1
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Braun-Cornejo M, Ornago C, Sonawane V, Haupenthal J, Kany AM, Diamanti E, Jézéquel G, Reiling N, Blankenfeldt W, Maas P, Hirsch AKH. Target-Directed Dynamic Combinatorial Chemistry Affords Binders of Mycobacterium tuberculosis IspE. ACS OMEGA 2024; 9:38160-38168. [PMID: 39281890 PMCID: PMC11391541 DOI: 10.1021/acsomega.4c05537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 09/18/2024]
Abstract
In the search for new antitubercular compounds, we leveraged target-directed dynamic combinatorial chemistry (tdDCC) as an efficient hit-identification method. In tdDCC, the target selects its own binders from a dynamic library generated in situ, reducing the number of compounds that require synthesis and evaluation. We combined a total of 12 hydrazides and six aldehydes to generate 72 structurally diverse N-acylhydrazones. To amplify the best binders, we employed anti-infective target 4-diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE) from Mycobacterium tuberculosis (Mtb). We successfully validated the use of tdDCC as hit-identification method for IspE and optimized the analysis of tdDCC hit determination. From the 72 possible N-acylhydrazones, we synthesized 12 of them, revealing several new starting points for the development of IspE inhibitors as antibacterial agents.
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Affiliation(s)
- Maria Braun-Cornejo
- Specs Compound Handling, B.V., Bleiswijkseweg 55, 2712 PB Zoetermeer, The Netherlands
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Camilla Ornago
- Department Structure and Function of Proteins Helmholtz Centre for Infection Research Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Vidhisha Sonawane
- RG Microbial Interface Biology, Research Center Borstel Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins Helmholtz Centre for Infection Research Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Peter Maas
- Specs Compound Handling, B.V., Bleiswijkseweg 55, 2712 PB Zoetermeer, The Netherlands
| | - Anna K H Hirsch
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
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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. 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] [MESH Headings] [Grants] [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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3
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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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4
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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5
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Zagiel B, Peker T, Marquant R, Cazals G, Webb G, Miclet E, Bich C, Sachon E, Moumné R. Dynamic Amino Acid Side‐Chains Grafting on Folded Peptide Backbone**. Chemistry 2022; 28:e202200454. [DOI: 10.1002/chem.202200454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin Zagiel
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Taleen Peker
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Rodrigue Marquant
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Guillaume Cazals
- UMR 5247-CNRS-UM-ENSCM Institut des Biomolécules Max Mousseron (IBMM) Université de Montpellier 34293 Montpellier France
| | - Gabrielle Webb
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Emeric Miclet
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM Institut des Biomolécules Max Mousseron (IBMM) Université de Montpellier 34293 Montpellier France
| | - Emmanuelle Sachon
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
- MS3 U platform UFR 926 UFR 927 Sorbonne Université 4 place Jussieu 75005 Paris France
| | - Roba Moumné
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
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6
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Fray M, Mathiron D, Pilard S, Lesur D, Abidi R, Barhoumi-Slimi T, Cragg PJ, BENAZZA M. Heteroglycoclusters through Unprecedented Orthogonal Chemistry Based on N‐Alkylation of N‐Acylhydrazone. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marwa Fray
- LG2A: Laboratoire de Glycochimie des Antimicrobiens et des Agroressources Chemistry 10 Rue Baudelocque 80039 Amiens FRANCE
| | - David Mathiron
- UPJV: Universite de Picardie Jules Verne Analytique 80039 Amiens FRANCE
| | - Serge Pilard
- UPJV: Universite de Picardie Jules Verne Analytique 80039 Amiens FRANCE
| | - David Lesur
- LG2A: Laboratoire de Glycochimie des Antimicrobiens et des Agroressources Analytique 10 Rue Baudelocque 80039 Amiens FRANCE
| | - Rym Abidi
- University of Carthage: Universite de Carthage Chemistry Zarzouna-Bizerte, TN 7021, Tunisia TN 7021 Bizerte TUNISIA
| | - Thouraya Barhoumi-Slimi
- University of Tunis El Manar: Universite de Tunis El Manar Structural Chemistry Faculty of Sciences of Tunis 2092 Tunis TUNISIA
| | - Peter J. Cragg
- University of Brighton School of Applied Sciences BN2 4GJ Brighton UNITED KINGDOM
| | - Mohammed BENAZZA
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources (LG2A UMR7378, CNRS), Université de Picardie Jules Verne Departement of organic Chemistry 10 Rue Baudelocque 80039 Amiens FRANCE
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7
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Jumde RP, Guardigni M, Gierse RM, Alhayek A, Zhu D, Hamid Z, Johannsen S, Elgaher WAM, Neusens PJ, Nehls C, Haupenthal J, Reiling N, Hirsch AKH. Hit-optimization using target-directed dynamic combinatorial chemistry: development of inhibitors of the anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase. Chem Sci 2021; 12:7775-7785. [PMID: 34168831 PMCID: PMC8188608 DOI: 10.1039/d1sc00330e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023] Open
Abstract
Target-directed dynamic combinatorial chemistry (tdDCC) enables identification, as well as optimization of ligands for un(der)explored targets such as the anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase (DXPS). We report the use of tdDCC to first identify and subsequently optimize binders/inhibitors of the anti-infective target DXPS. The initial hits were also optimized for their antibacterial activity against E. coli and M. tuberculosis during subsequent tdDCC runs. Using tdDCC, we were able to generate acylhydrazone-based inhibitors of DXPS. The tailored tdDCC runs also provided insights into the structure-activity relationship of this novel class of DXPS inhibitors. The competition tdDCC runs provided important information about the mode of inhibition of acylhydrazone-based inhibitors. This approach holds the potential to expedite the drug-discovery process and should be applicable to a range of biological targets.
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Affiliation(s)
- Ravindra P Jumde
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Melissa Guardigni
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- D3-PharmaChemistry, Istituto Italiano di Tecnologia Via Morego 30 16163 Genoa Italy
| | - Robin M Gierse
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Alaa Alhayek
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Di Zhu
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Zhoor Hamid
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Sandra Johannsen
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Walid A M Elgaher
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Philipp J Neusens
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Christian Nehls
- RG Biophysics, Research Center Borstel, Leibniz Lung Center Borstel Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center Borstel Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems Borstel Germany
| | - Anna K H Hirsch
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
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8
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Reznichenko O, Cucchiarini A, Gabelica V, Granzhan A. Quadruplex DNA-guided ligand selection from dynamic combinatorial libraries of acylhydrazones. Org Biomol Chem 2021; 19:379-386. [PMID: 33325973 DOI: 10.1039/d0ob01908a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic combinatorial libraries of acylhydrazones were prepared from diacylhydrazides and several cationic or neutral aldehydes in the presence of 5-methoxyanthranilic acid catalyst. Pull-down experiments with magnetic beads functionalized with a G-quadruplex (G4)-forming oligonucleotide led to the identification of putative ligands, which were resynthesized or emulated by close structural analogues. G4-binding properties of novel derivatives were assessed by fluorimetric titrations, mass spectrometry and thermal denaturation experiments, giving evidence of strong binding (Kd < 10 nM) for two compounds.
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Affiliation(s)
- Oksana Reznichenko
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France. and CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
| | - Anne Cucchiarini
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France. and CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, 33600 Pessac, France
| | - Anton Granzhan
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France. and CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
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9
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Biomimetic selenocystine based dynamic combinatorial chemistry for thiol-disulfide exchange. Nat Commun 2021; 12:163. [PMID: 33420034 PMCID: PMC7794297 DOI: 10.1038/s41467-020-20415-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
Dynamic combinatorial chemistry applied to biological environments requires the exchange chemistry of choice to take place under physiological conditions. Thiol-disulfide exchange, one of the most popular dynamic combinatorial chemistries, usually needs long equilibration times to reach the required equilibrium composition. Here we report selenocystine as a catalyst mimicking Nature's strategy to accelerate thiol-disulfide exchange at physiological pH and low temperatures. Selenocystine is able to accelerate slow thiol-disulfide systems and to promote the correct folding of an scrambled RNase A enzyme, thus broadening the practical range of pH conditions for oxidative folding. Additionally, dynamic combinatorial chemistry target-driven self-assembly processes are tested using spermine, spermidine and NADPH (casting) and glucose oxidase (molding). A non-competitive inhibitor is identified in the glucose oxidase directed dynamic combinatorial library.
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10
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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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11
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Troelsen NS, Clausen MH. Library Design Strategies To Accelerate Fragment‐Based Drug Discovery. Chemistry 2020; 26:11391-11403. [DOI: 10.1002/chem.202000584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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12
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Hartman AM, Jumde VR, Elgaher WAM, Te Poele EM, Dijkhuizen L, Hirsch AKH. Potential Dental Biofilm Inhibitors: Dynamic Combinatorial Chemistry Affords Sugar-Based Molecules that Target Bacterial Glucosyltransferase. ChemMedChem 2020; 16:113-123. [PMID: 32542998 PMCID: PMC7818428 DOI: 10.1002/cmdc.202000222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/15/2020] [Indexed: 12/21/2022]
Abstract
We applied dynamic combinatorial chemistry (DCC) to find novel ligands of the bacterial virulence factor glucosyltransferase (GTF) 180. GTFs are the major producers of extracellular polysaccharides, which are important factors in the initiation and development of cariogenic dental biofilms. Following a structure‐based strategy, we designed a series of 36 glucose‐ and maltose‐based acylhydrazones as substrate mimics. Synthesis of the required mono‐ and disaccharide‐based aldehydes set the stage for DCC experiments. Analysis of the dynamic combinatorial libraries (DCLs) by UPLC‐MS revealed major amplification of four compounds in the presence of GTF180. Moreover, we found that derivatives of the glucose‐acceptor maltose at the C1‐hydroxy group act as glucose‐donors and are cleaved by GTF180. The synthesized hits display medium to low binding affinity (KD values of 0.4–10.0 mm) according to surface plasmon resonance. In addition, they were investigated for inhibitory activity in GTF‐activity assays. The early‐stage DCC study reveals that careful design of DCLs opens up easy access to a broad class of novel compounds that can be developed further as potential inhibitors.
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Affiliation(s)
- Alwin M Hartman
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Varsha R Jumde
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Walid A M Elgaher
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Evelien M Te Poele
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen (The, Netherlands.,CarbExplore Research BV, Zernikepark 1, 9747 AN, Groningen (The, Netherlands
| | - Lubbert Dijkhuizen
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen (The, Netherlands.,CarbExplore Research BV, Zernikepark 1, 9747 AN, Groningen (The, Netherlands
| | - Anna K H Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
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13
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Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
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14
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Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020; 59:14965-14972. [PMID: 32436364 DOI: 10.1002/anie.202005070] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Indexed: 11/11/2022]
Abstract
Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.
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Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China.,Department of Chemistry, Southern University of Science and Technology China, 1088 Xueyuan Road, Shenzhen, China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
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15
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16
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Jiao T, Wu G, Zhang Y, Shen L, Lei Y, Wang C, Fahrenbach AC, Li H. Self‐Assembly in Water with N‐Substituted Imines. Angew Chem Int Ed Engl 2020; 59:18350-18367. [DOI: 10.1002/anie.201910739] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Tianyu Jiao
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Guangcheng Wu
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Yang Zhang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Libo Shen
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Ye Lei
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Cai‐Yun Wang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | | | - Hao Li
- Department of Chemistry Zhejiang University Hangzhou 310027 China
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17
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El-gendy AT, Youssef AA, Rizk SA. Which energetically favorable sustainable synthesis of 4-amino-8-azacoumarin ester or 4-hydroxy-3-cyano derivative based on new exact kinetic Arrhenius and DFT stimulation. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01838-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Insights into real-time chemical processes in a calcium sensor protein-directed dynamic library. Nat Commun 2019; 10:2798. [PMID: 31243268 PMCID: PMC6595003 DOI: 10.1038/s41467-019-10627-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
Dynamic combinatorial chemistry (DCC) has proven its potential in drug discovery speeding the identification of modulators of biological targets. However, the exchange chemistries typically take place under specific reaction conditions, with limited tools capable of operating under physiological parameters. Here we report a catalyzed protein-directed DCC working at low temperatures that allows the calcium sensor NCS-1 to find the best ligands in situ. Ultrafast NMR identifies the reaction intermediates of the acylhydrazone exchange, tracing the molecular assemblies and getting a real-time insight into the essence of DCC processes at physiological pH. Additionally, NMR, X-ray crystallography and computational methods are employed to elucidate structural and mechanistic aspects of the molecular recognition event. The DCC approach leads us to the identification of a compound stabilizing the NCS-1/Ric8a complex and whose therapeutic potential is proven in a Drosophila model of disease with synaptic alterations. Dynamic combinatorial chemistry (DCC) is instrumental in the discovery of ligands for pharmaceutical targets. Here, the authors adapted DCC to work at 4 degrees Celsius and used it to identify a ligand for Neuronal Calcium Sensor-1 that promotes NCS-1/Ric8a protein-protein interaction.
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19
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Hartman AM, Gierse RM, Hirsch AKH. Protein-Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol. European J Org Chem 2019; 2019:3581-3590. [PMID: 31680778 PMCID: PMC6813629 DOI: 10.1002/ejoc.201900327] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Indexed: 01/08/2023]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify bioactive compounds. This efficient technique allows the target to select its own binders and circumvents the need for synthesis and biochemical evaluation of all individual derivatives. An ever-increasing number of publications report the use of DCC on biologically relevant target proteins. This minireview complements previous reviews by focusing on the experimental protocol and giving detailed examples of essential steps and factors that need to be considered, such as protein stability, buffer composition and cosolvents.
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Affiliation(s)
- Alwin M. Hartman
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Robin M. Gierse
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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20
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Yoneyama K, Suzuki R, Kuramochi Y, Satake A. A Candidate for Multitopic Probes for Ligand Discovery in Dynamic Combinatorial Chemistry. Molecules 2019; 24:E2166. [PMID: 31181809 PMCID: PMC6600254 DOI: 10.3390/molecules24112166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022] Open
Abstract
Multifunctionalized materials are expected to be versatile probes to find specific interactions between a ligand and a target biomaterial. Thus, efficient methods to prepare possible combinations of the functionalities is desired. The concept of dynamic combinatorial chemistry (DCC) is ideal for the generation of any possible combination, as well as screening for target biomaterials. Here, we propose a new molecular design of multitopic probes for ligand discovery in DCC. We synthesized a new Gable Porphyrin, GP1, having prop-2-yne groups as a scaffold to introduce various functional groups. GP1 is a bis(imidazolylporphyrinatozinc) compound connected through a 1,3-phenylene moiety, and it gives macrocycles spontaneously and quantitatively by strong imidazole-to-zinc complementary coordination. Some different types of functional groups were introduced into GP1 in high yields. Formation of heterogeneous macrocycles composed of GP1 derivatives having different types of substituents was accomplished under equilibrium conditions. These results promise that enormous numbers of macrocycles having various functional groups can be provided when the kinds of GP components increase. These features are desirable for DCC, and the present system using GP1 is a potential candidate to provide a dynamic combinatorial library of multitopic probes to discover specific interactions between a ligand and a biomaterial.
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Affiliation(s)
- Keiko Yoneyama
- Graduate School of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Rina Suzuki
- Graduate School of Chemical Sciences and Technology, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Yusuke Kuramochi
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Akiharu Satake
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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21
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Dynamic combinatorial chemistry as a rapid method for discovering sequence-selective RNA-binding compounds. Methods Enzymol 2019; 623:67-84. [PMID: 31239058 DOI: 10.1016/bs.mie.2019.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ever-growing number of RNA species that are recognized as having a role in human disease is driving a demand for novel molecular probes and therapeutics. Producing sequence-selective RNA-binding molecules remains a substantial challenge, however. One approach that has been successful in producing molecules with high affinity and specificity for disease-relevant RNAs is the use of dynamic combinatorial chemistry, a fragment-based method in which fragments combine reversibly in the presence of the target. We describe methods for the design, synthesis, and screening of dynamic combinatorial libraries targeting RNA.
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22
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Sauer MM, Jakob RP, Luber T, Canonica F, Navarra G, Ernst B, Unverzagt C, Maier T, Glockshuber R. Binding of the Bacterial Adhesin FimH to Its Natural, Multivalent High-Mannose Type Glycan Targets. J Am Chem Soc 2018; 141:936-944. [PMID: 30543411 DOI: 10.1021/jacs.8b10736] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multivalent carbohydrate-lectin interactions at host-pathogen interfaces play a crucial role in the establishment of infections. Although competitive antagonists that prevent pathogen adhesion are promising antimicrobial drugs, the molecular mechanisms underlying these complex adhesion processes are still poorly understood. Here, we characterize the interactions between the fimbrial adhesin FimH from uropathogenic Escherichia coli strains and its natural high-mannose type N-glycan binding epitopes on uroepithelial glycoproteins. Crystal structures and a detailed kinetic characterization of ligand-binding and dissociation revealed that the binding pocket of FimH evolved such that it recognizes the terminal α(1-2)-, α(1-3)-, and α(1-6)-linked mannosides of natural high-mannose type N-glycans with similar affinity. We demonstrate that the 2000-fold higher affinity of the domain-separated state of FimH compared to its domain-associated state is ligand-independent and consistent with a thermodynamic cycle in which ligand-binding shifts the association equilibrium between the FimH lectin and the FimH pilin domain. Moreover, we show that a single N-glycan can bind up to three molecules of FimH, albeit with negative cooperativity, so that a molar excess of accessible N-glycans over FimH on the cell surface favors monovalent FimH binding. Our data provide pivotal insights into the adhesion properties of uropathogenic Escherichia coli strains to their target receptors and a solid basis for the development of effective FimH antagonists.
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Affiliation(s)
- Maximilian M Sauer
- Institute of Molecular Biology & Biophysics , ETH Zurich , Otto-Stern-Weg 5 , CH-8093 Zurich , Switzerland
| | - Roman P Jakob
- Biozentrum , University of Basel , Klingelbergstrasse 50/70 , CH-4056 Basel , Switzerland
| | - Thomas Luber
- Bioorganische Chemie , University of Bayreuth , D-95440 Bayreuth , Germany
| | - Fabia Canonica
- Institute of Molecular Biology & Biophysics , ETH Zurich , Otto-Stern-Weg 5 , CH-8093 Zurich , Switzerland
| | - Giulio Navarra
- Department of Pharmaceutical Sciences , University of Basel , Klingelbergstrasse 50 , CH-4056 Basel , Switzerland
| | - Beat Ernst
- Department of Pharmaceutical Sciences , University of Basel , Klingelbergstrasse 50 , CH-4056 Basel , Switzerland
| | - Carlo Unverzagt
- Bioorganische Chemie , University of Bayreuth , D-95440 Bayreuth , Germany
| | - Timm Maier
- Biozentrum , University of Basel , Klingelbergstrasse 50/70 , CH-4056 Basel , Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology & Biophysics , ETH Zurich , Otto-Stern-Weg 5 , CH-8093 Zurich , Switzerland
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23
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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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24
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Zhou Y, Li C, Peng J, Xie L, Meng L, Li Q, Zhang J, Li XD, Li X, Huang X, Li X. DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery. J Am Chem Soc 2018; 140:15859-15867. [DOI: 10.1021/jacs.8b09277] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Zhou
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Chen Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
| | - Jianzhao Peng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Liangxu Xie
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Ling Meng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Qingrong Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Jianfu Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
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25
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García P, Alonso VL, Serra E, Escalante AM, Furlan RLE. Discovery of a Biologically Active Bromodomain Inhibitor by Target-Directed Dynamic Combinatorial Chemistry. ACS Med Chem Lett 2018; 9:1002-1006. [PMID: 30344907 DOI: 10.1021/acsmedchemlett.8b00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Target-directed dynamic combinatorial chemistry (DCC) has emerged as a strategy for the identification of inhibitors of relevant therapeutic targets. In this contribution, we use this strategy for the identification of a high-affinity binder of a parasite target, the Trypanosoma cruzi bromodomain-containing protein TcBDF3. This protein is essential for viability of T. cruzi, the protozoan parasite that causes Chagas disease. A small dynamic library of acylhydrazones was prepared from aldehydes and acylhydrazides at neutral pH in the presence of aniline. The most amplified library member shows (a) high affinity for the template, (b) interesting antiparasitic activity against different parasite forms, and (c) low toxicity against Vero cells. In addition, parasites are rescued from the compound toxicity by TcBDF3 overexpression, suggesting that the toxicity of this compound is due to the TcBDF3 inhibition, i.e., the binding event that initially drives the molecular amplification is reproduced in the parasite, leading to selective toxicity.
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Affiliation(s)
- Paula García
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
| | - Victoria L. Alonso
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Esteban Serra
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Andrea M. Escalante
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
| | - Ricardo L. E. Furlan
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
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26
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Current Screening Methodologies in Drug Discovery for Selected Human Diseases. Mar Drugs 2018; 16:md16080279. [PMID: 30110923 PMCID: PMC6117650 DOI: 10.3390/md16080279] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/11/2018] [Indexed: 01/31/2023] Open
Abstract
The increase of many deadly diseases like infections by multidrug-resistant bacteria implies re-inventing the wheel on drug discovery. A better comprehension of the metabolisms and regulation of diseases, the increase in knowledge based on the study of disease-born microorganisms’ genomes, the development of more representative disease models and improvement of techniques, technologies, and computation applied to biology are advances that will foster drug discovery in upcoming years. In this paper, several aspects of current methodologies for drug discovery of antibacterial and antifungals, anti-tropical diseases, antibiofilm and antiquorum sensing, anticancer and neuroprotectors are considered. For drug discovery, two different complementary approaches can be applied: classical pharmacology, also known as phenotypic drug discovery, which is the historical basis of drug discovery, and reverse pharmacology, also designated target-based drug discovery. Screening methods based on phenotypic drug discovery have been used to discover new natural products mainly from terrestrial origin. Examples of the discovery of marine natural products are provided. A section on future trends provides a comprehensive overview on recent advances that will foster the pharmaceutical industry.
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