1
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. Angew Chem Int Ed Engl 2022; 61:e202211510. [PMID: 36112310 PMCID: PMC9827864 DOI: 10.1002/anie.202211510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 01/12/2023]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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2
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202211510. [PMID: 38505687 PMCID: PMC10947266 DOI: 10.1002/ange.202211510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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3
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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4
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Canal-Martín A, Pérez-Fernández R. Protein-Directed Dynamic Combinatorial Chemistry: An Efficient Strategy in Drug Design. ACS OMEGA 2020; 5:26307-26315. [PMID: 33110958 PMCID: PMC7581073 DOI: 10.1021/acsomega.0c03800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/24/2020] [Indexed: 05/05/2023]
Abstract
Protein-directed dynamic combinatorial chemistry (P-D DCC) is considered a powerful strategy to identify ligands to pharmacologically relevant protein targets. The protein selects its affinity ligands in situ through a thermodynamic templated effect in which the library composition shifts to the formation of specific library members at the expense of other (nonbinding) species. The increase in concentration of the selected species is known as amplification and leads to the discovery of new hit compounds for protein targets. This Mini-Review contains an updated overview of the protein-directed DCC applications and the fundamental aspects to take into account when designing a P-D DCC experiment such as the most biocompatible reversible reactions and the methodology used to analyze the experiments.
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5
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Frei P, Hevey R, Ernst B. Dynamic Combinatorial Chemistry: A New Methodology Comes of Age. Chemistry 2018; 25:60-73. [DOI: 10.1002/chem.201803365] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Priska Frei
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Rachel Hevey
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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6
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Ju LC, Cheng Z, Fast W, Bonomo RA, Crowder MW. The Continuing Challenge of Metallo-β-Lactamase Inhibition: Mechanism Matters. Trends Pharmacol Sci 2018; 39:635-647. [PMID: 29680579 DOI: 10.1016/j.tips.2018.03.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 01/16/2023]
Abstract
Metallo-β-lactamases (MBLs) are a significant clinical problem because they hydrolyze and inactivate nearly all β-lactam-containing antibiotics. These 'lifesaving drugs' constitute >50% of the available contemporary antibiotic arsenal. Despite the global spread of MBLs, MBL inhibitors have not yet appeared in clinical trials. Most MBL inhibitors target active site zinc ions and vary in mechanism from ternary complex formation to metal ion stripping. Importantly, differences in mechanism can impact pharmacology in terms of reversibility, target selectivity, and structure-activity relationship interpretation. This review surveys the mechanisms of MBL inhibitors and describes methods that determine the mechanism of inhibition to guide development of future therapeutics.
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Affiliation(s)
- Lin-Cheng Ju
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Robert A Bonomo
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics, and Bioinformatics and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, OH 44106, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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Sevaille L, Gavara L, Bebrone C, De Luca F, Nauton L, Achard M, Mercuri P, Tanfoni S, Borgianni L, Guyon C, Lonjon P, Turan-Zitouni G, Dzieciolowski J, Becker K, Bénard L, Condon C, Maillard L, Martinez J, Frère JM, Dideberg O, Galleni M, Docquier JD, Hernandez JF. 1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-β-lactamases. ChemMedChem 2017; 12:972-985. [DOI: 10.1002/cmdc.201700186] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/12/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Laurent Sevaille
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Carine Bebrone
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
- Present address: Symbiose Biomaterials S.A., GIGA Bât. B34; 1 avenue de l'Hôpital 4000 Liège Belgium
| | - Filomena De Luca
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Lionel Nauton
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS, CEA; Université Joseph Fourier; 41 rue Jules Horowitz 38027 Grenoble cedex 1 France
- Present address: Institut de Chimie de Clermont-Ferrand, UMR6296 CNRS; Université Clermont Auvergne; 63000 Clermont-Ferrand France
| | - Maud Achard
- EMBL Outstation c/o DESY; Notkestrasse 85 22603 Hamburg Germany
- Present address: School of Chemistry and Molecular Bioscience; University of Queensland, St. Lucia; Brisbane QLD 4072 Australia
| | - Paola Mercuri
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Silvia Tanfoni
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Luisa Borgianni
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Carole Guyon
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Pauline Lonjon
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
- Present address: CERN, HSE/SEE/SI; 1211 Geneva 23 Switzerland
| | - Gülhan Turan-Zitouni
- Department of Pharmaceutical Chemistry; Anadolu University, Faculty of Pharmacy; 26470 Eskisehir Turkey
| | - Julia Dzieciolowski
- Chair of Biochemistry and Molecular Biology, Interdisciplinary Research Center; Justus Liebig University; Heinrich-Buff-Ring 26-32 35392 Giessen Germany
| | - Katja Becker
- Chair of Biochemistry and Molecular Biology, Interdisciplinary Research Center; Justus Liebig University; Heinrich-Buff-Ring 26-32 35392 Giessen Germany
| | - Lionel Bénard
- UMR8226, CNRS, Université Pierre et Marie Curie; Institut de Biologie Physico-Chimique; 13 rue Pierre et Marie Curie 75005 Paris France
| | - Ciaran Condon
- UMR8261, CNRS, Université Paris-Diderot; Institut de Biologie Physico-Chimique; 13 rue Pierre et Marie Curie 75005 Paris France
| | - Ludovic Maillard
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Jean-Marie Frère
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Otto Dideberg
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS, CEA; Université Joseph Fourier; 41 rue Jules Horowitz 38027 Grenoble cedex 1 France
| | - Moreno Galleni
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
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8
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Li GB, Abboud MI, Brem J, Someya H, Lohans CT, Yang SY, Spencer J, Wareham DW, McDonough MA, Schofield CJ. NMR-filtered virtual screening leads to non-metal chelating metallo-β-lactamase inhibitors. Chem Sci 2016; 8:928-937. [PMID: 28451231 PMCID: PMC5369532 DOI: 10.1039/c6sc04524c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
There are no clinically useful inhibitors of metallo-β-lactamases (MBLs), which are a growing problem because they hydrolyse almost all β-lactam antibacterials. Inhibition by most reported MBL inhibitors involves zinc ion chelation. A structure-based virtual screening approach combined with NMR filtering led to the identification of inhibitors of the clinically relevant Verona Integron-encoded MBL (VIM)-2. Crystallographic analyses reveal a new mode of MBL inhibition involving binding adjacent to the active site zinc ions, but which does not involve metal chelation. The results will aid efforts to develop new types of clinically useful inhibitors targeting MBLs/MBL-fold metallo-enzymes involved in antibacterial and anticancer drug resistance.
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Affiliation(s)
- Guo-Bo Li
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , West China School of Pharmacy , Sichuan University , Chengdu , 610041 , China
| | - Martine I Abboud
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Jürgen Brem
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Hidenori Someya
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Medicinal Chemistry Research Laboratories , New Drug Research Division , Otsuka Pharmaceutical Co., Ltd. , 463-10 Kagasuno, Kawauchi-cho , Tokushima 771-0192 , Japan
| | - Christopher T Lohans
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy , West China Hospital , West China Medical School , Sichuan University , Sichuan 610041 , China
| | - James Spencer
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol BS8 1TD , UK
| | - David W Wareham
- Antimicrobial Research Group , Barts & The London School of Medicine and Dentistry , Queen Mary University of London , London , E1 2AT , UK
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
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9
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Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery. Molecules 2016; 21:molecules21070910. [PMID: 27438816 PMCID: PMC6273345 DOI: 10.3390/molecules21070910] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 01/16/2023] Open
Abstract
Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.
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10
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González MM, Vila AJ. An Elusive Task: A Clinically Useful Inhibitor of Metallo-β-Lactamases. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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11
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González MM, Kosmopoulou M, Mojica MF, Castillo V, Hinchliffe P, Pettinati I, Brem J, Schofield CJ, Mahler G, Bonomo RA, Llarrull LI, Spencer J, Vila AJ. Bisthiazolidines: A Substrate-Mimicking Scaffold as an Inhibitor of the NDM-1 Carbapenemase. ACS Infect Dis 2015; 1:544-54. [PMID: 27623409 DOI: 10.1021/acsinfecdis.5b00046] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pathogenic Gram-negative bacteria resistant to almost all β-lactam antibiotics are a major public health threat. Zn(II)-dependent or metallo-β-lactamases (MBLs) produced by these bacteria inactivate most β-lactam antibiotics, including the carbapenems, which are "last line therapies" for life-threatening Gram-negative infections. NDM-1 is a carbapenemase belonging to the MBL family that is rapidly spreading worldwide. Regrettably, inhibitors of MBLs are not yet developed. Here we present the bisthiazolidine (BTZ) scaffold as a structure with some features of β-lactam substrates, which can be modified with metal-binding groups to target the MBL active site. Inspired by known interactions of MBLs with β-lactams, we designed four BTZs that behave as in vitro NDM-1 inhibitors with Ki values in the low micromolar range (from 7 ± 1 to 19 ± 3 μM). NMR spectroscopy demonstrated that they inhibit hydrolysis of imipenem in NDM-1-producing Escherichia coli. In vitro time kill cell-based assays against a variety of bacterial strains harboring blaNDM-1 including Acinetobacter baumannii show that the compounds restore the antibacterial activity of imipenem. A crystal structure of the most potent heterocycle (L-CS319) in complex with NDM-1 at 1.9 Å resolution identified both structural determinants for inhibitor binding and opportunities for further improvements in potency.
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Affiliation(s)
- Mariano M. González
- Instituto de Biologı́a Molecular y Celular
de Rosario (IBR-CONICET), Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo
y Esmeralda, 2000 Rosario, Argentina
| | - Magda Kosmopoulou
- School of Cellular
and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Maria F. Mojica
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical
Center, and Departments of Pharmacology, Biochemistry, Microbiology,
and Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Valerie Castillo
- Laboratorio de Quı́mica Farmacéutica,
Facultad de Quı́mica, Universidad de la República (UdelaR), Montevideo 11800, Uruguay
| | - Philip Hinchliffe
- School of Cellular
and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Ilaria Pettinati
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Graciela Mahler
- Laboratorio de Quı́mica Farmacéutica,
Facultad de Quı́mica, Universidad de la República (UdelaR), Montevideo 11800, Uruguay
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical
Center, and Departments of Pharmacology, Biochemistry, Microbiology,
and Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Leticia I. Llarrull
- Instituto de Biologı́a Molecular y Celular
de Rosario (IBR-CONICET), Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo
y Esmeralda, 2000 Rosario, Argentina
| | - James Spencer
- School of Cellular
and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Alejandro J. Vila
- Instituto de Biologı́a Molecular y Celular
de Rosario (IBR-CONICET), Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo
y Esmeralda, 2000 Rosario, Argentina
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12
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Mondal M, Hirsch AKH. Dynamic combinatorial chemistry: a tool to facilitate the identification of inhibitors for protein targets. Chem Soc Rev 2015; 44:2455-88. [DOI: 10.1039/c4cs00493k] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dynamic combinatorial chemistry enables efficient identification of protein binder(s) from a library of interconverting compounds. The library responds to the addition of the target by amplifying the strongest binder.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
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13
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Mondal M, Groothuis DE, Hirsch AKH. Fragment growing exploiting dynamic combinatorial chemistry of inhibitors of the aspartic protease endothiapepsin. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00157a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel combination of fragment growing and DCC is a powerful and efficient strategy to convert a fragment into a hit.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Daphne E. Groothuis
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
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14
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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15
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Abstract
The production of β-lactamase is one of the primary resistance mechanisms used by Gram-negative bacterial pathogens to counter β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems. There is an urgent need to develop novel β-lactamase inhibitors in response to ever evolving β-lactamases possessing an expanded spectrum of β-lactam hydrolyzing activity. Whereas traditional high-throughput screening has proven ineffective against serine β-lactamases, fragment-based approaches have been successfully employed to identify novel chemical matter, which in turn has revealed much about the specific molecular interactions possible in the active site of serine and metallo β-lactamases. In this review, we summarize recent progress in the field, particularly: the identification of novel inhibitor chemotypes through fragment-based screening; the use of fragment-protein structures to understand key features of binding hot spots and inform the design of improved leads; lessons learned and new prospects for β-lactamase inhibitor development using fragment-based approaches.
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Affiliation(s)
- Derek A Nichols
- University of South Florida College of Medicine, Department of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry & Small Molecule Discovery Center, University of California San Francisco, 1700 4th Street, Byers Hall S504, San Francisco, CA 94158, USA
| | - Yu Chen
- University of South Florida College of Medicine, Department of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612, USA
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16
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van Berkel SS, Brem J, Rydzik AM, Salimraj R, Cain R, Verma A, Owens RJ, Fishwick CWG, Spencer J, Schofield CJ. Assay platform for clinically relevant metallo-β-lactamases. J Med Chem 2013; 56:6945-53. [PMID: 23898798 PMCID: PMC3910272 DOI: 10.1021/jm400769b] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Metallo-β-lactamases
(MBLs) are a growing threat to the use
of almost all clinically used β-lactam antibiotics. The identification
of broad-spectrum MBL inhibitors is hampered by the lack of a suitable
screening platform, consisting of appropriate substrates and a set
of clinically relevant MBLs. We report procedures for the preparation
of a set of clinically relevant metallo-β-lactamases (i.e.,
NDM-1 (New Delhi MBL), IMP-1 (Imipenemase), SPM-1 (São Paulo
MBL), and VIM-2 (Verona integron-encoded MBL)) and the identification
of suitable fluorogenic substrates (umbelliferone-derived cephalosporins).
The fluorogenic substrates were compared to chromogenic substrates
(CENTA, nitrocefin, and imipenem), showing improved sensitivity and
kinetic parameters. The efficiency of the fluorogenic substrates was
exemplified by inhibitor screening, identifying 4-chloroisoquinolinols
as potential pan MBL inhibitors.
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Affiliation(s)
- Sander S van Berkel
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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17
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Metallo-β-lactamase: Inhibitors and reporter substrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1648-59. [DOI: 10.1016/j.bbapap.2013.04.024] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/18/2013] [Accepted: 04/21/2013] [Indexed: 11/22/2022]
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18
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Faridoon, Ul Islam N. An Update on the Status of Potent Inhibitors of Metallo-β-Lactamases. Sci Pharm 2013; 81:309-27. [PMID: 23833706 PMCID: PMC3700068 DOI: 10.3797/scipharm.1302-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/28/2013] [Indexed: 11/22/2022] Open
Abstract
The production of metallo-β-lactamases is the most important strategy by which pathogenic bacteria become resistant to currently known β-lactam antibiotics. The emergence of these enzymes is particularly concerning for the future treatment of bacterial infections. There are no clinically available drugs capable of inhibiting any of the metallo-β-lactamases, so there is an urgent need to find such inhibitors. In this review, an up-to-date status of the inhibitors investigated for the inhibition of metallo-β-lactamases has been given so that this rich source of structural information of presently known metallo-β-lactamases could be helpful in generating a broad-spectrum potent inhibitor of metallo-β-lactamases.
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Affiliation(s)
- Faridoon
- Chemistry Department, Islamia College University, Peshawar-25120, Pakistan
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19
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Nour HF, Islam T, Fernández-Lahore M, Kuhnert N. Probing the dynamic reversibility and generation of dynamic combinatorial libraries in the presence of bacterial model oligopeptides as templating guests of tetra-carbohydrazide macrocycles using electrospray mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2865-2876. [PMID: 23136017 DOI: 10.1002/rcm.6401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Over the past few decades, bacterial resistance to antibiotics has emerged as a real threat to human health. Accordingly, there is an urgent demand for the development of innovative strategies for discovering new antibiotics. We present the first use of tetra-carbohydrazide cyclophane macrocycles in dynamic combinatorial chemistry (DCC) and molecular recognition as chiral hosts binding oligopeptides, which mimic bacterial cell wall. This study introduces an innovative application of electrospray ionisation time-of-flight mass spectrometry (ESI-TOF MS) to oligopeptides recognition using DCC. METHODS A small dynamic library composed of eight functionalised macrocycles has been generated in solution and all members were characterised by ESI-TOF MS. We also probed the dynamic reversibility and mechanism of formation of tetra-carbohydrazide cyclophanes in real-time using ESI-TOF MS. RESULTS Dynamic reversibility of tetra-carbohydrazide cyclophanes is favored under thermodynamic control. The mechanism of formation of tetra-carbohydrazide cyclophanes involves key dialdehyde intermediates, which have been detected and assigned according to their high-resolution m/z values. Three members of the dynamic library bind efficiently in the gas phase to a selection of oligopeptides, unique to bacteria, allowing observation of host/guest complex ions in the gas phase. CONCLUSIONS We probed the mechanism of the [2+2]-cyclocondensation reaction forming library members, proved dynamic reversibility of tetra-carbohydrazide cyclophanes and showed that complex ions formed between library members and hosts can be observed in the gas phase, allowing the solution of an important problem of biological interest.
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Affiliation(s)
- Hany F Nour
- School of Engineering and Science, Centre for Nano and Functional Materials (NanoFun), Jacobs University, 28759 Bremen, Germany
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20
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Clipson AJ, Bhat VT, McNae I, Caniard AM, Campopiano DJ, Greaney MF. Bivalent enzyme inhibitors discovered using dynamic covalent chemistry. Chemistry 2012; 18:10562-70. [PMID: 22782854 DOI: 10.1002/chem.201201507] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Indexed: 12/25/2022]
Abstract
A bivalent dynamic covalent chemistry (DCC) system has been designed to selectively target members of the homodimeric glutathione-S-transferase (GST) enzyme family. The dynamic covalent libraries (DCLs) use aniline-catalysed acylhydrazone exchange between bivalent hydrazides and glutathione-conjugated aldehydes and the bis-hydrazides act as linkers to bridge between each glutathione binding site. The resultant DCLs were found to be compatible and highly responsive to templating with different GST isozymes, with the best results coming from the M and Schistosoma japonicum (Sj) class of GSTs, targets in cancer and tropical disease, respectively. The approach yielded compounds with selective, nanomolar affinity (K(i) =61 nM for mGSTM1-1) and demonstrates that DCC can be used to simultaneously interrogate binding sites on different subunits of a dimeric protein.
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Affiliation(s)
- Alexandra J Clipson
- School of Chemistry, University of Edinburgh, King's Buildings, West Mains Rd., Edinburgh, UK
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21
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Sindelar M, Wanner KT. Library Screening by Means of Mass Spectrometry (MS) Binding Assays-Exemplarily Demonstrated for a Pseudostatic Library Addressing γ-Aminobutyric Acid (GABA) Transporter 1 (GAT1). ChemMedChem 2012; 7:1678-90. [DOI: 10.1002/cmdc.201200201] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Indexed: 11/06/2022]
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22
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202000] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012; 51:6672-5. [DOI: 10.1002/anie.201202000] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Indexed: 11/05/2022]
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24
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Woon ECY, Demetriades M, Bagg EAL, Aik W, Krylova SM, Ma JHY, Chan M, Walport LJ, Wegman DW, Dack KN, McDonough MA, Krylov SN, Schofield CJ. Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic acid demethylase. J Med Chem 2012; 55:2173-84. [PMID: 22263962 DOI: 10.1021/jm201417e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Oxoglutarate-dependent nucleic acid demethylases are of biological interest because of their roles in nucleic acid repair and modification. Although some of these enzymes are linked to physiology, their regulatory roles are unclear. Hence, there is a desire to develop selective inhibitors for them; we report studies on AlkB, which reveal it as being amenable to selective inhibition by small molecules. Dynamic combinatorial chemistry linked to mass spectrometric analyses (DCMS) led to the identification of lead compounds, one of which was analyzed by crystallography. Subsequent structure-guided studies led to the identification of inhibitors of improved potency, some of which were shown to be selective over two other 2OG oxygenases. The work further validates the use of the DCMS method and will help to enable the development of inhibitors of nucleic acid modifying 2OG oxygenases both for use as functional probes and, in the longer term, for potential therapeutic use.
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Affiliation(s)
- Esther C Y Woon
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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25
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Woon ECY, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JHY, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ. Linking of 2-oxoglutarate and substrate binding sites enables potent and highly selective inhibition of JmjC histone demethylases. Angew Chem Int Ed Engl 2012; 51:1631-4. [PMID: 22241642 DOI: 10.1002/anie.201107833] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Indexed: 12/19/2022]
Affiliation(s)
- Esther C Y Woon
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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26
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Woon ECY, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JHY, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ. Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107833] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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27
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Borra PS, Leiros HKS, Ahmad R, Spencer J, Leiros I, Walsh TR, Sundsfjord A, Samuelsen O. Structural and computational investigations of VIM-7: insights into the substrate specificity of vim metallo-β-lactamases. J Mol Biol 2011; 411:174-89. [PMID: 21645522 DOI: 10.1016/j.jmb.2011.05.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/16/2011] [Accepted: 05/23/2011] [Indexed: 11/24/2022]
Abstract
The presence of metallo-β-lactamases (MBLs) in many clinically important human bacterial pathogens limits treatment options, as these enzymes efficiently hydrolyze nearly all β-lactam antibiotics. VIM enzymes are among the most widely distributed MBLs, but many of the individual VIM subtypes remain poorly characterized. Pseudomonas aeruginosa VIM-7 is the most divergent among VIM-type MBLs in terms of amino acid sequence. Here we present crystal structures of VIM-7 as the native enzyme, with Cys221 oxidized (VIM-7-Ox), and with a sulfur atom bridging the two active-site zinc ions (VIM-7-S). Comparison with VIM-2 and VIM-4 structures suggests an explanation for the reduced catalytic efficiency of VIM-7 against cephalosporins with a positively charged cyclic substituent at the C3 position (e.g., ceftazidime). Kinetic variations are attributed to substitutions in residues 60-66 (that form a loop adjacent to the active site previously implicated in substrate binding) and to the disruption of two hydrogen-bonding clusters through substitutions at positions 218 and 224. Furthermore, the less negatively charged surface of VIM-7 (compared to VIM-2) may also contribute to the reduced hydrolytic efficiency. Docking of the cephalosporins ceftazidime and cefotaxime into the VIM-2 and VIM-7 structures reveals that amino acid substitutions may cause the mode of substrate binding to differ between the two enzymes. Our structures thus provide new insights into the variation in substrate specificity that is evident across this family of clinically important enzymes.
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Affiliation(s)
- Pardha Saradhi Borra
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
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28
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Capela MDF, Mosey NJ, Xing L, Wang R, Petitjean A. Amine Exchange in Formamidines: An Experimental and Theoretical Study. Chemistry 2011; 17:4598-612. [DOI: 10.1002/chem.201002389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Indexed: 11/05/2022]
Affiliation(s)
- Marinha dF. Capela
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Nicholas J. Mosey
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Liyan Xing
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Ruiyao Wang
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
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29
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Li DH, Shen JS, Chen N, Ruan YB, Jiang YB. A ratiometric luminescent sensing of Ag+ ion via in situ formation of coordination polymers. Chem Commun (Camb) 2011; 47:5900-2. [DOI: 10.1039/c0cc05519k] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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30
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Screening of fibrillogenesis inhibitors of β2-microglobulin: Integrated strategies by mass spectrometry capillary electrophoresis and in silico simulations. Anal Chim Acta 2011; 685:153-61. [DOI: 10.1016/j.aca.2010.11.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 11/10/2010] [Accepted: 11/11/2010] [Indexed: 11/18/2022]
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31
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Leung IKH, Brown Jr T, Schofield CJ, Claridge TDW. An approach to enzyme inhibition employing reversible boronate ester formation. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00011j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Ceborska M, Tarnowska A, Ziach K, Jurczak J. Dynamic combinatorial libraries of macrocycles derived from phthalic aldehydes and α,ω-diamines. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Bebrone C, Lassaux P, Vercheval L, Sohier JS, Jehaes A, Sauvage E, Galleni M. Current challenges in antimicrobial chemotherapy: focus on ß-lactamase inhibition. Drugs 2010; 70:651-79. [PMID: 20394454 DOI: 10.2165/11318430-000000000-00000] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The use of the three classical beta-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam) in combination with beta-lactam antibacterials is currently the most successful strategy to combat beta-lactamase-mediated resistance. However, these inhibitors are efficient in inactivating only class A beta-lactamases and the efficiency of the inhibitor/antibacterial combination can be compromised by several mechanisms, such as the production of naturally resistant class B or class D enzymes, the hyperproduction of AmpC or even the production of evolved inhibitor-resistant class A enzymes. Thus, there is an urgent need for the development of novel inhibitors. For serine active enzymes (classes A, C and D), derivatives of the beta-lactam ring such as 6-beta-halogenopenicillanates, beta-lactam sulfones, penems and oxapenems, monobactams or trinems seem to be potential starting points to design efficient molecules (such as AM-112 and LK-157). Moreover, a promising non-beta-lactam molecule, NXL-104, is now under clinical development. In contrast, an ideal inhibitor of metallo-beta-lactamases (class B) remains to be found, despite the huge number of potential molecules already described (biphenyl tetrazoles, cysteinyl peptides, mercaptocarboxylates, succinic acid derivatives, etc.). The search for such an inhibitor is complicated by the absence of a covalent intermediate in their catalytic mechanisms and the fact that beta-lactam derivatives often behave as substrates rather than as inhibitors. Currently, the most promising broad-spectrum inhibitors of class B enzymes are molecules presenting chelating groups (thiols, carboxylates, etc.) combined with an aromatic group. This review describes all the types of molecules already tested as potential beta-lactamase inhibitors and thus constitutes an update of the current status in beta-lactamase inhibitor discovery.
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Affiliation(s)
- Carine Bebrone
- Biological Macromolecules, Centre for Protein Engineering, University of Liège, Liège, Belgium.
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34
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Rose NR, Woon ECY, Kingham GL, King ONF, Mecinović J, Clifton IJ, Ng SS, Talib-Hardy J, Oppermann U, McDonough MA, Schofield CJ. Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches. J Med Chem 2010; 53:1810-8. [PMID: 20088513 PMCID: PMC2825117 DOI: 10.1021/jm901680b] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferrous ion and 2-oxoglutarate (2OG) oxygenases catalyze the demethylation of N(epsilon)-methylated lysine residues in histones. Here we report studies on the inhibition of the JMJD2 subfamily of histone demethylases, employing binding analyses by nondenaturing mass spectrometry (MS), dynamic combinatorial chemistry coupled to MS, turnover assays, and crystallography. The results of initial binding and inhibition assays directed the production and analysis of a set of N-oxalyl-d-tyrosine derivatives to explore the extent of a subpocket at the JMJD2 active site. Some of the inhibitors were shown to be selective for JMJD2 over the hypoxia-inducible factor prolyl hydroxylase PHD2. A crystal structure of JMJD2A in complex with one of the potent inhibitors was obtained; modeling other inhibitors based on this structure predicts interactions that enable improved inhibition for some compounds.
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Affiliation(s)
- Nathan R Rose
- The Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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35
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Besenius P, Cormack PAG, Ludlow RF, Otto S, Sherrington DC. Affinity chromatography in dynamic combinatorial libraries: one-pot amplification and isolation of a strongly binding receptor. Org Biomol Chem 2010; 8:2414-8. [PMID: 20448900 DOI: 10.1039/c000333f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the one-pot amplification and isolation of a nanomolar receptor in a multibuilding block aqueous dynamic combinatorial library using a polymer-bound template. By appropriate choice of a poly(N,N-dimethylacrylamide)-based support, nonselective ion-exchange type behaviour between the oppositely charged cationic guest and polyanionic hosts was overcome, such that the selective molecular recognition arising in aqueous solution reactions is manifest also in the analogous templated solid phase DCL syntheses. The ability of a polymer bound template to identify and isolate a synthetic receptor via dynamic combinatorial chemistry was not compromised by the large size of the library, consisting of well over 140 theoretical members, demonstrating the practical advantages of a polymer-supported DCL methodology.
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Affiliation(s)
- Pol Besenius
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK G1 1XL
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36
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Abstract
Since the introduction of penicillin, beta-lactam antibiotics have been the antimicrobial agents of choice. Unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial beta-lactamases. beta-Lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. In order to overcome beta-lactamase-mediated resistance, beta-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced into clinical practice. These inhibitors greatly enhance the efficacy of their partner beta-lactams (amoxicillin, ampicillin, piperacillin, and ticarcillin) in the treatment of serious Enterobacteriaceae and penicillin-resistant staphylococcal infections. However, selective pressure from excess antibiotic use accelerated the emergence of resistance to beta-lactam-beta-lactamase inhibitor combinations. Furthermore, the prevalence of clinically relevant beta-lactamases from other classes that are resistant to inhibition is rapidly increasing. There is an urgent need for effective inhibitors that can restore the activity of beta-lactams. Here, we review the catalytic mechanisms of each beta-lactamase class. We then discuss approaches for circumventing beta-lactamase-mediated resistance, including properties and characteristics of mechanism-based inactivators. We next highlight the mechanisms of action and salient clinical and microbiological features of beta-lactamase inhibitors. We also emphasize their therapeutic applications. We close by focusing on novel compounds and the chemical features of these agents that may contribute to a "second generation" of inhibitors. The goal for the next 3 decades will be to design inhibitors that will be effective for more than a single class of beta-lactamases.
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Affiliation(s)
- Sarah M. Drawz
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Robert A. Bonomo
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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37
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Scott DE, Dawes GJ, Ando M, Abell C, Ciulli A. A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry. Chembiochem 2009; 10:2772-9. [PMID: 19827080 PMCID: PMC4458376 DOI: 10.1002/cbic.200900537] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Indexed: 11/06/2022]
Abstract
A new strategy that combines the concepts of fragment-based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein-ligand complexes by X-ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta-nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine-recognition motifs in enzymes, our results provide a proof-of-concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate-forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H2) binding proteins.
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Affiliation(s)
- Duncan E. Scott
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Gwen J. Dawes
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Michiyo Ando
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Chris Abell
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Alessio Ciulli
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
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38
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Use of mass spectrometry to probe the nucleophilicity of cysteinyl residues of prolyl hydroxylase domain 2. Anal Biochem 2009; 393:215-21. [PMID: 19563769 DOI: 10.1016/j.ab.2009.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 06/22/2009] [Accepted: 06/22/2009] [Indexed: 12/22/2022]
Abstract
Prolyl hydroxylase domain 2 (PHD2) plays an important role in hypoxic sensing in humans. Here we report studies on the reactivity of cysteinyl residues of the catalytic domain of PHD2 using an approach in which nondenaturing electrospray ionization-mass spectrometry (ESI-MS) analyses were combined with the use of a thiol library and residue substitution. Among the seven cysteinyl residues of the PHD2 catalytic domain, Cys201 was found to be predominantly modified by thiols or N-ethylmaleimide. Selective modification of Cys201 was further demonstrated with methanethiosulfonate, a spin-labeled probe. The modified PHD2 will be useful in electron paramagnetic resonance studies on PHD2. The results demonstrate the use of a combined library/residue substitution/ESI-MS approach for analyzing residue reactivity.
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39
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Gareiss PC, Sobczak K, McNaughton BR, Palde PB, Thornton CA, Miller BL. Dynamic combinatorial selection of molecules capable of inhibiting the (CUG) repeat RNA-MBNL1 interaction in vitro: discovery of lead compounds targeting myotonic dystrophy (DM1). J Am Chem Soc 2008; 130:16254-61. [PMID: 18998634 PMCID: PMC2645920 DOI: 10.1021/ja804398y] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults, is an RNA-mediated disease. Dramatically expanded (CUG) repeats accumulate in nuclei and sequester RNA-binding proteins such as the splicing regulator MBNL1. We have employed resin-bound dynamic combinatorial chemistry (RBDCC) to identify the first examples of compounds able to inhibit MBNL1 binding to (CUG) repeat RNA. Screening an RBDCL with a theoretical diversity of 11 325 members yielded several molecules with significant selectivity for binding to (CUG) repeat RNA over other sequences. These compounds were also able to inhibit the interaction of GGG-(CUG)(109)-GGG RNA with MBNL1 in vitro, with K(i) values in the low micromolar range.
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Affiliation(s)
- Peter C. Gareiss
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
| | - Krzysztof Sobczak
- Department of Neurology, University of Rochester, Rochester, New York 14642
| | - Brian R. McNaughton
- Department of Chemistry, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
| | - Prakash B. Palde
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
| | | | - Benjamin L Miller
- Department of Dermatology, University of Rochester, Rochester, New York 14642
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
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40
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Nielsen MC, Ulven T. Selective Extraction of G-Quadruplex Ligands from a Rationally Designed Scaffold-Based Dynamic Combinatorial Library. Chemistry 2008; 14:9487-90. [DOI: 10.1002/chem.200801109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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41
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Clavaud C, Le Gal J, Thai R, Moutiez M, Dugave C. Dynamic Combinatorial Self‐Assembly of Cyclophilin hCyp‐18 Ligands through Oxorhenium Coordination. Chembiochem 2008; 9:1823-9. [DOI: 10.1002/cbic.200800187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Cancilla MT, He MM, Viswanathan N, Simmons RL, Taylor M, Fung AD, Cao K, Erlanson DA. Discovery of an Aurora kinase inhibitor through site-specific dynamic combinatorial chemistry. Bioorg Med Chem Lett 2008; 18:3978-81. [PMID: 18579375 DOI: 10.1016/j.bmcl.2008.06.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2008] [Revised: 05/30/2008] [Accepted: 06/04/2008] [Indexed: 01/14/2023]
Abstract
We demonstrate a fragment-based lead discovery method that combines site-directed ligand discovery with dynamic combinatorial chemistry. Our technique targets dynamic combinatorial screening to a specified region of a protein by using reversible disulfide chemistry. We have used this technology to rapidly identify inhibitors of the drug target Aurora A that span the purine-binding site and the adaptive pocket of the kinase. The binding mode of a noncovalent inhibitor has been further characterized through crystallography.
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Affiliation(s)
- Mark T Cancilla
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
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