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Coulibaly K, Thauvin M, Melenbacher A, Testard C, Trigoni E, Vincent A, Stillman MJ, Vriz S, Policar C, Delsuc N. A di-Copper Peptidyl Complex Mimics the Activity of Catalase, a Key Antioxidant Metalloenzyme. Inorg Chem 2021; 60:9309-9319. [PMID: 34109781 DOI: 10.1021/acs.inorgchem.0c03718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalases (CAT) are antioxidant metalloenzymes necessary for life in oxygen-metabolizing cells to regulate H2O2 concentration by accelerating its dismutation. Many physiopathological situations are associated with oxidative stress resulting from H2O2 overproduction, during which antioxidant defenses are overwhelmed. We have used a combinatorial approach associated with an activity-based screening to discover a first peptidyl di-copper complex mimicking CAT. The complex was studied in detail and characterized for its CAT activity both in solutions and in cells using different analytical methods. The complex exhibited CAT activity in solutions and, more interestingly, on HyPer HeLa cells that possess a genetically encoded ratiometric fluorescent sensors of H2O2. These results highlight the efficiency of a combinatorial approach for the discovery of peptidyl complexes that exhibit catalytic activity.
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Affiliation(s)
- Koudedja Coulibaly
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marion Thauvin
- Collège de France, Centre Interdisciplinaire de Recherche en Biologie (CIRB), CNRS UMR7241/INSERM U1050, 75231 Paris, Cedex 05, France.,Sorbonne Université, 4 place Jussieu, 75005 Paris, France
| | - Adyn Melenbacher
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Clara Testard
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Evangelia Trigoni
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Amandine Vincent
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Sophie Vriz
- Collège de France, Centre Interdisciplinaire de Recherche en Biologie (CIRB), CNRS UMR7241/INSERM U1050, 75231 Paris, Cedex 05, France.,Faculty of Science, Université de Paris, 75006 Paris, France
| | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Nicolas Delsuc
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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Vincent A, Fores JR, Tauziet E, Quévrain E, Dancs Á, Conte-Daban A, Bernard AS, Pelupessy P, Coulibaly K, Seksik P, Hureau C, Selmeczi K, Policar C, Delsuc N. An easy-to-implement combinatorial approach involving an activity-based assay for the discovery of a peptidyl copper complex mimicking superoxide dismutase. Chem Commun (Camb) 2020; 56:399-402. [DOI: 10.1039/c9cc07920c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy combining combinatorial chemistry and an activity-based screening leads to the development of a peptidyl catalytic drug that reduces the oxidative stress in cellular models.
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The best and the brightest: exploiting tryptophan-sensitized Tb(3+) luminescence to engineer lanthanide-binding tags. Methods Mol Biol 2015; 1248:201-20. [PMID: 25616335 DOI: 10.1007/978-1-4939-2020-4_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Consider the lanthanide metals, comprising lanthanum through lutetium. Lanthanides form stable cations with a +3 charge, and these ions exhibit a variety of useful physical properties (long-lifetime luminescence, paramagnetism, anomalous X-ray scattering) that are amenable to studies of biomolecules. The absence of lanthanide ions in living systems means that background signals are generally a nonissue; however, to exploit the advantageous properties it is necessary to engineer a robust lanthanide-binding sequence that can be appended to any macromolecules of interest. To this end, the luminescence produced by tryptophan-sensitized Tb(3+) has been used as a selection marker for peptide sequences that avidly chelate these ions. A combinatorial split-and-pool library that uses two orthogonal linkers-one that is cleaved for selection and one that is cleaved for sequencing and characterization-has been used to develop lanthanide-binding tags (LBTs): peptides of 15-20 amino acids with low-nM affinity for Tb(3+). Further validating the success of this screen, knowledge about LBTs has enabled the introduction of a lanthanide-binding loop in place of one of the four native calcium-binding loops within the protein calcineurin B.
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González-Vera JA, Luković E, Imperiali B. A rapid method for generation of selective Sox-based chemosensors of Ser/Thr kinases using combinatorial peptide libraries. Bioorg Med Chem Lett 2009; 19:1258-60. [PMID: 19157873 PMCID: PMC2838374 DOI: 10.1016/j.bmcl.2008.12.090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
Abstract
A novel screening method to identify selective Sox-based fluorescent probes for Ser/Thr kinases has been developed. Peptide libraries were exposed to a kinase of interest and the products of the timed reaction were analyzed by MALDI-TOF. To demonstrate the potential of this methodology, a selective substrate for Aurora A kinase was identified that showed a 7-fold improvement in catalytic efficiency over the best substrate described to date in the literature.
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Affiliation(s)
- Juan A González-Vera
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Abstract
The split-pool diversity orientated synthesis method, which requires some form of encoding to track the synthesis of discrete compounds, has been the lynchpin of most combinatorial synthesis efforts. The use of encoding methods in combinatorial chemistry has matured, and depending on their level of resources, chemists now have a diverse choice of encoding methods available. New methods of encoding have been developed that are inexpensive, simple to incorporate into any laboratory, and utilize analytical equipment such as MS, FTIR and NMR that are readily available to most organic chemists.
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Affiliation(s)
- Nicholas J Ede
- Mimotopes Pty. Ltd, 11 Duerdin Street, Clayton, Victoria 3168, Australia.
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7
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Nitz M, Franz KJ, Maglathlin RL, Imperiali B. A powerful combinatorial screen to identify high-affinity terbium(III)-binding peptides. Chembiochem 2003; 4:272-6. [PMID: 12672106 DOI: 10.1002/cbic.200390047] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Lanthanide-binding tags (LBTs) are protein fusion partners consisting of encoded amino acids that bind lanthanide ions with high affinity. Herein, we present a new screening methodology for the identification of new LBT sequences with high affinity for Tb(3+) ions and intense luminescence properties. This methodology utilizes solid-phase split-and-pool combinatorial peptide synthesis. Orthogonally cleavable linkers allow an efficient two-step screening procedure. The initial screen avoids the interference caused by on-bead screening by photochemically releasing a portion of the peptides into an agarose matrix for evaluation. The secondary screen further characterizes each winning sequence in a defined aqueous solution. Employment of this methodology on a series of focused combinatorial libraries yielded a linear peptide sequence of 17 encoded amino acids that demonstrated a 140-fold increase in affinity (57 nM dissociation constant, K(D)) over previously reported lanthanide-binding peptides. This linear sequence was macrocyclized by introducing a disulfide bond between flanking cysteine residues to produce a peptide with a 2-nM apparent dissociation constant for Tb(3+) ions.Supporting information for this article is available on the WWW under http://www.chemphyschem.org or from the author.
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Affiliation(s)
- Mark Nitz
- Department of Chemistry Massachusetts Institute of Technology Cambridge, MA 02139, USA
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Pastor JJ, Lingard I, Bhalay G, Bradley M. Ion-extraction ladder sequencing from bead-based libraries. JOURNAL OF COMBINATORIAL CHEMISTRY 2003; 5:85-90. [PMID: 12625697 DOI: 10.1021/cc0200437] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion-extraction mass spectrometry of ladders of mixtures of isotopically labeled compounds from single beads allows the unambiguous sequencing of bead-based peptides and offers significant advantages over traditional methods of library analysis.
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Affiliation(s)
- Jose J Pastor
- Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès, 1-11, 08028 Barcelona, Spain
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Abstract
The field of combinatorial peptide chemistry has emerged as a powerful tool in the study of many biological systems. This review focuses on combinatorial peptide library methodology, which includes biological library methods, spatially addressable parallel library methods, library methods requiring deconvolution, the "one-bead one-compound" library method, and affinity chromatography selection method. These peptide libraries have successfully been employed to study a vast array of cell surface receptors, as well as have been useful in identifying protein kinase substrates and inhibitors. In recent immunobiological applications, peptide libraries have proven monumental in the definition of MHC anchor residues, in lymphocyte epitope mapping, and in the development of peptide vaccines. Peptides identified from such libraries, when presented in a chemical microarray format, may prove useful in immunodiagnostics. Combinatorial peptide libraries offer a high-throughput approach to study limitless biological targets. Peptides discovered from such studies may be therapeutically and diagnostically useful agents.
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Affiliation(s)
- Ruiwu Liu
- UC Davis Cancer Center, Division of Hematology/Oncology, and Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
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Redman JE, Wilcoxen KM, Ghadiri MR. Automated mass spectrometric sequence determination of cyclic peptide library members. JOURNAL OF COMBINATORIAL CHEMISTRY 2003; 5:33-40. [PMID: 12523832 DOI: 10.1021/cc0200639] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic peptides have come under scrutiny as potential antimicrobial therapeutic agents. Combinatorial split-and-pool synthesis of cyclic peptides can afford single compound per well libraries for antimicrobial screening, new lead identification, and construction of quantitative structure-activity relationships (QSAR). Here, we report a new sequencing protocol for rapid identification of the members of a cyclic peptide library based on automated computer analysis of mass spectra, obviating the need for library encoding/decoding strategies. Furthermore, the software readily integrates with common spreadsheet and database packages to facilitate data visualization and archiving. The utility of the new MS-sequencing approach is demonstrated using sonic spray ionization ion trap MS and MS/MS spectrometry on a single compound per bead cyclic peptide library and validated with individually synthesized pure cyclic D,L-alpha-peptides.
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Affiliation(s)
- James E Redman
- Department of Chemistry, and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Pastor JJ, Fernández I, Rabanal F, Giralt E. A new method for the preparation of unprotected peptides on biocompatible resins with application in combinatorial chemistry. Org Lett 2002; 4:3831-3. [PMID: 12599470 DOI: 10.1021/ol026627z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[formula: see text] A synthetic strategy for the preparation of side chain free peptides on biocompatible solid supports is described. Final peptide detachment is afforded in mild basic conditions with no presence of scavengers or other additives, thus allowing single peptide-resin beads to be cleaved in mass spectrometry sample plates for direct sequencing using MALDI-TOF post-source decay. This methodology offers clear advantages for the development of one-bead--one-compound combinatorial libraries in addition to parallel and regular synthesis of peptides.
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Affiliation(s)
- Jose J Pastor
- Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona, Universitat de Barcelona, 08028 Barcelona, Spain
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