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Wang Z, Bosma R, Kuhne S, van den Bor J, Garabitian W, Vischer HF, Wijtmans M, Leurs R, de Esch IJ. Exploring the Effect of Cyclization of Histamine H 1 Receptor Antagonists on Ligand Binding Kinetics. ACS OMEGA 2021; 6:12755-12768. [PMID: 34056427 PMCID: PMC8154229 DOI: 10.1021/acsomega.0c06358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
There is an increasing interest in guiding hit optimization by considering the target binding kinetics of ligands. However, compared to conventional structure-activity relationships, structure-kinetics relationships have not been as thoroughly explored, even for well-studied archetypical drug targets such as the histamine H1 receptor (H1R), a member of the family A G-protein coupled receptor. In this study, we show that the binding kinetics of H1R antagonists at the H1R is dependent on the cyclicity of both the aromatic head group and the amine moiety of H1R ligands, the chemotypes that are characteristic for the first-generation H1R antagonists. Fusing the two aromatic rings of H1R ligands into one tricyclic aromatic head group prolongs the H1R residence time for benchmark H1R ligands as well as for tailored synthetic analogues. The effect of constraining the aromatic rings and the basic amines is systematically explored, leading to a coherent series and detailed discussions of structure-kinetics relationships. This study shows that cyclicity has a pronounced effect on the binding kinetics.
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Affiliation(s)
| | | | | | - Jelle van den Bor
- Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wrej Garabitian
- Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Henry F. Vischer
- Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J.P. de Esch
- Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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Jójárt B, Orgován Z, Márki Á, Pándy-Szekeres G, Ferenczy GG, Keserű GM. Allosteric activation of metabotropic glutamate receptor 5. J Biomol Struct Dyn 2019; 38:2624-2632. [DOI: 10.1080/07391102.2019.1638302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Szeged, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Márki
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, Hungary
| | - Gáspár Pándy-Szekeres
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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De Benedetti PG, Fanelli F. Computational modeling approaches to quantitative structure-binding kinetics relationships in drug discovery. Drug Discov Today 2018; 23:1396-1406. [PMID: 29574212 DOI: 10.1016/j.drudis.2018.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/22/2018] [Accepted: 03/19/2018] [Indexed: 11/22/2022]
Abstract
Simple comparative correlation analyses and quantitative structure-kinetics relationship (QSKR) models highlight the interplay of kinetic rates and binding affinity as an essential feature in drug design and discovery. The choice of the molecular series, and their structural variations, used in QSKR modeling is fundamental to understanding the mechanistic implications of ligand and/or drug-target binding and/or unbinding processes. Here, we discuss the implications of linear correlations between kinetic rates and binding affinity constants and the relevance of the computational approaches to QSKR modeling.
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Affiliation(s)
- Pier G De Benedetti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy.
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
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