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Voss JH, Crüsemann M, Bartling CR, Kehraus S, Inoue A, König GM, Strømgaard K, Müller CE. Structure-affinity and structure-residence time relationships of macrocyclic Gα q protein inhibitors. iScience 2023; 26:106492. [PMID: 37091255 PMCID: PMC10119753 DOI: 10.1016/j.isci.2023.106492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/02/2023] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
The macrocyclic depsipeptides YM-254890 (YM) and FR900359 (FR) are potent inhibitors of Gαq/11 proteins. They are important pharmacological tools and have potential as therapeutic drugs. The hydrogenated, tritium-labeled YM and FR derivatives display largely different residence times despite similar structures. In the present study we established a competition-association binding assay to determine the dissociation kinetics of unlabeled Gq protein inhibitors. Structure-affinity and structure-residence time relationships were analyzed. Small structural modifications had a large impact on residence time. YM and FR exhibited 4- to 10-fold higher residence times than their hydrogenated derivatives. While FR showed pseudo-irreversible binding, YM displayed much faster dissociation from its target. The isopropyl anchor present in FR and some derivatives was essential for slow dissociation. These data provide a basis for future drug design toward modulating residence times of macrocyclic Gq protein inhibitors, which has been recognized as a crucial determinant for therapeutic outcome.
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Affiliation(s)
- Jan H. Voss
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Christian R.O. Bartling
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Asuka Inoue
- Tohoku University, Graduate School of Pharmaceutical Sciences, Sendai, Miyagi 980-8578, Japan
| | - Gabriele M. König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Corresponding author
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2
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Vauquelin G, Maes D. Competition in drug binding and … the race to equilibrium. Fundam Clin Pharmacol 2023; 37:147-157. [PMID: 35981720 DOI: 10.1111/fcp.12824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023]
Abstract
Binding kinetics has become a popular topic in pharmacology due to its potential contribution to the selectivity and duration of drug action. Yet, the overall kinetic aspects of complex binding mechanisms are still merely described in terms of elaborate algebraic equations. Interestingly, it has been recommended some 10 years ago to examine such mechanisms in terms of binding fluxes instead of the conventional rate constants. Alike the velocity of product formation in enzymology, those fluxes refer to the velocity by which one target species converts into another one. Novel binding flux-based approaches are utilized to get a better visual insight into the "competition" between two drugs/ligands for a single target as well as between induced fit- and conformational selection pathways for a single ligand within a thermodynamic cycle. The present data were obtained by differential equation-based simulations. Early on, the ligand-binding steps "race" to equilibrium (i.e., when their forward and reverse fluxes are equal) at their individual pace. The overall/global equilibrium is only reached later on. For the competition association assays, this parting might produce a transient "overshoot" of one of the bound target species. A similar overshoot may also show up within a thermodynamic cycle and, at first glance, suggest that the induced fit pathway dominates. Yet, present findings show that under certain circumstances, it could rather be the other way round. Novel binding flux-based approaches offer visually attractive insights into crucial aspects of "complex" binding mechanisms under non-equilibrium conditions.
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Affiliation(s)
- Georges Vauquelin
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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3
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Gu X, Yuan H, Zhao W, Sun N, Yan W, Jiang C, He Y, Liu H, Cheng J, Guo D. Optical-Controlled Kinetic Switch: Fine-Tuning of the Residence Time of an Antagonist Binding to the Vasopressin V 2 Receptor in In Vitro, Ex Vivo, and In Vivo Models of ADPKD. J Med Chem 2023; 66:1454-1466. [PMID: 36563185 DOI: 10.1021/acs.jmedchem.2c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pharmacological activity of a small-molecule ligand is linked to its receptor residence time. Therefore, precise control of the duration for which a ligand binds to its receptor is highly desirable. Herein, we designed photoswitchable ligands targeting the vasopressin V2 receptor (V2R), a validated target for autosomal dominant polycystic kidney disease (ADPKD). We adapted the photoswitching trait of azobenzene to the parent V2R antagonist lixivaptan (LP) to generate azobenzene lixivaptan derivatives (aLPs). Among them, aLPs-5g was a potential optical-controlled kinetic switch. Upon irradiation, cis-aLPs-5g displayed a 4.3-fold prolonged V2R residence time compared to its thermally stable trans configuration. The optical-controlled kinetic variations led to distinct inhibitory effects on cellular functional readout. Furthermore, conversion of the cis/trans isomer of aLPs-5g resulted in different efficacies of inhibiting renal cystogenesis ex vivo and in vivo. Overall, aLPs-5g represents a photoswitch for precise control of ligand-receptor residence time and, consequently, the pharmacological activity.
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Affiliation(s)
- Xiaoke Gu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Haoxing Yuan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Wenchao Zhao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Nan Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Wenzhong Yan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chunyu Jiang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Yan He
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004 Jiangsu, China
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4
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Stampelou M, Suchankova A, Tzortzini E, Dhingra L, Barkan K, Lougiakis N, Marakos P, Pouli N, Ladds G, Kolocouris A. Dual A1/A3 Adenosine Receptor Antagonists: Binding Kinetics and Structure-Activity Relationship Studies Using Mutagenesis and Alchemical Binding Free Energy Calculations. J Med Chem 2022; 65:13305-13327. [PMID: 36173355 DOI: 10.1021/acs.jmedchem.2c01123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drugs targeting adenosine receptors (AR) can provide treatment for diseases. We report the identification of 7-(phenylamino)-pyrazolo[3,4-c]pyridines L2-L10, A15, and A17 as low-micromolar to low-nanomolar A1R/A3R dual antagonists, with 3-phenyl-5-cyano-7-(trimethoxyphenylamino)-pyrazolo[3,4-c]pyridine (A17) displaying the highest affinity at both receptors with a long residence time of binding, as determined using a NanoBRET-based assay. Two binding orientations of A17 produce stable complexes inside the orthosteric binding area of A1R in molecular dynamics (MD) simulations, and we selected the most plausible orientation based on the agreement with alanine mutagenesis supported by affinity experiments. Interestingly, for drug design purposes, the mutation of L2506.51 to alanine increased the binding affinity of A17 at A1R. We explored the structure-activity relationships against A1R using alchemical binding free energy calculations with the thermodynamic integration coupled with the MD simulation (TI/MD) method, applied on the whole G-protein-coupled receptor-membrane system, which showed a good agreement (r = 0.73) between calculated and experimental relative binding free energies.
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Affiliation(s)
- Margarita Stampelou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Anna Suchankova
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Lakshiv Dhingra
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Kerry Barkan
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Nikolaos Lougiakis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Panagiotis Marakos
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Nicole Pouli
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
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5
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IJzerman AP, Jacobson KA, Müller CE, Cronstein BN, Cunha RA. International Union of Basic and Clinical Pharmacology. CXII: Adenosine Receptors: A Further Update. Pharmacol Rev 2022; 74:340-372. [PMID: 35302044 PMCID: PMC8973513 DOI: 10.1124/pharmrev.121.000445] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.
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Affiliation(s)
- Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Kenneth A Jacobson
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Christa E Müller
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Bruce N Cronstein
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Rodrigo A Cunha
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
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6
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Hoare SRJ. The Problems of Applying Classical Pharmacology Analysis to Modern In Vitro Drug Discovery Assays: Slow Binding Kinetics and High Target Concentration. SLAS DISCOVERY 2021; 26:835-850. [PMID: 34112012 DOI: 10.1177/24725552211019653] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The analysis framework used to quantify drug potency in vitro (e.g., Kd or Ki) was initially developed for classical pharmacology bioassays, for example, organ bath experiments testing moderate-affinity natural products. Modern drug discovery can infringe the assumptions of the classical pharmacology analysis equations, owing to the reduction of assay volume in miniaturization, target overexpression, and the increase of compound-target affinity in medicinal chemistry. These assumptions are that (1) the compound concentration greatly exceeds the target concentration (i.e., minimal ligand depletion), and (2) the compound is at equilibrium with the receptor (i.e., rapid ligand binding kinetics). Unappreciated infringement of these assumptions can lead to substantial underestimation of compound affinity, which negatively impacts the drug discovery process, from early-stage lead optimization to prediction of human dosing. This study evaluates the real-world impact of these factors on the target interaction assays used in drug discovery using literature examples, database searches, and simulations. The ranges of compound affinity and the assay types that are prone to depletion and equilibration artifacts are identified. Importantly, the highest-affinity compounds, usually the highest value chemical matter in drug discovery, are the most affected. Methods and simulation tools are provided to enable investigators to evaluate, manage, and minimize depletion or equilibration artifacts. This study enables the correct application of pharmacological data analysis to accurately quantify affinity using modern drug discovery assay technology.
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7
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Xu X, Kaindl J, Clark MJ, Hübner H, Hirata K, Sunahara RK, Gmeiner P, Kobilka BK, Liu X. Binding pathway determines norepinephrine selectivity for the human β 1AR over β 2AR. Cell Res 2021; 31:569-579. [PMID: 33093660 PMCID: PMC8089101 DOI: 10.1038/s41422-020-00424-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023] Open
Abstract
Beta adrenergic receptors (βARs) mediate physiologic responses to the catecholamines epinephrine and norepinephrine released by the sympathetic nervous system. While the hormone epinephrine binds β1AR and β2AR with similar affinity, the smaller neurotransmitter norepinephrine is approximately tenfold selective for the β1AR. To understand the structural basis for this physiologically important selectivity, we solved the crystal structures of the human β1AR bound to an antagonist carazolol and different agonists including norepinephrine, epinephrine and BI-167107. Structural comparison revealed that the catecholamine-binding pockets are identical between β1AR and β2AR, but the extracellular vestibules have different shapes and electrostatic properties. Metadynamics simulations and mutagenesis studies revealed that these differences influence the path norepinephrine takes to the orthosteric pocket and contribute to the different association rates and thus different affinities.
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Affiliation(s)
- Xinyu Xu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084 China ,School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Jonas Kaindl
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich–Alexander University Erlangen–Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen, 91058 Germany
| | - Mary J. Clark
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich–Alexander University Erlangen–Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen, 91058 Germany
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo, 679-5148 Japan ,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Roger K. Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich–Alexander University Erlangen–Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen, 91058 Germany
| | - Brian K. Kobilka
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084 China ,School of Medicine, Tsinghua University, Beijing, 100084 China ,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084 China ,School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084 China
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8
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Wan S, Potterton A, Husseini FS, Wright DW, Heifetz A, Malawski M, Townsend-Nicholson A, Coveney PV. Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors. Interface Focus 2020; 10:20190128. [PMID: 33178414 PMCID: PMC7653344 DOI: 10.1098/rsfs.2019.0128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A1 and A2A adenosine receptors, members of a subclass of the GPCR (G protein-coupled receptor) superfamily. Our predicted binding free energies, calculated using ESMACS, show a good correlation with previously reported experimental values of the ligands studied. Relative binding free energies, calculated using TIES, accurately predict experimentally determined values within a mean absolute error of approximately 1 kcal mol-1. Our methodology may be applied widely within the GPCR superfamily and to other small molecule-receptor protein systems.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew Potterton
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Fouad S. Husseini
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - David W. Wright
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Alexander Heifetz
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, UK
| | - Maciej Malawski
- ACK Cyfronet, AGH University of Science and Technology, Nawojki 11, 30-950, Kraków, Poland
| | - Andrea Townsend-Nicholson
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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9
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Yang X, Dilweg MA, Osemwengie D, Burggraaff L, van der Es D, Heitman LH, IJzerman AP. Design and pharmacological profile of a novel covalent partial agonist for the adenosine A 1 receptor. Biochem Pharmacol 2020; 180:114144. [PMID: 32653590 DOI: 10.1016/j.bcp.2020.114144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/29/2022]
Abstract
Partial agonists for G protein-coupled receptors (GPCRs) provide opportunities for novel pharmacotherapies with enhanced on-target safety compared to full agonists. For the human adenosine A1 receptor (hA1AR) this has led to the discovery of capadenoson, which has been in phase IIa clinical trials for heart failure. Accordingly, the design and profiling of novel hA1AR partial agonists has become an important research focus. In this study, we report on LUF7746, a capadenoson derivative bearing an electrophilic fluorosulfonyl moiety, as an irreversibly binding hA1AR modulator. Meanwhile, a nonreactive ligand bearing a methylsulfonyl moiety, LUF7747, was designed as a control probe in our study. In a radioligand binding assay, LUF7746's apparent affinity increased to nanomolar range with longer pre-incubation time, suggesting an increasing level of covalent binding over time. Moreover, compared to the reference full agonist CPA, LUF7746 was a partial agonist in a hA1AR-mediated G protein activation assay and resistant to blockade with an antagonist/inverse agonist. An in silico structure-based docking study combined with site-directed mutagenesis of the hA1AR demonstrated that amino acid Y2717.36 was the primary anchor point for the covalent interaction. Additionally, a label-free whole-cell assay was set up to identify LUF7746's irreversible activation of an A1 receptor-mediated cell morphological response. These results led us to conclude that LUF7746 is a novel covalent hA1AR partial agonist and a valuable chemical probe for further mapping the receptor activation process. It may also serve as a prototype for a therapeutic approach in which a covalent partial agonist may cause less on-target side effects, conferring enhanced safety compared to a full agonist.
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Affiliation(s)
- Xue Yang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands
| | - Majlen A Dilweg
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands
| | - Dion Osemwengie
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands
| | - Lindsey Burggraaff
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands
| | - Daan van der Es
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300RA Leiden, The Netherlands.
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10
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Huang S, Chen L, Mei H, Zhang D, Shi T, Kuang Z, Heng Y, Xu L, Pan X. In Silico Prediction of the Dissociation Rate Constants of Small Chemical Ligands by 3D-Grid-Based VolSurf Method. Int J Mol Sci 2020; 21:ijms21072456. [PMID: 32252223 PMCID: PMC7177943 DOI: 10.3390/ijms21072456] [Citation(s) in RCA: 4] [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: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022] Open
Abstract
Accumulated evidence suggests that binding kinetic properties—especially dissociation rate constant or drug-target residence time—are crucial factors affecting drug potency. However, quantitative prediction of kinetic properties has always been a challenging task in drug discovery. In this study, the VolSurf method was successfully applied to quantitatively predict the koff values of the small ligands of heat shock protein 90α (HSP90α), adenosine receptor (AR) and p38 mitogen-activated protein kinase (p38 MAPK). The results showed that few VolSurf descriptors can efficiently capture the key ligand surface properties related to dissociation rate; the resulting models demonstrated to be extremely simple, robust and predictive in comparison with available prediction methods. Therefore, it can be concluded that the VolSurf-based prediction method can be widely applied in the ligand-receptor binding kinetics and de novo drug design researches.
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Affiliation(s)
- Shuheng Huang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing 400044, China; (S.H.); (L.C.)
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Linxin Chen
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing 400044, China; (S.H.); (L.C.)
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing 400044, China; (S.H.); (L.C.)
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
- Correspondence: (H.M.); (X.P.); Tel.: +86-23-65112677 (H.M.)
| | - Duo Zhang
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Tingting Shi
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Zuyin Kuang
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Yu Heng
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Lei Xu
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Xianchao Pan
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
- Department of Medicinal Chemistry, College of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Correspondence: (H.M.); (X.P.); Tel.: +86-23-65112677 (H.M.)
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11
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van der Velden WJC, Heitman LH, Rosenkilde MM. Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacol Transl Sci 2020; 3:179-189. [PMID: 32296761 DOI: 10.1021/acsptsci.0c00012] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 12/16/2022]
Abstract
The concept of ligand-receptor binding kinetics has been broadly applied in drug development pipelines focusing on G protein-coupled receptors (GPCRs). The ligand residence time (RT) for a receptor describes how long a ligand-receptor complex exists, and is defined as the reciprocal of the dissociation rate constant (k off). RT has turned out to be a valuable parameter for GPCR researchers focusing on drug development as a good predictor of in vivo efficacy. The positive correlation between RT and in vivo efficacy has been established for several drugs targeting class A GPCRs (e.g., the neurokinin-1 receptor (NK1R), the β2 adrenergic receptor (β2AR), and the muscarinic 3 receptor (M3R)) and for drugs targeting class B1 (e.g., the glucagon-like peptide 1 receptor (GLP-1R)). Recently, the association rate constant (k on) has gained similar attention as another parameter affecting in vivo efficacy. In the current perspective, we address the importance of studying ligand-receptor binding kinetics for therapeutic targeting of GPCRs, with an emphasis on how binding kinetics can be altered by subtle molecular changes in the ligands and/or the receptors and how such changes affect treatment outcome. Moreover, we speculate on the impact of binding kinetic parameters for functional selectivity and sustained receptor signaling from endosomal compartments; phenomena that have gained increasing interest in attempts to improve therapeutic targeting of GPCRs.
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Affiliation(s)
- Wijnand J C van der Velden
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
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12
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Azalim P, do Monte FM, Rendeiro MM, Liu X, O'Doherty GA, Fontes CF, Leitão SG, Quintas LEM, Noël F. Conformational states of the pig kidney Na+/K+-ATPase differently affect bufadienolides and cardenolides: A directed structure-activity and structure-kinetics study. Biochem Pharmacol 2020; 171:113679. [DOI: 10.1016/j.bcp.2019.113679] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
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13
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The importance of target binding kinetics for measuring target binding affinity in drug discovery: a case study from a CRF1 receptor antagonist program. Drug Discov Today 2020; 25:7-14. [DOI: 10.1016/j.drudis.2019.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/16/2019] [Accepted: 09/13/2019] [Indexed: 12/28/2022]
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14
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Georgi V, Dubrovskiy A, Steigele S, Fernández-Montalván AE. Considerations for improved performance of competition association assays analysed with the Motulsky-Mahan's "kinetics of competitive binding" model. Br J Pharmacol 2019; 176:4731-4744. [PMID: 31444916 PMCID: PMC7029771 DOI: 10.1111/bph.14841] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 06/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022] Open
Abstract
Background and Purpose Target engagement dynamics can influence drugs' pharmacological effects. Kinetic parameters for drug:target interactions are often quantified by evaluating competition association experiments—measuring simultaneous protein binding of labelled tracers and unlabelled test compounds over time—with Motulsky–Mahan's “kinetics of competitive binding” model. Despite recent technical improvements, the current assay formats impose practical limitations to this approach. This study aims at the characterisation, understanding and prevention of these experimental constraints, and associated analytical challenges. Experimental Approach Monte Carlo simulations were used to run virtual kinetic and equilibrium tracer binding and competition experiments in both normal and perturbed assay conditions. Data were fitted to standard equations derived from the mass action law (including Motulsky–Mahan's) and to extended versions aiming to cope with frequently observed deviations of the canonical traces. Results were compared to assess the precision and accuracy of these models and identify experimental factors influencing their performance. Key Results Key factors influencing the precision and accuracy of the Motulsky–Mahan model are the interplay between compound dissociation rates, measurement time and interval frequency, tracer concentration and binding kinetics and the relative abundance of equilibrium complexes in vehicle controls. Experimental results produced recommendations for better design of tracer characterisation experiments and new strategies to deal with systematic signal decay. Conclusions and Implications Our data advances our comprehension of the Motulsky–Mahan kinetics of competitive binding models and provides experimental design recommendations, data analysis tools, and general guidelines for its practical application to in vitro pharmacology and drug screening.
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Affiliation(s)
| | - Alexey Dubrovskiy
- Research and Development, Genedata AG, Basel, Switzerland.,Software Engineering, Google Inc., Zürich, Switzerland
| | | | - Amaury E Fernández-Montalván
- Drug Discovery, Pharmaceuticals, Bayer AG, Berlin, Germany.,Compound Screening, Institut de Recherches Servier, Croissy-sur-Seine, France
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15
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Bosma R, Wang Z, Kooistra AJ, Bushby N, Kuhne S, van den Bor J, Waring MJ, de Graaf C, de Esch IJ, Vischer HF, Sheppard RJ, Wijtmans M, Leurs R. Route to Prolonged Residence Time at the Histamine H 1 Receptor: Growing from Desloratadine to Rupatadine. J Med Chem 2019; 62:6630-6644. [PMID: 31274307 PMCID: PMC6750840 DOI: 10.1021/acs.jmedchem.9b00447] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Drug–target
binding kinetics are an important predictor of in vivo drug efficacy,
yet the relationship
between ligand structures and their binding kinetics is often poorly
understood. We show that both rupatadine (1) and desloratadine
(2) have a long residence time at the histamine H1 receptor (H1R). Through development of a [3H]levocetirizine radiolabel, we find that the residence time
of 1 exceeds that of 2 more than 10-fold.
This was further explored with 22 synthesized rupatadine and desloratadine
analogues. Methylene-linked cycloaliphatic or β-branched substitutions
of desloratadine increase the residence time at the H1R,
conveying a longer duration of receptor antagonism. However, cycloaliphatic
substituents directly attached to the piperidine amine (i.e., lacking
the spacer) have decreased binding affinity and residence time compared
to their methylene-linked structural analogues. Guided by docking
studies, steric constraints within the binding pocket are hypothesized
to explain the observed differences in affinity and binding kinetics
between analogues.
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Affiliation(s)
- Reggie Bosma
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Zhiyong Wang
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Albert J Kooistra
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Nick Bushby
- Operations, BioPharmaceuticals R&D , AstraZeneca , Alderley Park , Macclesfield SK10 4TG , United Kingdom
| | - Sebastiaan Kuhne
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Jelle van den Bor
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Michael J Waring
- Medicinal Chemistry, Research and Early Development, Oncology R&D , AstraZeneca , Alderley Park , Macclesfield SK10 4TG , United Kingdom
| | - Chris de Graaf
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Iwan J de Esch
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Henry F Vischer
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Robert J Sheppard
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D , AstraZeneca , Gothenburg 431 50 , Sweden
| | - Maikel Wijtmans
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
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16
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Abstract
The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/ koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). There are many experimental and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time. We first introduce the theoretical background of drug binding kinetics from a physicochemical standpoint. We then analyze the recent literature in the field, starting from the experimental methodologies and applications thereof and moving to theoretical and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of molecular dynamics and related methods, which comprise a great number of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
| | - Walter Rocchia
- CONCEPT Laboratory, Istituto Italiano di Tecnologia, I-16163 Genova, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
- Computational Sciences Domain, Istituto Italiano di Tecnologia, I-16163 Genova, Italy
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17
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Long residence time adenosine A1 receptor agonists produce sustained wash-resistant antilipolytic effect in rat adipocytes. Biochem Pharmacol 2019; 164:45-52. [DOI: 10.1016/j.bcp.2019.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/20/2019] [Indexed: 02/06/2023]
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18
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Probe dependency in the determination of ligand binding kinetics at a prototypical G protein-coupled receptor. Sci Rep 2019; 9:7906. [PMID: 31133718 PMCID: PMC6536503 DOI: 10.1038/s41598-019-44025-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 01/28/2023] Open
Abstract
Drug-target binding kinetics are suggested to be important parameters for the prediction of in vivo drug-efficacy. For G protein-coupled receptors (GPCRs), the binding kinetics of ligands are typically determined using association binding experiments in competition with radiolabelled probes, followed by analysis with the widely used competitive binding kinetics theory developed by Motulsky and Mahan. Despite this, the influence of the radioligand binding kinetics on the kinetic parameters derived for the ligands tested is often overlooked. To address this, binding rate constants for a series of histamine H1 receptor (H1R) antagonists were determined using radioligands with either slow (low koff) or fast (high koff) dissociation characteristics. A correlation was observed between the probe-specific datasets for the kinetic binding affinities, association rate constants and dissociation rate constants. However, the magnitude and accuracy of the binding rate constant-values was highly dependent on the used radioligand probe. Further analysis using recently developed fluorescent binding methods corroborates the finding that the Motulsky-Mahan methodology is limited by the employed assay conditions. The presented data suggest that kinetic parameters of GPCR ligands depend largely on the characteristics of the probe used and results should therefore be viewed within the experimental context and limitations of the applied methodology.
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19
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Philippe C, Zeilinger M, Dumanic M, Pichler F, Fetty L, Vraka C, Balber T, Wadsak W, Pallitsch K, Spreitzer H, Lanzenberger R, Hacker M, Mitterhauser M. SNAPshots of the MCHR1: a Comparison Between the PET-Tracers [ 18F]FE@SNAP and [ 11C]SNAP-7941. Mol Imaging Biol 2019; 21:257-268. [PMID: 29948643 PMCID: PMC6449294 DOI: 10.1007/s11307-018-1212-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE The melanin-concentrating hormone receptor 1 (MCHR1) has become an important pharmacological target, since it may be involved in various diseases, such as diabetes, insulin resistance, and obesity. Hence, a suitable positron emission tomography radiotracer for the in vivo assessment of the MCHR1 pharmacology is imperative. The current paper contrasts the extensive in vitro, in vivo, and ex vivo assessments of the radiotracers [18F]FE@SNAP and [11C]SNAP-7941 and provides comprehensive information about their biological and physicochemical properties. Furthermore, it examines their suitability for first-in-man imaging studies. PROCEDURES Kinetic real-time cell-binding studies with [18F]FE@SNAP and [11C]SNAP-7941 were conducted on adherent Chines hamster ovary (CHO-K1) cells stably expressing the human MCHR1 and MCHR2. Small animal imaging studies on mice and rats were performed under displacement and baseline conditions, as well as after pretreatment with the P-glycoprotein/breast cancer resistant protein inhibitor tariquidar. After the imaging studies, detailed analyses of the ex vivo biodistribution were performed. Ex vivo metabolism was determined in rat blood and brain and analyzed at various time points using a quantitative radio-HPLC assay. RESULTS [11C]SNAP-7941 demonstrates high uptake on CHO-K1-hMCHR1 cells, whereas no uptake was detected for the CHO-K1-hMCHR2 cells. In contrast, [18F]FE@SNAP evinced binding to CHO-K1-hMCHR1 and CHO-K1-hMCHR2 cells. Imaging studies with [18F]FE@SNAP and [11C]SNAP-7941 showed an increased brain uptake after tariquidar pretreatment in mice, as well as in rats, and exhibited a significant difference between the time-activity curves of the baseline and blocking groups. Biodistribution of both tracers demonstrated a decreased uptake after displacement. [11C]SNAP-7941 revealed a high metabolic stability in rats, whereas [18F]FE@SNAP was rapidly metabolized. CONCLUSIONS Both radiotracers demonstrate appropriate imaging properties for the MCHR1. However, the pronounced metabolic stability as well as superior selectivity and affinity of [11C]SNAP-7941 underlines the decisive superiority over [18F]FE@SNAP.
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Affiliation(s)
- Cécile Philippe
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Markus Zeilinger
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Faculty of Engineering, University of Applied Sciences Wiener Neustadt, Neustadt, Austria
| | - Monika Dumanic
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Florian Pichler
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Faculty of Engineering, University of Applied Sciences Wiener Neustadt, Neustadt, Austria
| | - Lukas Fetty
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Radiotherapy, Division of Medical Physics, Medical University of Vienna, Vienna, Austria
| | - Chrysoula Vraka
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Theresa Balber
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Wolfgang Wadsak
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Inorganic Chemistry, University of Vienna, Vienna, Austria
- CBmed, Graz, Austria
| | | | - Helmut Spreitzer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Marcus Hacker
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Markus Mitterhauser
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria.
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.
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20
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Structure-kinetic relationship studies of cannabinoid CB 2 receptor agonists reveal substituent-specific lipophilic effects on residence time. Biochem Pharmacol 2018; 152:129-142. [DOI: 10.1016/j.bcp.2018.03.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/16/2018] [Indexed: 02/05/2023]
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21
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Guo D, Peletier LA, Bridge L, Keur W, de Vries H, Zweemer A, Heitman LH, IJzerman AP. A two-state model for the kinetics of competitive radioligand binding. Br J Pharmacol 2018; 175:1719-1730. [PMID: 29486053 PMCID: PMC5913406 DOI: 10.1111/bph.14184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 12/11/2017] [Accepted: 02/19/2018] [Indexed: 01/09/2023] Open
Abstract
Background and Purpose Ligand–receptor binding kinetics is receiving increasing attention in the drug research community. The Motulsky and Mahan model, a one‐state model, offers a method for measuring the binding kinetics of an unlabelled ligand, with the assumption that the labelled ligand has no preference while binding to distinct states or conformations of a drug target. As such, the one‐state model is not applicable if the radioligand displays biphasic binding kinetics to the receptor. Experimental Approach We extended the Motulsky and Mahan model to a two‐state model, in which the kinetics of the unlabelled competitor binding to different receptor states (R1 and R2) can be measured. With this extended model, we determined the binding kinetics of unlabelled N‐5′‐ethylcarboxamidoadenosine (NECA), a representative agonist for the adenosine A1 receptor. Subsequently, an application of the model was exemplified by measuring the binding kinetics of other A1 receptor ligands. In addition, limitations of the model were investigated as well. Key Results The kinetic rate constants of unlabelled NECA were comparable with the results of kinetic radioligand binding assays in which [3H]‐NECA was used. The model was further validated by good correlation between simulated results and the experimental data. Conclusion The two‐state model is sufficient to analyse the binding kinetics of an unlabelled ligand, when a radioligand shows biphasic association characteristics. We expect this two‐state model to have general applicability for other targets as well.
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Affiliation(s)
- Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | - Lloyd Bridge
- Department of Mathematics, Swansea University, Swansea, UK.,Department of Engineering Design and Mathematics, University of the West of England, Bristol, UK
| | - Wesley Keur
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Annelien Zweemer
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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22
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Doornbos MLJ, Wang X, Vermond SC, Peeters L, Pérez-Benito L, Trabanco AA, Lavreysen H, Cid JM, Heitman LH, Tresadern G, IJzerman AP. Covalent Allosteric Probe for the Metabotropic Glutamate Receptor 2: Design, Synthesis, and Pharmacological Characterization. J Med Chem 2018; 62:223-233. [PMID: 29494768 PMCID: PMC6331142 DOI: 10.1021/acs.jmedchem.8b00051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Covalent labeling
of G protein-coupled receptors (GPCRs) by small
molecules is a powerful approach to understand binding modes, mechanism
of action, pharmacology, and even facilitate structure elucidation.
We report the first covalent positive allosteric modulator (PAM) for
a class C GPCR, the mGlu2 receptor. Three putatively covalent
mGlu2 PAMs were designed and synthesized. Pharmacological
characterization identified 2 to bind the receptor covalently.
Computational modeling combined with receptor mutagenesis revealed
T7917.29×30 as the likely position of covalent interaction.
We show how this covalent ligand can be used to characterize the PAM
binding mode and that it is a valuable tool compound in studying receptor
function and binding kinetics. Our findings advance the understanding
of the mGlu2 PAM interaction and suggest that 2 is a valuable probe for further structural and chemical biology
approaches.
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Affiliation(s)
- Maarten L J Doornbos
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Xuesong Wang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Sophie C Vermond
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Luc Peeters
- Janssen Research and Development , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Laura Pérez-Benito
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain.,Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Andrés A Trabanco
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain
| | - Hilde Lavreysen
- Janssen Research and Development , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - José María Cid
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Gary Tresadern
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
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23
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A binding kinetics study of human adenosine A 3 receptor agonists. Biochem Pharmacol 2018; 153:248-259. [PMID: 29305857 DOI: 10.1016/j.bcp.2017.12.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/29/2017] [Indexed: 02/07/2023]
Abstract
The human adenosine A3 (hA3) receptor has been suggested as a viable drug target in inflammatory diseases and in cancer. So far, a number of selective hA3 receptor agonists (e.g. IB-MECA and 2-Cl-IB-MECA) inducing anti-inflammatory or anticancer effects are under clinical investigation. Drug-target binding kinetics is increasingly recognized as another pharmacological parameter, next to affinity, for compound triage in the early phases of drug discovery. However, such a kinetics-driven analysis has not yet been performed for the hA3 receptor. In this study, we first validated a competition association assay for adenosine A3 receptor agonists to determine the target interaction kinetics. Affinities and Kinetic Rate Index (KRI) values of 11 ribofurano and 10 methanocarba nucleosides were determined in radioligand binding assays. Afterwards, 15 analogues were further selected (KRI <0.70 or KRI >1.35) for full kinetics characterization. The structure-kinetics relationships (SKR) were derived and longer residence times were associated with methanocarba and enlarged adenine N6 and C2 substitutions. In addition, from a kon-koff-KD kinetic map we divided the agonists into three subgroups. A residence time "cliff" was observed, which might be relevant to (N)-methanocarba derivatives' rigid C2-arylalkynyl substitutions. Our findings provide substantial evidence that, next to affinity, additional knowledge of binding kinetics is useful for developing and selecting new hA3R agonists in the early phase of the drug discovery process.
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Xia L, de Vries H, Lenselink EB, Louvel J, Waring MJ, Cheng L, Pahlén S, Petersson MJ, Schell P, Olsson RI, Heitman LH, Sheppard RJ, IJzerman AP. Structure-Affinity Relationships and Structure-Kinetic Relationships of 1,2-Diarylimidazol-4-carboxamide Derivatives as Human Cannabinoid 1 Receptor Antagonists. J Med Chem 2017; 60:9545-9564. [PMID: 29111736 PMCID: PMC5734604 DOI: 10.1021/acs.jmedchem.7b00861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
We
report on the synthesis and biological evaluation of a series of 1,2-diarylimidazol-4-carboxamide
derivatives developed as CB1 receptor antagonists. These
were evaluated in a radioligand displacement binding assay, a [35S]GTPγS binding assay, and in a competition association
assay that enables the relatively fast kinetic screening of multiple
compounds. The compounds show high affinities and a diverse range
of kinetic profiles at the CB1 receptor and their structure–kinetic
relationships (SKRs) were established. Using the recently resolved
hCB1 receptor crystal structures, we also performed a modeling
study that sheds light on the crucial interactions for both the affinity
and dissociation kinetics of this family of ligands. We provide evidence
that, next to affinity, additional knowledge of binding kinetics is
useful for selecting new hCB1 receptor antagonists in the
early phases of drug discovery.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Julien Louvel
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | | | | | - Sara Pahlén
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca , Gothenburg SE-431 83, Sweden
| | - Maria J Petersson
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca , Gothenburg SE-431 83, Sweden
| | | | | | - Laura H Heitman
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Robert J Sheppard
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge SK10 2NA, United Kingdom
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
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25
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Xia L, de Vries H, Yang X, Lenselink EB, Kyrizaki A, Barth F, Louvel J, Dreyer MK, van der Es D, IJzerman AP, Heitman LH. Kinetics of human cannabinoid 1 (CB1) receptor antagonists: Structure-kinetics relationships (SKR) and implications for insurmountable antagonism. Biochem Pharmacol 2017; 151:166-179. [PMID: 29102677 DOI: 10.1016/j.bcp.2017.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
While equilibrium binding affinities and in vitro functional antagonism of CB1 receptor antagonists have been studied in detail, little is known on the kinetics of their receptor interaction. In this study, we therefore conducted kinetic assays for nine 1-(4,5-diarylthiophene-2-carbonyl)-4-phenylpiperidine-4-carboxamide derivatives and included the CB1 antagonist rimonabant as a comparison. For this we newly developed a dual-point competition association assay with [3H]CP55940 as the radioligand. This assay yielded Kinetic Rate Index (KRI) values from which structure-kinetics relationships (SKR) of hCB1 receptor antagonists could be established. The fast dissociating antagonist 6 had a similar receptor residence time (RT) as rimonabant, i.e. 19 and 14 min, respectively, while the slowest dissociating antagonist (9) had a very long RT of 2222 min, i.e. pseudo-irreversible dissociation kinetics. In functional assays, 9 displayed insurmountable antagonism, while the effects of the shortest RT antagonist 6 and rimonabant were surmountable. Taken together, this study shows that hCB1 receptor antagonists can have very divergent RTs, which are not correlated to their equilibrium affinities. Furthermore, their RTs appear to define their mode of functional antagonism, i.e. surmountable vs. insurmountable. Finally, based on the recently resolved hCB1 receptor crystal structure, we propose that the differences in RT can be explained by a different binding mode of antagonist 9 from short RT antagonists that is able to displace unfavorable water molecules. Taken together, these findings are of importance for future design and evaluation of potent and safe hCB1 receptor antagonists.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Xue Yang
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Athina Kyrizaki
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Francis Barth
- Sanofi-Aventis Research and Development, 371, Rue du Professeur Blayac, 34184 Montpellier Cedex 04, France
| | - Julien Louvel
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Matthias K Dreyer
- Sanofi-Aventis Deutschland GmbH R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt, Germany
| | - Daan van der Es
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands.
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26
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Nederpelt I, Kuzikov M, de Witte WEA, Schnider P, Tuijt B, Gul S, IJzerman AP, de Lange ECM, Heitman LH. From receptor binding kinetics to signal transduction; a missing link in predicting in vivo drug-action. Sci Rep 2017; 7:14169. [PMID: 29075004 PMCID: PMC5658448 DOI: 10.1038/s41598-017-14257-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/09/2017] [Indexed: 11/12/2022] Open
Abstract
An important question in drug discovery is how to overcome the significant challenge of high drug attrition rates due to lack of efficacy and safety. A missing link in the understanding of determinants for drug efficacy is the relation between drug-target binding kinetics and signal transduction, particularly in the physiological context of (multiple) endogenous ligands. We hypothesized that the kinetic binding parameters of both drug and endogenous ligand play a crucial role in determining cellular responses, using the NK1 receptor as a model system. We demonstrated that the binding kinetics of both antagonists (DFA and aprepitant) and endogenous agonists (NKA and SP) have significantly different effects on signal transduction profiles, i.e. potency values, in vitro efficacy values and onset rate of signal transduction. The antagonistic effects were most efficacious with slowly dissociating aprepitant and slowly associating NKA while the combination of rapidly dissociating DFA and rapidly associating SP had less significant effects on the signal transduction profiles. These results were consistent throughout different kinetic assays and cellular backgrounds. We conclude that knowledge of the relationship between in vitro drug-target binding kinetics and cellular responses is important to ultimately improve the understanding of drug efficacy in vivo.
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Affiliation(s)
- Indira Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Maria Kuzikov
- Fraunhofer IME Screening Port, Schnackenburgallee 114, D-22525, Hamburg, Germany
| | - Wilbert E A de Witte
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Patrick Schnider
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Bruno Tuijt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Sheraz Gul
- Fraunhofer IME Screening Port, Schnackenburgallee 114, D-22525, Hamburg, Germany
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Elizabeth C M de Lange
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
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27
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Xia L, Burger WAC, van Veldhoven JPD, Kuiper BJ, van Duijl TT, Lenselink EB, Paasman E, Heitman LH, IJzerman AP. Structure-Affinity Relationships and Structure-Kinetics Relationships of Pyrido[2,1-f]purine-2,4-dione Derivatives as Human Adenosine A 3 Receptor Antagonists. J Med Chem 2017; 60:7555-7568. [PMID: 28806076 PMCID: PMC5601358 DOI: 10.1021/acs.jmedchem.7b00950] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
We
expanded on a series of pyrido[2,1-f]purine-2,4-dione
derivatives as human adenosine A3 receptor (hA3R) antagonists to determine their kinetic profiles and affinities.
Many compounds showed high affinities and a diverse range of kinetic
profiles. We found hA3R antagonists with very short residence
time (RT) at the receptor (2.2 min for 5) and much longer
RTs (e.g., 376 min for 27 or 391 min for 31). Two representative antagonists (5 and 27) were tested in [35S]GTPγS binding assays, and
their RTs appeared correlated to their (in)surmountable antagonism.
From a kon–koff–KD kinetic map, we divided
the antagonists into three subgroups, providing a possible direction
for the further development of hA3R antagonists. Additionally,
we performed a computational modeling study that sheds light on the
crucial receptor interactions, dictating the compounds’ binding
kinetics. Knowledge of target binding kinetics appears useful for
developing and triaging new hA3R antagonists in the early
phase of drug discovery.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Wessel A C Burger
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Jacobus P D van Veldhoven
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Boaz J Kuiper
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Tirsa T van Duijl
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Ellen Paasman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
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28
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Abstract
Previously, drugs were developed focusing on target affinity and selectivity. However, it is becoming evident that the drug-target residence time, related to the off-rate, is an important parameter for successful drug development. The residence time influences both the on-rate and overall effectiveness of drugs. Furthermore, ligand binding is now appreciated to be a multistep process because metastable and/or intermediate binding sites in the extracellular region have been identified. In this review, we summarize experimental ligand-binding data for G-protein-coupled receptors (GPCRs), and their binding pathways, analyzed by molecular dynamics (MD). The kinetics of drug binding to GPCRs are complex and depend on several factors, including charge distribution on the receptor surface, ligand-receptor interactions in the binding channel and the binding site, or solvation.
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Affiliation(s)
- Andrea Strasser
- Department of Pharmaceutical/Medicinal Chemistry II, University of Regensburg, Regensburg, Germany.
| | | | - Roland Seifert
- Institute of Pharmacology, Hannover Medical School, Hannover, Germany
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29
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Schuetz DA, de Witte WEA, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Heitman LH, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, Hill S, Cooke RM, De Graaf C, Leurs R, Frech M, Wade RC, de Lange ECM, IJzerman AP, Müller-Fahrnow A, Ecker GF. Kinetics for Drug Discovery: an industry-driven effort to target drug residence time. Drug Discov Today 2017; 22:896-911. [PMID: 28412474 DOI: 10.1016/j.drudis.2017.02.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/24/2017] [Accepted: 02/17/2017] [Indexed: 01/05/2023]
Abstract
A considerable number of approved drugs show non-equilibrium binding characteristics, emphasizing the potential role of drug residence times for in vivo efficacy. Therefore, a detailed understanding of the kinetics of association and dissociation of a target-ligand complex might provide crucial insight into the molecular mechanism-of-action of a compound. This deeper understanding will help to improve decision making in drug discovery, thus leading to a better selection of interesting compounds to be profiled further. In this review, we highlight the contributions of the Kinetics for Drug Discovery (K4DD) Consortium, which targets major open questions related to binding kinetics in an industry-driven public-private partnership.
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Affiliation(s)
- Doris A Schuetz
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | | | - Yin Cheong Wong
- Division of Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bernhard Knasmueller
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Reggie Bosma
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Indira Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Elena Segala
- Heptares Therapeutics,Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Marta Amaral
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany; Instituto de Biologia Experimental e Tecnológica, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Dong Guo
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Dorothee Andres
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Victoria Georgi
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Leigh A Stoddart
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Steve Hill
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Robert M Cooke
- Heptares Therapeutics,Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Chris De Graaf
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Rob Leurs
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Matthias Frech
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Elizabeth Cunera Maria de Lange
- Division of Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Anke Müller-Fahrnow
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria.
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30
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Zeilinger M, Pichler F, Nics L, Wadsak W, Spreitzer H, Hacker M, Mitterhauser M. New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. EJNMMI Res 2017; 7:22. [PMID: 28271461 PMCID: PMC5340791 DOI: 10.1186/s13550-016-0249-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/15/2016] [Indexed: 12/02/2022] Open
Abstract
Background Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A3R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the Ki of eight different A3R antagonists, using CHO-K1 cells stably expressing the hA3R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants kon and koff, as well as the dedicated Kd of the A3R agonist [125I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Results Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A3R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Conclusions Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.
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Affiliation(s)
- Markus Zeilinger
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Faculty of Engineering, University of Applied Sciences Wiener Neustadt, Wiener Neustadt, Austria
| | - Florian Pichler
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Faculty of Engineering, University of Applied Sciences Wiener Neustadt, Wiener Neustadt, Austria
| | - Lukas Nics
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Wolfgang Wadsak
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Department of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Helmut Spreitzer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Marcus Hacker
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Markus Mitterhauser
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria. .,Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria. .,Ludwig Boltzmann Institute for Applied Diagnostics, Vienna, Austria.
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31
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Bot I, Ortiz Zacarías NV, de Witte WEA, de Vries H, van Santbrink PJ, van der Velden D, Kröner MJ, van der Berg DJ, Stamos D, de Lange ECM, Kuiper J, IJzerman AP, Heitman LH. A novel CCR2 antagonist inhibits atherogenesis in apoE deficient mice by achieving high receptor occupancy. Sci Rep 2017; 7:52. [PMID: 28246398 PMCID: PMC5427923 DOI: 10.1038/s41598-017-00104-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 02/06/2017] [Indexed: 12/21/2022] Open
Abstract
CC Chemokine Receptor 2 (CCR2) and its endogenous ligand CCL2 are involved in a number of diseases, including atherosclerosis. Several CCR2 antagonists have been developed as potential therapeutic agents, however their in vivo clinical efficacy was limited. In this report, we aimed to determine whether 15a, an antagonist with a long residence time on the human CCR2, is effective in inhibiting the development of atherosclerosis in a mouse disease model. First, radioligand binding assays were performed to determine affinity and binding kinetics of 15a on murine CCR2. To assess the in vivo efficacy, western-type diet fed apoE-/- mice were treated daily with 15a or vehicle as control. Treatment with 15a reduced the amount of circulating CCR2+ monocytes and the size of the atherosclerotic plaques in both the carotid artery and the aortic root. We then showed that the long pharmacokinetic half-life of 15a combined with the high drug concentrations ensured prolonged CCR2 occupancy. These data render 15a a promising compound for drug development and confirms high receptor occupancy as a key parameter when targeting chemokine receptors.
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Affiliation(s)
- Ilze Bot
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Natalia V Ortiz Zacarías
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Wilhelmus E A de Witte
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Peter J van Santbrink
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Daniël van der Velden
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Mara J Kröner
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Dirk-Jan van der Berg
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | | | - Elizabeth C M de Lange
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Johan Kuiper
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands.
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32
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Link R, Veiksina S, Rinken A, Kopanchuk S. Characterization of ligand binding to melanocortin 4 receptors using fluorescent peptides with improved kinetic properties. Eur J Pharmacol 2017; 799:58-66. [DOI: 10.1016/j.ejphar.2017.01.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 12/24/2022]
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Alachouzos G, Lenselink EB, Mulder-Krieger T, de Vries H, IJzerman AP, Louvel J. Synthesis and evaluation of N-substituted 2-amino-4,5-diarylpyrimidines as selective adenosine A1 receptor antagonists. Eur J Med Chem 2017; 125:586-602. [DOI: 10.1016/j.ejmech.2016.09.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/04/2016] [Accepted: 09/25/2016] [Indexed: 02/01/2023]
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Hothersall JD, Guo D, Sarda S, Sheppard RJ, Chen H, Keur W, Waring MJ, IJzerman AP, Hill SJ, Dale IL, Rawlins PB. Structure-Activity Relationships of the Sustained Effects of Adenosine A2A Receptor Agonists Driven by Slow Dissociation Kinetics. Mol Pharmacol 2016; 91:25-38. [PMID: 27803241 PMCID: PMC5198511 DOI: 10.1124/mol.116.105551] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/28/2016] [Indexed: 12/02/2022] Open
Abstract
The duration of action of adenosine A2A receptor (A2A) agonists is critical for their clinical efficacy, and we sought to better understand how this can be optimized. The in vitro temporal response profiles of a panel of A2A agonists were studied using cAMP assays in recombinantly (CHO) and endogenously (SH-SY5Y) expressing cells. Some agonists (e.g., 3cd; UK-432,097) but not others (e.g., 3ac; CGS-21680) demonstrated sustained wash-resistant agonism, where residual receptor activation continued after washout. The ability of an antagonist to reverse pre-established agonist responses was used as a surrogate read-out for agonist dissociation kinetics, and together with radioligand binding studies suggested a role for slow off-rate in driving sustained effects. One compound, 3ch, showed particularly marked sustained effects, with a reversal t1/2 > 6 hours and close to maximal effects that remained for at least 5 hours after washing. Based on the structure-activity relationship of these compounds, we suggest that lipophilic N6 and bulky C2 substituents can promote stable and long-lived binding events leading to sustained agonist responses, although a high compound logD is not necessary. This provides new insight into the binding interactions of these ligands and we anticipate that this information could facilitate the rational design of novel long-acting A2A agonists with improved clinical efficacy.
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Affiliation(s)
- J Daniel Hothersall
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Dong Guo
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Sunil Sarda
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Robert J Sheppard
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Hongming Chen
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Wesley Keur
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Michael J Waring
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Adriaan P IJzerman
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Stephen J Hill
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Ian L Dale
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Philip B Rawlins
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
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A new, simple and robust radioligand binding method used to determine kinetic off-rate constants for unlabeled ligands. Application at α 2A - and α 2C -adrenoceptors. Eur J Pharmacol 2016; 788:113-121. [DOI: 10.1016/j.ejphar.2016.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/12/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
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Costa B, Da Pozzo E, Cavallini C, Taliani S, Da Settimo F, Martini C. Long Residence Time at the Neurosteroidogenic 18 kDa Translocator Protein Characterizes the Anxiolytic Ligand XBD173. ACS Chem Neurosci 2016; 7:1041-6. [PMID: 27385308 DOI: 10.1021/acschemneuro.6b00149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Recent data have demonstrated a positive correlation between the residence time (RT) and neurosteroidogenic efficacy of a ligand at the translocator protein (TSPO), an attractive anxyolitic target. To explore the potential impact of RT on TSPO ligand anxiolytic activity, the RT and the steroidogenic activity of XBD173, a ligand exerting anxiolytic activity in humans, were retrospectively evaluated. To this aim, XBD173 association and dissociation rate constants were measured (1.23 × 10(7) M(-1) min(-1) and 0.0079 min(-1), respectively). XBD173 resulted to have a long RT (127 min) and to stimulate efficaciously neurosteroidogenesis, in terms of pregnenolone production. The present findings corroborate the importance of TSPO ligand RT to predict their effective neurosteroidogenic activity and promising anxiolytic action. These positive results prompted us to set up a fast and high-throughput kinetic method to improve the efficiency of RT-based TSPO drug-discovery process.
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Affiliation(s)
- Barbara Costa
- Department of Pharmacy, University of Pisa, via Bonanno, 6-56126 Pisa, Italy
| | - Eleonora Da Pozzo
- Department of Pharmacy, University of Pisa, via Bonanno, 6-56126 Pisa, Italy
| | - Chiara Cavallini
- Department of Pharmacy, University of Pisa, via Bonanno, 6-56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, via Bonanno, 6-56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, via Bonanno, 6-56126 Pisa, Italy
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, via Bonanno, 6-56126 Pisa, Italy
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Shimizu Y, Ogawa K, Nakayama M. Characterization of Kinetic Binding Properties of Unlabeled Ligands via a Preincubation Endpoint Binding Approach. ACTA ACUST UNITED AC 2016; 21:729-37. [PMID: 27270099 DOI: 10.1177/1087057116652065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022]
Abstract
The dissociation rates of unlabeled drugs have been well studied by kinetic binding analyses. Since kinetic assays are laborious, we developed a simple method to determine the kinetic binding parameters of unlabeled competitors by a preincubation endpoint assay. The probe binding after preincubation of a competitor can be described by a single equation as a function of time. Simulations using the equation revealed the degree of IC50 change induced by preincubation of a competitor depended on the dissociation rate koff of the competitor but not on the association rate kon To validate the model, an in vitro binding assay was performed using a smoothened receptor (SMO) and [(3)H]TAK-441, a SMO antagonist. The equilibrium dissociation constants (KI) and koff of SMO antagonists determined by globally fitting the model to the concentration-response curves obtained with and without 24 h preincubation correlated well with those determined by other methods. This approach could be useful for early-stage optimization of drug candidates by enabling determination of binding kinetics in a high-throughput manner because it does not require kinetic measurements, an intermediate washout step during the reaction, or prior determination of competitors' KI values.
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Affiliation(s)
- Yuji Shimizu
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Kazumasa Ogawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Masaharu Nakayama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
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Ferruz N, De Fabritiis G. Binding Kinetics in Drug Discovery. Mol Inform 2016; 35:216-26. [PMID: 27492236 DOI: 10.1002/minf.201501018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/20/2016] [Indexed: 12/19/2022]
Abstract
Over the last years, researchers have increasingly become interested in measuring and understanding drugs' binding kinetics, namely the time in which drug and its target associate and dissociate. Historically, drug discovery programs focused on the optimization of target affinity as a proxy of in-vivo efficacy. However, often the efficacy of a ligand is not appropriately described by the in-vitro measured drug-receptor affinity, but rather depends on the lifetime of the in-vivo drug-receptor interaction. In this review we review recent works that highlight the importance of binding kinetics, molecular determinants for rational optimization and the recent emergence of computational methods as powerful tools in measuring and understanding binding kinetics.
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Affiliation(s)
- Noelia Ferruz
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain.,Acellera, Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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Guo D, Heitman LH, IJzerman AP. Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors. Chem Rev 2016; 117:38-66. [DOI: 10.1021/acs.chemrev.6b00025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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40
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Equilibrium and kinetic selectivity profiling on the human adenosine receptors. Biochem Pharmacol 2016; 105:34-41. [DOI: 10.1016/j.bcp.2016.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 11/23/2022]
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41
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Swinney ZT, Haubrich BA, Xia S, Ramesha C, Gomez SR, Guyett P, Mensa-Wilmot K, Swinney DC. A Four-Point Screening Method for Assessing Molecular Mechanism of Action (MMOA) Identifies Tideglusib as a Time-Dependent Inhibitor of Trypanosoma brucei GSK3β. PLoS Negl Trop Dis 2016; 10:e0004506. [PMID: 26942720 PMCID: PMC4778863 DOI: 10.1371/journal.pntd.0004506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/10/2016] [Indexed: 01/01/2023] Open
Abstract
Background New therapeutics are needed for neglected tropical diseases including Human African trypanosomiasis (HAT), a progressive and fatal disease caused by the protozoan parasites Trypanosoma brucei gambiense and T. b. rhodesiense. There is a need for simple, efficient, cost effective methods to identify new molecules with unique molecular mechanisms of action (MMOAs). The mechanistic features of a binding mode, such as competition with endogenous substrates and time-dependence can affect the observed inhibitory IC50, and differentiate molecules and their therapeutic usefulness. Simple screening methods to determine time-dependence and competition can be used to differentiate compounds with different MMOAs in order to identify new therapeutic opportunities. Methodology/Principal Findings In this work we report a four point screening methodology to evaluate the time-dependence and competition for inhibition of GSK3β protein kinase isolated from T. brucei. Using this method, we identified tideglusib as a time-dependent inhibitor whose mechanism of action is time-dependent, ATP competitive upon initial binding, which transitions to ATP non-competitive with time. The enzyme activity was not recovered following 100-fold dilution of the buffer consistent with an irreversible mechanism of action. This is in contrast to the T. brucei GSK3β inhibitor GW8510, whose inhibition was competitive with ATP, not time-dependent at all measured time points and reversible in dilution experiments. The activity of tideglusib against T. brucei parasites was confirmed by inhibition of parasite proliferation (GI50 of 2.3 μM). Conclusions/Significance Altogether this work demonstrates a straightforward method for determining molecular mechanisms of action and its application for mechanistic differentiation of two potent TbGSK3β inhibitors. The four point MMOA method identified tideglusib as a mechanistically differentiated TbGSK3β inhibitor. Tideglusib was shown to inhibit parasite growth in this work, and has been reported to be well tolerated in one year of dosing in human clinical studies. Consequently, further supportive studies on the potential therapeutic usefulness of tideglusib for HAT are justified. Drug discovery for neglected tropical diseases must use efficient methods due to limited resources. One preferred drug discovery strategy is target-based drug discovery. In this strategy it is assumed that drug action begins with binding of a drug to its target. However, while binding is required, it is not sufficient to describe all the molecular interactions that translate binding to a therapeutically useful response. The contribution of aspects of the molecular mechanism of action (MMOA) such as time-dependence and substrate competition can influence concentration response relationships. To address this, a four point MMOA methodology was developed to evaluate time-dependence and substrate competition. We used this method to evaluate the MMOA for T.brucei GSK3β inhibitors, and observed tideglusib to have a time-dependent, ATP-competitive mechanism that differentiated it from rapidly reversible inhibitors, such as GW8510. Adjusting the enzyme assays to account for these mechanisms showed that GW8510 and tideglusib had similar activities for TbGSK3β. However, this similarity did not translate to cellular activity, where GW-8510 was more active than tideglusib (0.12 μM to 2.3 μM, respectively). These data suggest that factors other than TbGSK3β MMOA differentiate the effect of these molecules against T. brucei.
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Affiliation(s)
- Zachary T. Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Brad A. Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Shuangluo Xia
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Chakk Ramesha
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Stephen R. Gomez
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Paul Guyett
- Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Kojo Mensa-Wilmot
- Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - David C. Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
- * E-mail:
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Xia L, de Vries H, IJzerman AP, Heitman LH. Scintillation proximity assay (SPA) as a new approach to determine a ligand's kinetic profile. A case in point for the adenosine A1 receptor. Purinergic Signal 2015; 12:115-26. [PMID: 26647040 PMCID: PMC4749533 DOI: 10.1007/s11302-015-9485-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/19/2015] [Indexed: 01/11/2023] Open
Abstract
Scintillation proximity assay (SPA) is a radio-isotopic technology format used to measure a wide range of biological interactions, including drug-target binding affinity studies. The assay is homogeneous in nature, as it relies on a “mix and measure” format. It does not involve a filtration step to separate bound from free ligand as is the case in a traditional receptor-binding assay. For G protein-coupled receptors (GPCRs), it has been shown that optimal binding kinetics, next to a high affinity of a ligand, can result in more desirable pharmacological profiles. However, traditional techniques to assess kinetic parameters tend to be cumbersome and laborious. We thus aimed to evaluate whether SPA can be an alternative platform for real-time receptor-binding kinetic measurements on GPCRs. To do so, we first validated the SPA technology for equilibrium binding studies on a prototypic class A GPCR, the human adenosine A1 receptor (hA1R). Differently to classic kinetic studies, the SPA technology allowed us to study binding kinetic processes almost real time, which is impossible in the filtration assay. To demonstrate the reliability of this technology for kinetic purposes, we performed the so-called competition association experiments. The association and dissociation rate constants (kon and koff) of unlabeled hA1R ligands were reliably and quickly determined and agreed very well with the same parameters from a traditional filtration assay performed simultaneously. In conclusion, SPA is a very promising technique to determine the kinetic profile of the drug-target interaction. Its robustness and potential for high-throughput may render this technology a preferred choice for further kinetic studies.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Ad P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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de Witte WEA, Wong YC, Nederpelt I, Heitman LH, Danhof M, van der Graaf PH, Gilissen RAHJ, de Lange ECM. Mechanistic models enable the rational use of in vitro drug-target binding kinetics for better drug effects in patients. Expert Opin Drug Discov 2015; 11:45-63. [PMID: 26484747 DOI: 10.1517/17460441.2016.1100163] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Drug-target binding kinetics are major determinants of the time course of drug action for several drugs, as clearly described for the irreversible binders omeprazole and aspirin. This supports the increasing interest to incorporate newly developed high-throughput assays for drug-target binding kinetics in drug discovery. A meaningful application of in vitro drug-target binding kinetics in drug discovery requires insight into the relation between in vivo drug effect and in vitro measured drug-target binding kinetics. AREAS COVERED In this review, the authors discuss both the relation between in vitro and in vivo measured binding kinetics and the relation between in vivo binding kinetics, target occupancy and effect profiles. EXPERT OPINION More scientific evidence is required for the rational selection and development of drug-candidates on the basis of in vitro estimates of drug-target binding kinetics. To elucidate the value of in vitro binding kinetics measurements, it is necessary to obtain information on system-specific properties which influence the kinetics of target occupancy and drug effect. Mathematical integration of this information enables the identification of drug-specific properties which lead to optimal target occupancy and drug effect in patients.
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Affiliation(s)
- Wilhelmus E A de Witte
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
| | - Yin Cheong Wong
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
| | - Indira Nederpelt
- b Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
| | - Laura H Heitman
- b Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
| | - Meindert Danhof
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
| | - Piet H van der Graaf
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
| | - Ron A H J Gilissen
- c A Division of Janssen Pharmaceutica N.V., Janssen Research and Development , Turnhoutseweg 30, Beerse 2340 , Belgium
| | - Elizabeth C M de Lange
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Einsteinweg 55, 2333 CC Leiden , The Netherlands
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Massink A, Holzheimer M, Hölscher A, Louvel J, Guo D, Spijksma G, Hankemeier T, IJzerman AP. Mass spectrometry-based ligand binding assays on adenosine A1 and A2A receptors. Purinergic Signal 2015; 11:581-94. [PMID: 26482925 PMCID: PMC4648803 DOI: 10.1007/s11302-015-9477-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/02/2015] [Indexed: 12/01/2022] Open
Abstract
Conventional methods to measure ligand-receptor binding parameters typically require radiolabeled ligands as probes. Despite the robustness of radioligand binding assays, they carry inherent disadvantages in terms of safety precautions, expensive synthesis, special lab requirements, and waste disposal. Mass spectrometry (MS) is a method that can selectively detect ligands without the need of a label. The sensitivity of MS equipment increases progressively, and currently, it is possible to detect low ligand quantities that are usually found in ligand binding assays. We developed a label-free MS ligand binding (MS binding) assay on the adenosine A1 and A2A receptors (A1AR and A2AAR), which are well-characterized members of the class A G protein-coupled receptor (GPCR) family. Radioligand binding assays for both receptors are well established, and ample data is available to compare and evaluate the performance of an MS binding assay. 1,3-Dipropyl-8-cyclopentyl-xanthine (DPCPX) and 4-(2-((7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a]-[1,3,5]triazin-5-yl)amino)ethyl)phenol (ZM-241,385) are high-affinity ligands selective for the A1AR and A2AAR, respectively. To proof the feasibility of MS binding on the A1AR and A2AAR, we first developed an MS detection method for unlabeled DPCPX and ZM-241,385. To serve as internal standards, both compounds were also deuterium-labeled. Subsequently, we investigated whether the two unlabeled compounds could substitute for their radiolabeled counterparts as marker ligands in binding experiments, including saturation, displacement, dissociation, and competition association assays. Furthermore, we investigated the accuracy of these assays if the use of internal standards was excluded. The results demonstrate the feasibility of the MS binding assay, even in the absence of a deuterium-labeled internal standard, and provide great promise for the further development of label-free assays based on MS for other GPCRs.
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Affiliation(s)
- A Massink
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - M Holzheimer
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - A Hölscher
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - J Louvel
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - D Guo
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - G Spijksma
- Division of Analytical Biosciences, LACDR, Leiden University, Leiden, The Netherlands
| | - T Hankemeier
- Division of Analytical Biosciences, LACDR, Leiden University, Leiden, The Netherlands
| | - A P IJzerman
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands. .,Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
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Vauquelin G, Van Liefde I, Swinney DC. Radioligand binding to intact cells as a tool for extended drug screening in a representative physiological context. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 17:28-34. [PMID: 26724334 DOI: 10.1016/j.ddtec.2015.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Radioligand binding assays on intact cells offer distinct advantages to those on membrane suspensions. Major pharmacological properties like drug affinity and binding kinetics are more physiologically relevant. Complex mechanisms can be studied with a wider choice of experimental approaches and so provide insights into induced-fit type binding, receptor internalisation and even into pharmacomicrokinetic phenomena like drug rebinding and partitioning into the membrane. Hence, intact cell binding constitutes a valuable addition to the pharmacologist's toolbox.
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Affiliation(s)
- Georges Vauquelin
- Dept. of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Isabelle Van Liefde
- Dept. of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - David C Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, 897 Independence Ave, Suite 2C, Mountain View, CA 94043, United States
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Pompeu TET, Monteiro do Monte F, Bosier B, Fraga CAM, Barreiro EJ, Menegatti R, Hermans E, Noël F. Partial agonism and fast dissociation of LASSBio-579 at dopamine D2 receptor. Prog Neuropsychopharmacol Biol Psychiatry 2015; 62:1-6. [PMID: 25891249 DOI: 10.1016/j.pnpbp.2015.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/30/2015] [Accepted: 04/11/2015] [Indexed: 01/09/2023]
Abstract
In an attempt to better understand the molecular mechanism of action of the antipsychotic lead LASSBio-579 and of its main metabolite LQFM 037, the aim of this work was to evaluate their intrinsic activity and binding kinetics at the dopamine D2 receptor. In transfected HEK cells expressing the D2L receptor under an inducible promoter, LASSBio-579 and LQFM 037, but not clozapine, behaved as weak partial agonists in [(35)S]-GTPγS binding assays performed in optimized conditions previously shown to evidence the partial agonist profile of aripiprazole. Besides, data obtained in radioligand competition assays on rat striatal membranes suggested a rapid association to and dissociation from the D2-like receptors. Using the kinetic rate index based on the strategy of the dual-point competition association assay, we showed that our compounds share a similar kinetic profile with clozapine, distinct from the typical antipsychotic haloperidol. These two characteristics could contribute to the atypical-like profile observed after administration of LASSBio-579 to rodents, in models of positive and negative symptoms of schizophrenia.
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Affiliation(s)
- Thais Emanoelle T Pompeu
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala J1-17, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala K2-27, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Fernando Monteiro do Monte
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala J1-17, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala K2-27, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Barbara Bosier
- Institute of Neuroscience (IoNS), Group of Neuropharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Carlos A M Fraga
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala K2-27, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil; Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Bloco Bss 022, CEP 21944-971 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Eliezer J Barreiro
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala K2-27, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil; Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Bloco Bss 022, CEP 21944-971 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Ricardo Menegatti
- Laboratório de Bioconversão, LabMol and Laboratório de Química Farmacêutica, Medicinal, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Emmanuel Hermans
- Institute of Neuroscience (IoNS), Group of Neuropharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - François Noël
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala J1-17, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Sala K2-27, CEP 21941-912 Ilha do Fundão, Rio de Janeiro, Brazil.
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Guo D, IJzerman AP, Heitman LH. Importance of Drug-Target Residence Time at G Protein-Coupled Receptors - a Case for the Adenosine Receptors. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Vauquelin G, Huber W, Swinney DC. Experimental Methods to Determine Binding Kinetics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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49
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Louvel J, Guo D, Soethoudt M, Mocking TA, Lenselink EB, Mulder-Krieger T, Heitman LH, IJzerman AP. Structure-kinetics relationships of Capadenoson derivatives as adenosine A 1 receptor agonists. Eur J Med Chem 2015. [DOI: 10.1016/j.ejmech.2015.07.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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50
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van Veldhoven JPD, Liu R, Thee SA, Wouters Y, Verhoork SJM, Mooiman C, Louvel J, IJzerman AP. Affinity and kinetics study of anthranilic acids as HCA2 receptor agonists. Bioorg Med Chem 2015; 23:4013-25. [PMID: 25737085 DOI: 10.1016/j.bmc.2015.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/05/2015] [Accepted: 02/10/2015] [Indexed: 12/25/2022]
Abstract
Structure-affinity relationship (SAR) and structure-kinetics relationship (SKR) studies were combined to investigate a series of biphenyl anthranilic acid agonists for the HCA2 receptor. In total, 27 compounds were synthesized and twelve of them showed higher affinity than nicotinic acid. Two compounds, 6g (IC50=75nM) and 6z (IC50=108nM) showed a longer residence time profile compared to nicotinic acid, exemplified by their kinetic rate index (KRI) values of 1.31 and 1.23, respectively. The SAR study resulted in the novel 2-F, 4-OH derivative (6x) with an IC50 value of 23nM as the highest affinity HCA2 agonist of the biphenyl series, although it showed a similar residence time as nicotinic acid. The SAR and SKR data suggest that an early compound selection based on binding kinetics is a promising addition to the lead optimization process.
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Affiliation(s)
- Jacobus P D van Veldhoven
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Rongfang Liu
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Stephanie A Thee
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Yessica Wouters
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Sanne J M Verhoork
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Christiaan Mooiman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Julien Louvel
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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