/s11030-005-1295-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The preparation of solid supported glycine phosphonate and its utilization for the total synthesis of two natural products is presented. The proposed protocol combines diversity with accessibility and speed, which makes this scaffold suitable for automated parallel synthesis and combinatorial chemistry. The preparation of a small library of dehydro-2,5-diketopiperazines, combining several natural amino acids with diverse heterocycles (including thiazoles, pyridines, indoles and imidazoles), is also demonstrated.
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Affiliation(s)
- Elias A Couladouros
- Chemistry Laboratories, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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31
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Besada P, Mamedova L, Thomas CJ, Costanzi S, Jacobson KA. Design and synthesis of new bicyclic diketopiperazines as scaffolds for receptor probes of structurally diverse functionality. Org Biomol Chem 2005; 3:2016-25. [PMID: 15889186 PMCID: PMC3476468 DOI: 10.1039/b416349d] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diketopiperazines (DKPs) are a common motif in various biologically active natural products, and hence they may be useful scaffolds for the rational design of receptor probes and therapeutic agents. We constructed a new bicyclic scaffold that combines a DKP bridged with a 10-membered ring. In this way we obtained a three-dimensional molecular skeleton, with several amendable sites that provide a starting point to design a new combinatorial library having diverse substituent groups. Structural variation is based upon the flexibility of alkylation of the nitrogen atoms of the DKP and on the side-chain olefin. We obtained a 10-membered secondary ring through a ring-closure metathesis reaction using the second generation Grubbs catalyst. Rings containing both O-ethers and S-ethers were compared. N-Alkyl or arylalkyl groups were introduced optionally at the two Nalpha-atoms. This is a general scheme that will allow us to test rings of varying sizes, linkages, and stereochemical parameters. The DKP derivatives were tested for activity in astrocytoma cells expressing receptors coupled to phospholipase C. Inhibitory effects were observed for signaling elicited by activation of human nucleotide P2Y receptors but not m3 muscarinic receptors. Compound 20 selectively inhibited calcium mobilization (IC50 value of 486 +/- 16 nM) and phosphoinositide turnover elicited by a selective P2Y1 receptor agonist, but this compound did not compete for binding of a radiolabeled nucleotide-competitive receptor antagonist. Therefore, the new class of DKP derivatives shows utility as pharmacological tools for P2Y receptors.
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Affiliation(s)
- Pedro Besada
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA. Fax: (301) 480-8422; Tel: (301) 496-9024
| | - Liaman Mamedova
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA. Fax: (301) 480-8422; Tel: (301) 496-9024
| | - Craig J. Thomas
- Chemical Biology Core Facility, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA
| | - Stefano Costanzi
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA. Fax: (301) 480-8422; Tel: (301) 496-9024
- Chemical Biology Core Facility, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA. Fax: (301) 480-8422; Tel: (301) 496-9024
- Chemical Biology Core Facility, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA
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32
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Vasudevan A, Verzal MK. A post-Ugi carbonylation/intramolecular amidation approach toward the synthesis of macrolactams. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.01.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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34
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Ramón DJ, Yus M. Neue Entwicklungen in der asymmetrischen Mehrkomponenten-Reaktion. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200460548] [Citation(s) in RCA: 352] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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Abstract
Constricting the peptide backbone into a more defined conformational form through cyclization is an activity evolved in nature and in synthetic work, the latter straddling only the most recent decades. The resulting conformational constraints increase the probability of an optimum response with bio-receptors. The purpose of this review is to highlight developments that have proved to be reasonably efficient in the macrocyclization of linear precursors into cyclic peptides and depsipeptides.
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Affiliation(s)
- John S Davies
- Department of Chemistry, University of Wales, Swansea, Singleton Park, Swansea SA2 8PP, UK.
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36
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Horton DA, Bourne GT, Smythe ML. Exploring privileged structures: the combinatorial synthesis of cyclic peptides. Mol Divers 2003; 5:289-304. [PMID: 12549678 DOI: 10.1023/a:1021365402751] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. They may therefore be considered to be privileged structures. This review outlines the strategies by which both macrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines have been synthesised in combinatorial libraries. It also briefly outlines some of the biological applications of these molecules, thereby justifying their inclusion as privileged structures.
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Affiliation(s)
- Douglas A Horton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Qld., Australia
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37
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Kuhnast B, Bodenstein C, Wester HJ, Weber W. Carbon-11 labelling of anN-sulfonylamino acid derivative: a potential tracer for MMP-2 and MMP-9 imaging. J Labelled Comp Radiopharm 2003. [DOI: 10.1002/jlcr.695] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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38
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Abstract
Diketopiperazines (DKPs), the smallest cyclic peptides, represent an important class of biologically active natural products and their research has been fundamental to many aspects of peptide chemistry. The advent of combinatorial chemistry has revived interest in DKPs for two reasons: firstly, they are simple heterocyclic scaffolds in which diversity can be introduced and stereochemically controlled at up to four positions; secondly, they can be prepared from readily available alpha-amino acids using very robust chemistry. Here synthetic methods, conformation, as well as applications of DKPs are summarized and discussed critically.
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39
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Zaragoza F. New Strategies for the Solid-Phase Synthesis of Highly Functionalized, Small Molecules: Sequential Nucleophilic Substitutions on Polymer-Bound Polyelectrophiles. Methods Enzymol 2003; 369:517-27. [PMID: 14722970 DOI: 10.1016/s0076-6879(03)69026-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Carbonell T, Masip I, Sánchez-Baeza F, Delgado M, Araya E, Llorens O, Corcho F, Pérez JJ, Pérez-Payá E, Messeguer A. Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones. Mol Divers 2002; 5:131-43. [PMID: 12197070 DOI: 10.1023/a:1016230600162] [Citation(s) in RCA: 10] [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
The potentiation of central cholinergic activity has been proposed as a therapeutic approach for improving cognitive function in patients with Alzheimer's disease. Increasing the acetylcholine concentration in brain by modulating acetylcholinesterase (AChE) activity is among the most promising strategies. We have used a combinatorial approach to identify different 2,5-piperazinediones (DKP) with AChE inhibitory activity. Our goal was to find inhibitors exhibiting high AChE/BuChE (butyrylcholinesterase) selectivity, in order to reduce the undesirable side effects elicited by most of the inhibitors that have been developed to date. Screening of a DKP library constructed on solid-phase using the multiple parallel synthesis format, resulted in the identification of several compounds with moderate efficacy on AChE. In particular, DKP-80 had an IC50 = 2.2 microM with no significant inhibitory activity on BuChE. Moreover, estimated values of Clog P and log BB for the most active compounds fulfilled the bioavailability requirements for enzyme inhibitors acting on the central nervous system. In order to understand the inhibitory properties of the ligand at the molecular level, molecular dynamics simulations were computed on DKP-80 complexed to AChE, and the most relevant binding interactions of this inhibitor to the active center of the enzyme were characterized. Overall the present results indicate that the DKP-based compounds identified are novel AChE inhibitors which may be considered likely lead compounds for further development of drug candidates against Alzheimer's disease.
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Affiliation(s)
- T Carbonell
- Department of Biochemistry and Molecular Biology, Universitat de València, E-46100 Burjassot, Spain
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41
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Horton DA, Bourne GT, Smythe ML. Exploring privileged structures: the combinatorial synthesis of cyclic peptides. J Comput Aided Mol Des 2002; 16:415-30. [PMID: 12489688 DOI: 10.1023/a:1020863921840] [Citation(s) in RCA: 68] [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
Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. They may therefore be considered to be privileged structures. This review outlines the strategies by which both macrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines have been synthesised in combinatorial libraries. It also briefly outlines some of the biological applications of these molecules, thereby justifying their inclusion as privileged structures.
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Affiliation(s)
- Douglas A Horton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Qld., Australia
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42
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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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43
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Li WR, Yang JH. Solid-phase synthesis of unsaturated 3-substituted piperazine-2,5-diones. JOURNAL OF COMBINATORIAL CHEMISTRY 2002; 4:106-8. [PMID: 11886282 DOI: 10.1021/cc010055c] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wen-Ren Li
- Department of Chemistry, National Central University, Chung-Li, Taiwan 32054, ROC.
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44
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Acharya AN, Ostresh JM, Houghten RA. Solid-phase synthesis of substituted imidazoline-tethered 2,3-diketopiperazines, cyclic ureas, and cyclic thioureas. JOURNAL OF COMBINATORIAL CHEMISTRY 2001; 3:612-23. [PMID: 11703159 DOI: 10.1021/cc010030d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient methods for the solid-phase synthesis of imidazoline-tethered 2,3-diketopiperazines, cyclic ureas, and cyclic thioureas are described. Following the exhaustive reduction of resin-bound dipeptides derived from orthogonally protected diamino acids, the primary amine of the resulting tetraamines was selectively protected with Dde. The compounds were then selectively cyclized via their secondary amines with three different diimidazole derivatives ((COIm)(2), COIm(2), CSIm(2)). Upon Dde removal, the compounds were selectively N-acylated and dehydratively cyclized with POCl(3) to afford the imidazoline-tethered analogues in moderate yield and high purity. These procedures have been extended to prepare mixture-based combinatorial libraries. Details of the selection of building blocks for preparation of the positional scanning libraries based on the "libraries from libraries" approach are discussed.
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Affiliation(s)
- A N Acharya
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, CA 92121, USA
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45
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Perrotta E, Altamura M, Barani T, Bindi S, Giannotti D, Harmat NJ, Nannicini R, Maggi CA. 2,6-Diketopiperazines from amino acids, from solution-phase to solid-phase organic synthesis. JOURNAL OF COMBINATORIAL CHEMISTRY 2001; 3:453-60. [PMID: 11549363 DOI: 10.1021/cc0000904] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method to prepare 1,3-disubstituted 2,6-diketopiperazines (2,6-DKP) as useful heterocyclic library scaffolds in the search of new leads for drug discovery is described. The method can be used in solution-phase and solid-phase conditions. In the key step of the synthesis, the imido portion of the new molecule is formed in solution through intramolecular cyclization, under basic conditions, of a secondary amide nitrogen on a benzyl ester. A Wang resin carboxylic ester is used as the acylating agent under solid-phase conditions, allowing the cyclization to take place with simultaneous cleavage of the product from the resin ("cyclocleavage"). The synthetic method worked well with several couples of amino acids, independently from their configuration, and was used for the parallel synthesis of a series of fully characterized compounds. The use of iterative conditions in the solid phase (repeated addition of fresh solvent and potassium carbonate to the resin after filtering out the product-containing solution) allowed us to keep diastereoisomer content below the detection limit by HPLC and (1)H NMR (200 MHz).
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Affiliation(s)
- E Perrotta
- Department of Chemistry, Menarini Ricerche S.p.A., I-50131 Firenze, Italy
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46
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Abstract
A continuous assay method, such as one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors and to aid in the design of MMP inhibitors, a variety of sequence specificity, phage display, and combinatorial chemistry studies have been performed. Results of these studies have been valuable for defining the differences in MMPs and for creating quenched fluorescent substrates that utilize fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET). FRET triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. The present chapter provides an overview of MMP and related FRET substrates and describes how to construct and utilize these substrates.
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Affiliation(s)
- Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 U.S.A. Phone 561-297-2093, Fax 561-297-2759
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47
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Groth T, Meldal M. N-Terminal peptide aldehydes as electrophiles in combinatorial solid phase synthesis of novel peptide isosteres. JOURNAL OF COMBINATORIAL CHEMISTRY 2001; 3:45-63. [PMID: 11148063 DOI: 10.1021/cc000058+] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Terminal peptide aldehydes were synthesized on a solid support and utilized as electrophiles in nucleophilic reactions in order to furnish novel and diverse peptide isosteres. The aldehyde moiety of the peptide was synthesized by coupling a protected aldehyde building block to the peptide and deprotecting it quantitatively in less than 3 min. It was found that protection of the two succeeding amide nitrogens was necessary in order to avoid reaction between the aldehyde and backbone amides. The N-terminal peptide aldehydes were successfully reacted in the following way: (a) reductive amination with a large variety of amines, leading to N-alkyl-gamma-aminobutyric peptide isosteres positioned centrally in the peptide; (b) reductive amination with amino esters, leading to N-terminal 2,5-diketopiperazine peptides; (c) Horner-Wadsworth-Emmons olefination, leading to unsaturated peptide isosteres positioned centrally in the peptide; and (d) Pictet-Spengler condensations, leading to tetrahydro-beta-carbolines either positioned centrally in a peptide or fused with a diketopiperazine ring in the N-terminus of the peptide.
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Affiliation(s)
- T Groth
- Center for Solid Phase Organic Combinatorial Chemistry, Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
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48
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Abstract
Chemical genetics is the study of gene-product function in a cellular or organismal context using exogenous ligands. In this approach, small molecules that bind directly to proteins are used to alter protein function, enabling a kinetic analysis of the in vivo consequences of these changes. Recent advances have strongly enhanced the power of exogenous ligands such that they can resemble genetic mutations in terms of their general applicability and target specificity. The growing sophistication of this approach raises the possibility of its application to any biological process.
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Affiliation(s)
- B R Stockwell
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
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49
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Bianco A, Furrer J, Limal D, Guichard G, Elbayed K, Raya J, Piotto M, Briand JP. Multistep synthesis of 2,5-diketopiperazines on different solid supports monitored by high resolution magic angle spinning NMR spectroscopy. JOURNAL OF COMBINATORIAL CHEMISTRY 2000; 2:681-90. [PMID: 11126296 DOI: 10.1021/cc0000489] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solid-phase synthesis of 2,5-diketopiperazines containing the trans-4-hydroxy-L-proline amino acid residue (Hyp) was performed on Ellman polystyrene, polyoxyethylene-polyoxypropylene (POEPOP), polystyrene-polyoxyethylene NovaSyn, and Wang resins, respectively. The reaction pathway allowed the introduction of different functional groups around the bicyclic scaffold in a combinatorial approach, and it generated mixtures of isomers. A detailed characterization of the single reaction steps by high resolution magic angle spinning (HRMAS) NMR spectroscopy was performed. The NMR spectral resolution of the resin-bound intermediates and final products was greatly influenced by the polymer matrix. The POEPOP resin permitted to obtain HRMAS NMR spectra with a resolution comparable with that of the spectra of the molecules in solution. Moreover, configurational and conformational isomers formed during the solid-phase reaction steps could be detected and easily assigned. Therefore, the combination of the HRMAS NMR technique with the use of nonaromatic resins may become an extremely powerful tool in solid-phase organic synthesis. This approach will allow the monitoring of multistep reactions and the conception of on-bead structural studies either on small molecules or on natural and/or synthetic oligomers.
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Affiliation(s)
- A Bianco
- Institut de Biologie Moléculaire et Cellulaire, Laboratoire de Chimie Immunologique, UPR 9021 CNRS, Strasbourg, France
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50
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Abstract
Multicomponent reactions (MCRs) are fundamentally different from two-component reactions in several aspects. Among the MCRs, those with isocyanides have developed into popular organic-chemical reactions in the pharmaceutical industry for the preparation of compound libraries of low-molecular druglike compounds. With a small set of starting materials, very large libraries can be built up within a short time, which can then be used for research on medicinal substances. Due to the intensive research of the last few years, many new backbone types have become accessible. MCRs are also increasingly being employed in the total synthesis of natural products. MCRs and especially MCRs with isocyanides offer many opportunities to attain new reactions and basic structures. However, this requires that the chemist learns the "language" of MCRs, something that this review wishes to stimulate.
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Affiliation(s)
- A Dömling
- Morphochem AG Gmunderstrasse 37-37 a, 81379 München (Germany)
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