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Su H, Xu Y. Application of ITC-Based Characterization of Thermodynamic and Kinetic Association of Ligands With Proteins in Drug Design. Front Pharmacol 2018; 9:1133. [PMID: 30364164 PMCID: PMC6193069 DOI: 10.3389/fphar.2018.01133] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
A comprehensive characterization of the thermodynamic and kinetic profiling of ligands binding to a given target protein is crucial for the hit selection as well as the hit-to-lead-to-drug evolution. Isothermal titration calorimetry (ITC), widely known as an invaluable tool to measure the thermodynamic data, has recently found its way to determine the binding kinetics too. The extensive application of ITC in measurement of both thermodynamic and kinetic data manifests unique roles of ITC in drug discovery and development. This mini-review concentrates on elaborating how to gain the thermodynamic and kinetic data using ITC, highlighting the importance of these data in lead discovery and optimization, and intends to provide an overview of the technical and conceptual advances that offer unprecedented access to protein–ligand recognition by ITC measurement.
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Affiliation(s)
- Haixia Su
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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2
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Movsisyan LD, Schäfer E, Nguyen A, Ehrmann FR, Schwab A, Rossolini T, Zimmerli D, Wagner B, Daff H, Heine A, Klebe G, Diederich F. Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry 2018; 24:9957-9967. [PMID: 29939431 DOI: 10.1002/chem.201801756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/10/2018] [Indexed: 11/09/2022]
Abstract
The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.
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Affiliation(s)
- Levon D Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anatol Schwab
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Thomas Rossolini
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Daniel Zimmerli
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Hamina Daff
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
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3
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Sun H, Horatscheck A, Martos V, Bartetzko M, Uhrig U, Lentz D, Schmieder P, Nazaré M. Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Han Sun
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - André Horatscheck
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
- Drug Discovery and Development Centre (H3D); Department of Chemistry; University of Cape Town; Rondebosch 7701 South Africa
| | - Vera Martos
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Max Bartetzko
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL); Chemical Biology Core Facility; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstrasse 34-36 14195 Berlin Germany
| | - Peter Schmieder
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Marc Nazaré
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
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4
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Sun H, Horatscheck A, Martos V, Bartetzko M, Uhrig U, Lentz D, Schmieder P, Nazaré M. Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances. Angew Chem Int Ed Engl 2017; 56:6454-6458. [PMID: 28452102 DOI: 10.1002/anie.201700520] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/24/2022]
Abstract
We dissected halogen-aryl π interactions experimentally using a bicyclic N-arylimide based molecular torsion balances system, which is based on the influence of the non-bonded interaction on the equilibria between folded and unfolded states. Through comparison of balances modulated by higher halogens with fluorine balances, we determined the magnitude of the halogen-aryl π interactions in our unimolecular systems to be larger than -5.0 kJ mol-1 , which is comparable with the magnitude estimated in the biomolecular systems. Our study provides direct experimental evidence of halogen-aryl π interactions in solution, which until now have only been revealed in the solid state and evaluated theoretically by quantum-mechanical calculations.
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Affiliation(s)
- Han Sun
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - André Horatscheck
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany.,Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Vera Martos
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Max Bartetzko
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany.,Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34-36, 14195, Berlin, Germany
| | - Peter Schmieder
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Marc Nazaré
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
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5
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Neeb M, Hohn C, Ehrmann FR, Härtsch A, Heine A, Diederich F, Klebe G. Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding? Bioorg Med Chem 2016; 24:4900-4910. [DOI: 10.1016/j.bmc.2016.07.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/24/2016] [Indexed: 11/29/2022]
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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Thelemann J, Illarionov B, Barylyuk K, Geist J, Kirchmair J, Schneider P, Anthore L, Root K, Trapp N, Bacher A, Witschel M, Zenobi R, Fischer M, Schneider G, Diederich F. Aryl Bis-Sulfonamide Inhibitors of IspF from Arabidopsis thaliana and Plasmodium falciparum. ChemMedChem 2015; 10:2090-8. [PMID: 26435072 DOI: 10.1002/cmdc.201500382] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Indexed: 01/23/2023]
Abstract
2-Methylerythritol 2,4-cyclodiphosphate synthase (IspF) is an essential enzyme for the biosynthesis of isoprenoid precursors in plants and many human pathogens. The protein is an attractive target for the development of anti-infectives and herbicides. Using a photometric assay, a screen of 40 000 compounds on IspF from Arabidopsis thaliana afforded symmetrical aryl bis-sulfonamides that inhibit IspF from A. thaliana (AtIspF) and Plasmodium falciparum (PfIspF) with IC50 values in the micromolar range. The ortho-bis-sulfonamide structural motif is essential for inhibitory activity. The best derivatives obtained by parallel synthesis showed IC50 values of 1.4 μm against PfIspF and 240 nm against AtIspF. Substantial herbicidal activity was observed at a dose of 2 kg ha(-1) . Molecular modeling studies served as the basis for an in silico search targeted at the discovery of novel, non-symmetrical sulfonamide IspF inhibitors. The designed compounds were found to exhibit inhibitory activities in the double-digit micromolar IC50 range.
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Affiliation(s)
- Jonas Thelemann
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Konstantin Barylyuk
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Julie Geist
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Johannes Kirchmair
- Zentrum für Bioinformatik, Universität Hamburg, Bundesstr. 43, 20146, Hamburg, Germany
| | - Petra Schneider
- Institut für Pharmazeutische Wissenschaften, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Lucile Anthore
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Katharina Root
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Adelbert Bacher
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergerstr. 4, 85748, Garching, Germany
| | | | - Renato Zenobi
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany.
| | - Gisbert Schneider
- Institut für Pharmazeutische Wissenschaften, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.
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Thermodynamics of protein–ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. J Comput Aided Mol Des 2015; 29:867-83. [DOI: 10.1007/s10822-015-9867-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/05/2015] [Indexed: 12/11/2022]
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9
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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12
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Klebe G. The Use of Thermodynamic and Kinetic Data in Drug Discovery: Decisive Insight or Increasing the Puzzlement? ChemMedChem 2014; 10:229-31. [DOI: 10.1002/cmdc.201402521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 11/07/2022]
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Barandun LJ, Ehrmann FR, Zimmerli D, Immekus F, Giroud M, Grünenfelder C, Schweizer WB, Bernet B, Betz M, Heine A, Klebe G, Diederich F. Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appendedlin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT). Chemistry 2014; 21:126-35. [DOI: 10.1002/chem.201405764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 11/09/2022]
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