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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024; 23:626-644. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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2
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Servant G, Kenakin T. A Pharmacological perspective on the temporal properties of sweeteners. Pharmacol Res 2024; 204:107211. [PMID: 38744400 DOI: 10.1016/j.phrs.2024.107211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Several non-caloric sweeteners exhibit a delay in sweetness onset and a sweetness linger after sampling. These temporal properties are thought to be the result of non-specific interactions with cell membranes and proteins in the oral cavity. Data and analysis presented in this report also support the potential involvement of receptor affinity and binding kinetics to this phenomenon. In general, affected sweeteners exhibit distinctly higher binding affinity compared to carbohydrate sweeteners, which do not have temporal issues. In addition, binding kinetic simulations illustrate much slower receptor binding association and dissociation kinetics for a set of non-caloric sweeteners presenting temporal issues, in comparison to carbohydrate sweeteners. So, the higher affinity of some non-caloric sweeteners, dictating lower use levels, and affecting binding kinetics, could contribute to their delay and linger in sweetness perception. Simple pharmacology principles could explain, at least in part, some of the temporal issues of sweeteners.
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Affiliation(s)
- Guy Servant
- dsm-firmenich, 10636 Scripps Summit Court #201, San Diego, CA 92131, USA.
| | - Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, 120 Mason Farm Rd., 4042 Genetic Medicine CB #7365, Chapel Hill, NC 27599, USA
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3
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Scott-Dennis M, Rafani FA, Yi Y, Perera T, Harwood CR, Guba W, Rufer AC, Grether U, Veprintsev DB, Sykes DA. Development of a membrane-based Gi-CASE biosensor assay for profiling compounds at cannabinoid receptors. Front Pharmacol 2023; 14:1158091. [PMID: 37637423 PMCID: PMC10450933 DOI: 10.3389/fphar.2023.1158091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/05/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction: The cannabinoid receptor (CBR) subtypes 1 (CB1R) and 2 (CB2R) are key components of the endocannabinoid system (ECS), playing a central role in the control of peripheral pain, inflammation and the immune response, with further roles in the endocrine regulation of food intake and energy balance. So far, few medicines targeting these receptors have reached the clinic, suggesting that a better understanding of the receptor signalling properties of existing tool compounds and clinical candidates may open the door to the development of more effective and safer treatments. Both CB1R and CB2R are Gαi protein-coupled receptors but detecting Gαi protein signalling activity reliably and reproducibly is challenging. This is due to the inherent variability in live cell-based assays and restrictions around the use of radioactive [35S]-GTPγS, a favoured technology for developing higher-throughput membrane-based Gαi protein activity assays. Methods: Here, we describe the development of a membrane-based Gαi signalling system, produced from membrane preparations of HEK293TR cells, stably overexpressing CB1R or CB2R, and components of the Gαi-CASE biosensor. This BRET-based system allows direct detection of Gαi signalling in both cells and membranes by monitoring bioluminescence resonance energy transfer (BRET) between the α and the βγ subunits. Cells and membranes were subject to increasing concentrations of reference cannabinoid compounds, with 10 μM furimazine added to generate RET signals, which were detected on a PHERAstar FSX plate reader, then processed using MARS software and analysed in GraphPad PRISM 9.2. Results: In membranes expressing the Gi-CASE biosensor, the cannabinoid ligands profiled were found to show agonist and inverse agonist activity. Agonist activity elicited a decrease in the BRET signal, indicative of receptor activation and G protein dissociation. Inverse agonist activity caused an increase in BRET signal, indicative of receptor inactivation, and the accumulation of inactive G protein. Our membrane-based Gi-CASE NanoBRET system successfully characterised the potency (pEC50) and efficacy (Emax) of CBR agonists and inverse agonists in a 384-well screening format. Values obtained were in-line with whole-cell Gi-CASE assays and consistent with literature values obtained in the GTPγS screening format. Discussion: This novel, membrane-based Gαi protein activation assay is applicable to other Gαi-coupled GPCRs, including orphan receptors, allowing real-time higher-throughput measurements of receptor activation.
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Affiliation(s)
- Morgan Scott-Dennis
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Fikri A. Rafani
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Yicheng Yi
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Themiya Perera
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Clare R. Harwood
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Wolfgang Guba
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Arne C. Rufer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Uwe Grether
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Dmitry B. Veprintsev
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
- Z7 Biotech Limited, London, United Kingdom
| | - David A. Sykes
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
- Z7 Biotech Limited, London, United Kingdom
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4
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Indurthi DC, Auerbach A. Agonist efficiency links binding and gating in a nicotinic receptor. eLife 2023; 12:e86496. [PMID: 37399234 DOI: 10.7554/elife.86496] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023] Open
Abstract
Receptors signal by switching between resting (C) and active (O) shapes ('gating') under the influence of agonists. The receptor's maximum response depends on the difference in agonist binding energy, O minus C. In nicotinic receptors, efficiency (η) represents the fraction of agonist binding energy applied to a local rearrangement (an induced fit) that initiates gating. In this receptor, free energy changes in gating and binding can be interchanged by the conversion factor η. Efficiencies estimated from concentration-response curves (23 agonists, 53 mutations) sort into five discrete classes (%): 0.56 (17), 0.51(32), 0.45(13), 0.41(26), and 0.31(12), implying that there are 5 C versus O binding site structural pairs. Within each class efficacy and affinity are corelated linearly, but multiple classes hide this relationship. η unites agonist binding with receptor gating and calibrates one link in a chain of coupled domain rearrangements that comprises the allosteric transition of the protein.
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Affiliation(s)
- Dinesh C Indurthi
- Department of Physiology and Biophysics, University at Buffalo, State University of New York, Buffalo, United States
| | - Anthony Auerbach
- Department of Physiology and Biophysics, University at Buffalo, State University of New York, Buffalo, United States
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5
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Galvani F, Pala D, Cuzzolin A, Scalvini L, Lodola A, Mor M, Rizzi A. Unbinding Kinetics of Muscarinic M3 Receptor Antagonists Explained by Metadynamics Simulations. J Chem Inf Model 2023; 63:2842-2856. [PMID: 37053454 PMCID: PMC10170513 DOI: 10.1021/acs.jcim.3c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 04/15/2023]
Abstract
The residence time (RT), the time for which a drug remains bound to its biological target, is a critical parameter for drug design. The prediction of this key kinetic property has been proven to be challenging and computationally demanding in the framework of atomistic simulations. In the present work, we setup and applied two distinct metadynamics protocols to estimate the RTs of muscarinic M3 receptor antagonists. In the first method, derived from the conformational flooding approach, the kinetics of unbinding is retrieved from a physics-based parameter known as the acceleration factor α (i.e., the running average over time of the potential deposited in the bound state). Such an approach is expected to recover the absolute RT value for a compound of interest. In the second method, known as the tMETA-D approach, a qualitative estimation of the RT is given by the time of simulation required to drive the ligand from the binding site to the solvent bulk. This approach has been developed to reproduce the change of experimental RTs for compounds targeting the same target. Our analysis shows that both computational protocols are able to rank compounds in agreement with their experimental RTs. Quantitative structure-kinetics relationship (SKR) models can be identified and employed to predict the impact of a chemical modification on the experimental RT once a calibration study has been performed.
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Affiliation(s)
- Francesca Galvani
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Daniele Pala
- Chemistry
Research and Drug Design Department, Chiesi
Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Alberto Cuzzolin
- Chemistry
Research and Drug Design Department, Chiesi
Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Laura Scalvini
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Marco Mor
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
- Microbiome
Research Hub, University of Parma, Parco Area delle Scienze 11/A, I-43124 Parma, Italy
| | - Andrea Rizzi
- Chemistry
Research and Drug Design Department, Chiesi
Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
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6
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Fan H, Huang X, Zhang Z, Wang T, Wang L, Zhang Y. Immobilization of M3 Muscarinic Receptor to Rapidly Analyze Drug-Protein Interactions and Bioactive Components in a Natural Plant. Int J Mol Sci 2023; 24:ijms24087171. [PMID: 37108332 PMCID: PMC10139132 DOI: 10.3390/ijms24087171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Despite its increasing application in pursing potential ligands, the capacity of receptor affinity chromatography is greatly challenged as most current research studies lack a comprehensive characterization of the ligand-receptor interaction, particularly when simultaneously determining their binding thermodynamics and kinetics. This work developed an immobilized M3 muscarinic receptor (M3R) affinity column by fixing M3R on amino polystyrene microspheres via the interaction of a 6-chlorohexanoic acid linker with haloalkane dehalogenase. The efficiency of the immobilized M3R was tested by characterizing the binding thermodynamics and kinetics of three known drugs to immobilized M3R using a frontal analysis and the peak profiling method, as well as by analyzing the bioactive compounds in Daturae Flos (DF) extract. The data showed that the immobilized M3R demonstrated good specificity, stability, and competence for analyzing drug-protein interactions. The association constants of (-)-scopolamine hydrochloride, atropine sulfate, and pilocarpine to M3R were determined to be (2.39 ± 0.03) × 104, (3.71 ± 0.03) × 104, and (2.73 ± 0.04) × 104 M-1, respectively, with dissociation rate constants of 27.47 ± 0.65, 14.28 ± 0.17, and 10.70 ± 0.35 min-1, respectively. Hyoscyamine and scopolamine were verified as the bioactive compounds that bind to M3R in the DF extract. Our results suggest that the immobilized M3R method was capable of determining drug-protein binding parameters and probing specific ligands in a natural plant, thus enhancing the effectiveness of receptor affinity chromatography in diverse stages of drug discovery.
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Affiliation(s)
- Hushuai Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaomin Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ziru Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ting Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ludan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yajun Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
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7
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Allosteric binding cooperativity in a kinetic context. Drug Discov Today 2023; 28:103441. [PMID: 36372329 DOI: 10.1016/j.drudis.2022.103441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Allosteric modulators are of prime interest in drug discovery. These drugs regulate the binding and function of endogenous ligands, with some advantages over orthosteric ligands. A typical pharmacological parameter in allosteric modulation is binding cooperativity. This property can yield unexpected but illuminating results when decomposed into its kinetic parameters. Using two reference models (the allosteric ternary complex receptor model and a heterodimer receptor model), a relationship has been derived for the cooperativity rate constant parameters. This relationship allows many combinations of the cooperativity kinetic parameters for a single binding cooperativity value obtained under equilibrium conditions. This assessment may help understand striking experimental results involving allosteric modulation and suggest further investigations in the field.
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8
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Zhang H, Yan W, Sun Y, Yuan H, Su L, Cao X, Wang P, Xu Z, Hu Y, Wang Z, Wang Y, Fu K, Sun Y, Chen Y, Cheng J, Guo D. Long Residence Time at the Vasopressin V 2 Receptor Translates into Superior Inhibitory Effects in Ex Vivo and In Vivo Models of Autosomal Dominant Polycystic Kidney Disease. J Med Chem 2022; 65:7717-7728. [PMID: 35363466 DOI: 10.1021/acs.jmedchem.2c00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Prevailing strategies directing early-phase drug discovery heavily rely on equilibrium-based metrics such as affinity, which overlooks the kinetic process of a drug molecule interacting with its target. Herein, we developed a number of vasopressin V2 receptor (V2R) antagonists with divergent binding affinities and kinetics for autosomal dominant polycystic kidney disease (ADPKD). Surprisingly, the residence time of the V2R antagonists, but not their affinity, was correlated with the efficacy in both ex vivo and in vivo models of ADPKD. We envision that the kinetics-directed drug candidate selection and development may have general applicability for ADPKD and other therapeutic areas as well.
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Affiliation(s)
- Haoran Zhang
- 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
| | - Yongzhan Sun
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Tianjin Medical University, Tianjin 300070, China
| | - Haoxing Yuan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Limin Su
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Xudong Cao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Peng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Zhou Xu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Youhui Hu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Zhongjian Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Yinan Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Kequan Fu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Ying Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Yupeng Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Tianjin Medical University, Tianjin 300070, China
| | - Jianjun Cheng
- iHuman Institute, 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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9
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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: 70] [Impact Index Per Article: 35.0] [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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10
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Potterton A, Heifetz A, Townsend-Nicholson A. Predicting Residence Time of GPCR Ligands with Machine Learning. Methods Mol Biol 2022; 2390:191-205. [PMID: 34731470 DOI: 10.1007/978-1-0716-1787-8_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Drug-target residence time, the duration of binding at a given protein target, has been shown in some protein families to be more significant for conferring efficacy than binding affinity. To carry out efficient optimization of residence time in drug discovery, machine learning models that can predict that value need to be developed. One of the main challenges with predicting residence time is the paucity of data. This chapter outlines all of the currently available ligand kinetic data, providing a repository that contains the largest publicly available source of GPCR-ligand kinetic data to date. To help decipher the features of kinetic data that might be beneficial to include in computational models for the prediction of residence time, the experimental evidence for properties that influence residence time are summarized. Finally, two different workflows for predicting residence time with machine learning are outlined. The first is a single-target model trained on ligand features; the second is a multi-target model trained on features generated from molecular dynamics simulations.
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Affiliation(s)
- Andrew Potterton
- Structural and Molecular Biology, University College London, London, UK
- Evotec (U.K.) Ltd., Abingdon, Oxfordshire, UK
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11
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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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12
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Glaser T, Shimojo H, Ribeiro DE, Martins PPL, Beco RP, Kosinski M, Sampaio VFA, Corrêa-Velloso J, Oliveira-Giacomelli Á, Lameu C, de Jesus Santos AP, de Souza HDN, Teng YD, Kageyama R, Ulrich H. ATP and spontaneous calcium oscillations control neural stem cell fate determination in Huntington's disease: a novel approach for cell clock research. Mol Psychiatry 2021; 26:2633-2650. [PMID: 32350390 DOI: 10.1038/s41380-020-0717-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/12/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
Calcium, the most versatile second messenger, regulates essential biology including crucial cellular events in embryogenesis. We investigated impacts of calcium channels and purinoceptors on neuronal differentiation of normal mouse embryonic stem cells (ESCs), with outcomes being compared to those of in vitro models of Huntington's disease (HD). Intracellular calcium oscillations tracked via real-time fluorescence and luminescence microscopy revealed a significant correlation between calcium transient activity and rhythmic proneuronal transcription factor expression in ESCs stably expressing ASCL-1 or neurogenin-2 promoters fused to luciferase reporter genes. We uncovered that pharmacological manipulation of L-type voltage-gated calcium channels (VGCCs) and purinoceptors induced a two-step process of neuronal differentiation. Specifically, L-type calcium channel-mediated augmentation of spike-like calcium oscillations first promoted stable expression of ASCL-1 in differentiating ESCs, which following P2Y2 purinoceptor activation matured into GABAergic neurons. By contrast, there was neither spike-like calcium oscillations nor responsive P2Y2 receptors in HD-modeling stem cells in vitro. The data shed new light on mechanisms underlying neurogenesis of inhibitory neurons. Moreover, our approach may be tailored to identify pathogenic triggers of other developmental neurological disorders for devising targeted therapies.
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Affiliation(s)
- Talita Glaser
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Hiromi Shimojo
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Deidiane Elisa Ribeiro
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Renata Pereira Beco
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Michal Kosinski
- Departments of Physical Medicine & Rehabilitation and Neurosurgery, Harvard Medical School, Spaulding Rehabilitation Hospital and Brigham and Women's Hospital, Boston, MA, USA.,Translative Plataform for Regenerative Medicine, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | | | - Juliana Corrêa-Velloso
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Claudiana Lameu
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | | | | | - Yang D Teng
- Departments of Physical Medicine & Rehabilitation and Neurosurgery, Harvard Medical School, Spaulding Rehabilitation Hospital and Brigham and Women's Hospital, Boston, MA, USA
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil.
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13
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Pettmann J, Huhn A, Abu Shah E, Kutuzov MA, Wilson DB, Dustin ML, Davis SJ, van der Merwe PA, Dushek O. The discriminatory power of the T cell receptor. eLife 2021; 10:e67092. [PMID: 34030769 PMCID: PMC8219380 DOI: 10.7554/elife.67092] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/15/2021] [Indexed: 12/20/2022] Open
Abstract
T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity non-self peptides presented on major histocompatibility complex (pMHC) antigens. Although the discriminatory power of the TCR is widely believed to be near-perfect, technical difficulties have hampered efforts to precisely quantify it. Here, we describe a method for measuring very low TCR/pMHC affinities and use it to measure the discriminatory power of the TCR and the factors affecting it. We find that TCR discrimination, although enhanced compared with conventional cell-surface receptors, is imperfect: primary human T cells can respond to pMHC with affinities as low as KD ∼ 1 mM. The kinetic proofreading mechanism fit our data, providing the first estimates of both the time delay (2.8 s) and number of biochemical steps (2.67) that are consistent with the extraordinary sensitivity of antigen recognition. Our findings explain why self pMHC frequently induce autoimmune diseases and anti-tumour responses, and suggest ways to modify TCR discrimination.
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Affiliation(s)
- Johannes Pettmann
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
- Radcliffe Department of Medicine, Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Anna Huhn
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Enas Abu Shah
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
- Kennedy Institute of Rheumatology, University of OxfordOxfordUnited Kingdom
| | - Mikhail A Kutuzov
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Daniel B Wilson
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
- Boston University, Department of Mathematics and StatisticsBostonUnited States
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of OxfordOxfordUnited Kingdom
| | - Simon J Davis
- Radcliffe Department of Medicine, Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
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14
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Yuyama M, Ito T, Arai Y, Kadowaki Y, Iiyama N, Keino A, Hiraoka Y, Kanaya T, Momose Y, Kurihara M. Risk Prediction Method for Anticholinergic Action Using Auto-quantitative Structure-Activity Relationship and Docking Study with Molecular Operating Environment. Chem Pharm Bull (Tokyo) 2021; 68:773-778. [PMID: 32741919 DOI: 10.1248/cpb.c20-00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lower urinary tract symptoms (LUTS) induced by anticholinergic drug action impair the QOL of patients and are associated with a poor prognosis. Therefore, it is expedient to develop methods of predicting the anticholinergic side effects of drugs, which we aimed to achieve in this study using a quantitative structure-activity relationship (QSAR) and docking study with molecular operations environment (MOE; Molecular Simulation Informatics Systems [MOLSIS], Inc.) In the QSAR simulation, the QSAR model built using the partial least squares regression (PLS) and genetic algorithm-multiple linear regression (GA-MLR) methods showed remarkable coefficient of determination (R2) and XR2 values. In the docking study, a specific relationship was identified between the adjusted docking score (-S) and bioactivity (pKi) values. In conclusion, the methods developed could be useful for in silico risk assessment of LUTS, and plans are potentially applicable to numerous drugs with anticholinergic activity that induce serious side effects, limiting their use.
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Affiliation(s)
- Materu Yuyama
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare Graduate School
| | - Takeshi Ito
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare Graduate School.,Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Yumiko Arai
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare Graduate School
| | - Yuki Kadowaki
- Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Natsumi Iiyama
- Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Ayako Keino
- Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Yurina Hiraoka
- Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Takayuki Kanaya
- Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Yasuyuki Momose
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare Graduate School.,Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Masaaki Kurihara
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare Graduate School.,Department of Pharmaceutical Sciences, International University of Health and Welfare
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15
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Amangeldiuly N, Karlov D, Fedorov MV. Baseline Model for Predicting Protein–Ligand Unbinding Kinetics through Machine Learning. J Chem Inf Model 2020; 60:5946-5956. [DOI: 10.1021/acs.jcim.0c00450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nurlybek Amangeldiuly
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitry Karlov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maxim V. Fedorov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, Glasgow G4 0NG, U.K
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16
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Herrera-Zúñiga LD, Moreno-Vargas LM, Ballaud L, Correa-Basurto J, Prada-Gracia D, Pastré D, Curmi PA, Arrang JM, Maroun RC. Molecular dynamics of the histamine H3 membrane receptor reveals different mechanisms of GPCR signal transduction. Sci Rep 2020; 10:16889. [PMID: 33037273 PMCID: PMC7547658 DOI: 10.1038/s41598-020-73483-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/11/2020] [Indexed: 02/02/2023] Open
Abstract
In this work, we studied the mechanisms of classical activation and inactivation of signal transduction by the histamine H3 receptor, a 7-helix transmembrane bundle G-Protein Coupled Receptor through long-time-scale atomistic molecular dynamics simulations of the receptor embedded in a hydrated double layer of dipalmitoyl phosphatidyl choline, a zwitterionic polysaturated ordered lipid. Three systems were prepared: the apo receptor, representing the constitutively active receptor; and two holo-receptors-the receptor coupled to the antagonist/inverse agonist ciproxifan, representing the inactive state of the receptor, and the receptor coupled to the endogenous agonist histamine and representing the active state of the receptor. An extensive analysis of the simulation showed that the three states of H3R present significant structural and dynamical differences as well as a complex behavior given that the measured properties interact in multiple and interdependent ways. In addition, the simulations described an unexpected escape of histamine from the orthosteric binding site, in agreement with the experimental modest affinities and rapid off-rates of agonists.
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Affiliation(s)
- Leonardo David Herrera-Zúñiga
- UMR-S U1204, Structure et Activité de Biomolécules Normales et Pathologiques, INSERM/Université d'Evry-Val d'Essonne/Université Paris-Saclay, 91000, Evry, France
- Laboratoire de Neurobiologie et Pharmacologie Moléculaire, INSERM U894, Centre de Psychiatrie et Neurosciences, 75014, Paris, France
- Área de Estudios de Posgrado e Investigación, Tecnológico de Estudios Superiores del Oriente del Estado de México, Los Reyes Acaquilpan, Mexico
| | - Liliana Marisol Moreno-Vargas
- Computational Biology and Drug Design Research Unit, Federico Gómez Children's Hospital of Mexico City, Mexico City, Mexico
- Laboratoire de Neurobiologie et Pharmacologie Moléculaire, INSERM U894, Centre de Psychiatrie et Neurosciences, 75014, Paris, France
| | - Luck Ballaud
- Laboratoire de Neurobiologie et Pharmacologie Moléculaire, INSERM U894, Centre de Psychiatrie et Neurosciences, 75014, Paris, France
| | - José Correa-Basurto
- UMR-S U1204, Structure et Activité de Biomolécules Normales et Pathologiques, INSERM/Université d'Evry-Val d'Essonne/Université Paris-Saclay, 91000, Evry, France
- Laboratorio de Modelado Molecular y Bioinformática, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Diego Prada-Gracia
- Computational Biology and Drug Design Research Unit, Federico Gómez Children's Hospital of Mexico City, Mexico City, Mexico
| | - David Pastré
- UMR-S U1204, Structure et Activité de Biomolécules Normales et Pathologiques, INSERM/Université d'Evry-Val d'Essonne/Université Paris-Saclay, 91000, Evry, France
| | - Patrick A Curmi
- UMR-S U1204, Structure et Activité de Biomolécules Normales et Pathologiques, INSERM/Université d'Evry-Val d'Essonne/Université Paris-Saclay, 91000, Evry, France
| | - Jean Michel Arrang
- Laboratoire de Neurobiologie et Pharmacologie Moléculaire, INSERM U894, Centre de Psychiatrie et Neurosciences, 75014, Paris, France
| | - Rachid C Maroun
- UMR-S U1204, Structure et Activité de Biomolécules Normales et Pathologiques, INSERM/Université d'Evry-Val d'Essonne/Université Paris-Saclay, 91000, Evry, France.
- Laboratoire de Neurobiologie et Pharmacologie Moléculaire, INSERM U894, Centre de Psychiatrie et Neurosciences, 75014, Paris, France.
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17
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Buchwald P. A single unified model for fitting simple to complex receptor response data. Sci Rep 2020; 10:13386. [PMID: 32770075 PMCID: PMC7414914 DOI: 10.1038/s41598-020-70220-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
The fitting of complex receptor-response data where fractional response and occupancy do not match is challenging. They encompass important cases including (a) the presence of "receptor reserve" and/or partial agonism, (b) multiple responses assessed at different vantage points along a pathway, (c) responses that are different along diverging downstream pathways (biased agonism), and (d) constitutive activity. For these, simple models such as the well-known Clark or Hill equations cannot be used. Those that can, such as the operational (Black&Leff) model, do not provide a unified approach, have multiple nonintuitive parameters that are challenging to fit in well-defined manner, have difficulties incorporating binding data, and cannot be reduced or connected to simpler forms. We have recently introduced a quantitative receptor model (SABRE) that includes parameters for Signal Amplification (γ), Binding affinity (Kd), Receptor activation Efficacy (ε), and constitutive activity (εR0). It provides a single equation to fit complex cases within a full two-state framework with the possibility of incorporating receptor occupancy data (i.e., experimental Kds). Simpler cases can be fit by using consecutively reduced forms obtained by constraining parameters to specific values, e.g., εR0 = 0: no constitutive activity, γ = 1: no amplification (Emax-type fitting), and ε = 1: no partial agonism (Clark equation). Here, a Hill-type extension is introduced (n ≠ 1), and simulated and experimental receptor-response data from simple to increasingly complex cases are fitted within the unified framework of SABRE with differently constrained parameters.
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Affiliation(s)
- Peter Buchwald
- Department of Molecular and Cellular Pharmacology and Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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18
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Stephens BS, Ngo T, Kufareva I, Handel TM. Functional anatomy of the full-length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis. Sci Signal 2020; 13:eaay5024. [PMID: 32665413 PMCID: PMC7437921 DOI: 10.1126/scisignal.aay5024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because of their prominent roles in development, cancer, and HIV, the chemokine receptor CXCR4 and its ligand CXCL12 have been the subject of numerous structural and functional studies, but the determinants of ligand binding, selectivity, and signaling are still poorly understood. Here, building on our latest structural model, we used a systematic mutagenesis strategy to dissect the functional anatomy of the CXCR4-CXCL12 complex. Key charge swap mutagenesis experiments provided evidence for pairwise interactions between oppositely charged residues in the receptor and chemokine, confirming the accuracy of the predicted orientation of the chemokine relative to the receptor and providing insight into ligand selectivity. Progressive deletion of N-terminal residues revealed an unexpected contribution of the receptor N terminus to chemokine signaling. This finding challenges a longstanding "two-site" hypothesis about the essential features of the receptor-chemokine interaction in which the N terminus contributes only to binding affinity. Our results suggest that although the interaction of the chemokine N terminus with the receptor-binding pocket is the key driver of signaling, the signaling amplitude depends on the extent to which the receptor N terminus binds the chemokine. Together with systematic characterization of other epitopes, these data enable us to propose an experimentally consistent structural model for how CXCL12 binds CXCR4 and initiates signal transmission through the receptor transmembrane domain.
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Affiliation(s)
- Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tony Ngo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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19
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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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20
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Fyfe TJ, Kellam B, Sykes DA, Capuano B, Scammells PJ, Lane JR, Charlton SJ, Mistry SN. Structure-Kinetic Profiling of Haloperidol Analogues at the Human Dopamine D 2 Receptor. J Med Chem 2019; 62:9488-9520. [PMID: 31580666 DOI: 10.1021/acs.jmedchem.9b00864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Haloperidol is a typical antipsychotic drug (APD) associated with an increased risk of extrapyramidal side effects (EPSs) and hyperprolactinemia relative to atypical APDs such as clozapine. Both drugs are dopamine D2 receptor (D2R) antagonists, with contrasting kinetic profiles. Haloperidol displays fast association/slow dissociation at the D2R, whereas clozapine exhibits relatively slow association/fast dissociation. Recently, we have provided evidence that slow dissociation from the D2R predicts hyperprolactinemia, whereas fast association predicts EPS. Unfortunately, clozapine can cause severe side effects independent of its D2R action. Our results suggest an optimal kinetic profile for D2R antagonist APDs that avoids EPS. To begin exploring this hypothesis, we conducted a structure-kinetic relationship study of haloperidol and revealed that subtle structural modifications dramatically change binding kinetic rate constants, affording compounds with a clozapine-like kinetic profile. Thus, optimization of these kinetic parameters may allow development of novel APDs based on the haloperidol scaffold with improved side-effect profiles.
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Affiliation(s)
- Tim J Fyfe
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Barrie Kellam
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Sykes
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K
| | | | | | - J Robert Lane
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K
| | - Steven J Charlton
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K.,Excellerate Bioscience Ltd., BioCity , Nottingham NG1 1GF , U.K
| | - Shailesh N Mistry
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
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21
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Zhao P, Furness SGB. The nature of efficacy at G protein-coupled receptors. Biochem Pharmacol 2019; 170:113647. [PMID: 31585071 DOI: 10.1016/j.bcp.2019.113647] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/27/2019] [Indexed: 12/31/2022]
Abstract
G protein-coupled receptors (GPCRs) participate in many pathophysiological processes as well as almost all aspects of normal physiology. They are present at the surface of all cell types making them amenable and attractive targets for pharmaceutical therapeutics. GPCRs possess complex pharmacology with the ability to be turned on to various extents, have their constitutive activity suppressed and even switch between signaling pathways to which they couple. Underlying this complex pharmacology is GPCR signaling efficacy, and differences in efficacy promoted by alternative ligands and in different tissues is of great interest to biology in general and also the pharmaceutical industry. In this review we hope to discuss what the molecular foundations of efficacy are and whether a new approach utilizing a rate-dependent model may provide new insights into this phenomenon.
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Affiliation(s)
- Peishen Zhao
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia.
| | - Sebastian G B Furness
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia.
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22
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Narita T, Qi B, Murakami M, Sugiya H. Pilocarpine induces the residual secretion of salivary fluid in perfused submandibular glands of rats. PLoS One 2019; 14:e0221832. [PMID: 31461497 PMCID: PMC6713442 DOI: 10.1371/journal.pone.0221832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/15/2019] [Indexed: 12/19/2022] Open
Abstract
Pilocarpine is an M3 muscarinic agonist that is widely used for the treatment of xerostomia caused by various diseases and medical conditions. Pilocarpine induced the secretion of salivary fluid in perfused submandibular glands of rats. The secretion of salivary fluid observed after removal of pilocarpine was referred to as residual fluid secretion. The volume of fluid and time of the residual secretion depended on the dose of pilocarpine. Such a residual effect of pilocarpine was observed on fluid secretion via the paracellular pathway and oxygen consumption. When a muscarinic antagonist was added to the perfusate immediately after cessation of pilocarpine, residual secretion of salivary fluid did not occur. These observations indicate that the residual secretion of salivary fluid is a characteristics of the interaction of pilocarpine with muscarinic receptors.
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Affiliation(s)
- Takanori Narita
- Laboratory of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan.,Department of Physiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Bing Qi
- Department of Physiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Masataka Murakami
- Department of Nano-structure Physiology, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
| | - Hiroshi Sugiya
- Laboratory of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan.,Department of Physiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
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23
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Sykes DA, Jain P, Charlton SJ. Investigating the Influence of Tracer Kinetics on Competition-Kinetic Association Binding Assays: Identifying the Optimal Conditions for Assessing the Kinetics of Low-Affinity Compounds. Mol Pharmacol 2019; 96:378-392. [PMID: 31436538 DOI: 10.1124/mol.119.116764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 06/22/2019] [Indexed: 12/16/2022] Open
Abstract
An increased appreciation of the importance of optimizing drug-binding kinetics has lead to the development of various techniques for measuring the kinetics of unlabeled compounds. One approach is the competition-association kinetic binding method first described in the 1980s. The kinetic characteristics of the tracer employed greatly affects the reliability of estimated kinetic parameters, a barrier to successfully introducing these kinetic assays earlier in the drug discovery process. Using a modeling and Monte Carlo simulation approach, we identify the optimal tracer characteristics for determining the kinetics of the range of unlabeled ligands typically encountered during the different stages of a drug discovery program (i.e., rapidly dissociating, e.g., k off = 10 minute-1 low-affinity "hits" through to slowly dissociating e.g., k off = 0.01 minute-1 high-affinity "candidates"). For more rapidly dissociating ligands (e.g., k off = 10 minute-1), the key to obtaining accurate kinetic parameters was to employ a tracer with a relatively fast off-rate (e.g., k off = 1 minute-1) or, alternatively, to increase the tracer concentration. Reductions in assay start-time ≤1second and read frequency ≤5 seconds significantly improved the reliability of curve fitting. Timing constraints are largely dictated by the method of detection, its inherent sensitivity (e.g., TR-FRET versus radiometric detection), and the ability to inject samples online. Furthermore, we include data from TR-FRET experiments that validate this simulation approach, confirming its practical utility. These insights into the optimal experimental parameters for development of competition-association assays provide a framework for identifying and testing novel tracers necessary for profiling unlabeled competitors, particularly rapidly dissociating low-affinity competitors.
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Affiliation(s)
- David A Sykes
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom (D.A.S., P.J., S.J.C.); Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (D.A.S., P.J., S.J.C.); and Excellerate Bioscience Ltd, Discovery Building, BioCity, Nottingham, United Kingdom (S.J.C.)
| | - Palash Jain
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom (D.A.S., P.J., S.J.C.); Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (D.A.S., P.J., S.J.C.); and Excellerate Bioscience Ltd, Discovery Building, BioCity, Nottingham, United Kingdom (S.J.C.)
| | - Steven J Charlton
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom (D.A.S., P.J., S.J.C.); Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (D.A.S., P.J., S.J.C.); and Excellerate Bioscience Ltd, Discovery Building, BioCity, Nottingham, United Kingdom (S.J.C.)
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24
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Buchwald P. A Receptor Model With Binding Affinity, Activation Efficacy, and Signal Amplification Parameters for Complex Fractional Response Versus Occupancy Data. Front Pharmacol 2019; 10:605. [PMID: 31244653 PMCID: PMC6580154 DOI: 10.3389/fphar.2019.00605] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/14/2019] [Indexed: 12/28/2022] Open
Abstract
In quantitative pharmacology, multi-parameter receptor models are needed to account for the complex nonlinear relationship between fractional occupancy and response that can occur due to the intermixing of the effects of partial receptor activation and post-receptor signal amplification. Here, a general two-state receptor model and corresponding quantitative forms are proposed that unify three distinct processes, each characterized with its own parameter: 1) receptor binding, characterized by Kd, the equilibrium dissociation constant used for binding affinity; 2) receptor activation, characterized by an (intrinsic) efficacy parameter ε; and 3) post-activation signal transduction (amplification), characterized by a gain parameter γ. Constitutive activity is accommodated via an additional εR0 parameter quantifying the activation of the ligand-free receptor. Receptors can be active or inactive in both their ligand-free and ligand-bound states (two-state receptor theory), but ligand binding alters the likelihood of activation (induced fit). Because structural data now confirm that for most receptors in their active conformation, the small-molecule ligand-binding site is buried inside, straightforward binding to the active form (direct conformational selection) is unlikely. The proposed general equation has parameters that are more intuitive and better suited for optimization by nonlinear regression than those of the operational (Black and Leff) or del Castillo–Katz model. The model provides a unified framework for fitting complex data including a) fractional responses that do not match independently measured fractional occupancies, b) responses measured after partial irreversible inactivation of the “receptor reserve” (Furchgott method), c) fractional responses that are different along distinct downstream pathways (biased agonism), and d) responses with constitutive receptor activity. Furthermore, unlike previous models, the present one can be reduced back for special cases of its parameters to consecutively nested simplified forms that can be used on their own when adequate (e.g., εR0 = 0, no constitutive activity; γ = 1: Emax model for partial agonism; ε = 1: Clark equation).
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Affiliation(s)
- Peter Buchwald
- Department of Molecular and Cellular Pharmacology, Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, United States
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25
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IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
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Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - 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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26
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Potterton A, Husseini FS, Southey MWY, Bodkin MJ, Heifetz A, Coveney PV, Townsend-Nicholson A. Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders. J Chem Theory Comput 2019; 15:3316-3330. [PMID: 30893556 DOI: 10.1021/acs.jctc.8b01270] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drug-target residence time, the length of time for which a small molecule stays bound to its receptor target, has increasingly become a key property for optimization in drug discovery programs. However, its in silico prediction has proven difficult. Here we describe a method, using atomistic ensemble-based steered molecular dynamics (SMD), to observe the dissociation of ligands from their target G protein-coupled receptor in a time scale suitable for drug discovery. These dissociation simulations accurately, precisely, and reproducibly identify ligand-residue interactions and quantify the change in ligand energy values for both protein and water. The method has been applied to 17 ligands of the A2A adenosine receptor, all with published experimental kinetic binding data. The residues that interact with the ligand as it dissociates are known experimentally to have an effect on binding affinities and residence times. There is a good correlation ( R2 = 0.79) between the computationally calculated change in water-ligand interaction energy and experimentally determined residence time. Our results indicate that ensemble-based SMD is a rapid, novel, and accurate semi-empirical method for the determination of drug-target relative residence time.
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Affiliation(s)
- Andrew Potterton
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom
| | - Fouad S Husseini
- Centre for Computational Science, Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Mike J Bodkin
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Alexander Heifetz
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom.,Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom.,Computational Science Laboratory, Institute for Informatics, Faculty of Science , University of Amsterdam , Amsterdam 1098XH , The Netherlands
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom
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27
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Sykes DA, Stoddart LA, Kilpatrick LE, Hill SJ. Binding kinetics of ligands acting at GPCRs. Mol Cell Endocrinol 2019; 485:9-19. [PMID: 30738950 PMCID: PMC6406023 DOI: 10.1016/j.mce.2019.01.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/19/2019] [Accepted: 01/19/2019] [Indexed: 12/31/2022]
Abstract
The influence of drug-receptor binding kinetics has often been overlooked during the development of new therapeutics that target G protein-coupled receptors (GPCRs). Over the last decade there has been a growing understanding that an in-depth knowledge of binding kinetics at GPCRs is required to successfully target this class of proteins. Ligand binding to a GPCR is often not a simple single step process with ligand freely diffusing in solution. This review will discuss the experiments and equations that are commonly used to measure binding kinetics and how factors such as allosteric regulation, rebinding and ligand interaction with the plasma membrane may influence these measurements. We will then consider the molecular characteristics of a ligand and if these can be linked to association and dissociation rates.
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Affiliation(s)
- David A Sykes
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Leigh A Stoddart
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Laura E Kilpatrick
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Stephen J Hill
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
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28
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Nayak TK, Vij R, Bruhova I, Shandilya J, Auerbach A. Efficiency measures the conversion of agonist binding energy into receptor conformational change. J Gen Physiol 2019; 151:465-477. [PMID: 30635369 PMCID: PMC6445574 DOI: 10.1085/jgp.201812215] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/11/2018] [Indexed: 12/19/2022] Open
Abstract
Receptors alternate between resting↔active conformations that bind agonists with low↔high affinity. Here, we define a new agonist attribute, energy efficiency (η), as the fraction of ligand-binding energy converted into the mechanical work of the activation conformational change. η depends only on the resting/active agonist-binding energy ratio. In a plot of activation energy versus binding energy (an "efficiency" plot), the slope gives η and the y intercept gives the receptor's intrinsic activation energy (without agonists; ΔG0). We used single-channel electrophysiology to estimate η for eight different agonists and ΔG0 in human endplate acetylcholine receptors (AChRs). From published equilibrium constants, we also estimated η for agonists of KCa1.1 (BK channels) and muscarinic, γ-aminobutyric acid, glutamate, glycine, and aryl-hydrocarbon receptors, and ΔG0 for all of these except KCa1.1. Regarding AChRs, η is 48-56% for agonists related structurally to acetylcholine but is only ∼39% for agonists related to epibatidine; ΔG0 is 8.4 kcal/mol in adult and 9.6 kcal/mol in fetal receptors. Efficiency plots for all of the above receptors are approximately linear, with η values between 12% and 57% and ΔG0 values between 2 and 12 kcal/mol. Efficiency appears to be a general attribute of agonist action at receptor binding sites that is useful for understanding binding mechanisms, categorizing agonists, and estimating concentration-response relationships.
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Affiliation(s)
- Tapan K Nayak
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Iva Bruhova
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Jayasha Shandilya
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
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29
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Mocking TAM, Verweij EWE, Vischer HF, Leurs R. Homogeneous, Real-Time NanoBRET Binding Assays for the Histamine H 3 and H 4 Receptors on Living Cells. Mol Pharmacol 2018; 94:1371-1381. [PMID: 30249614 DOI: 10.1124/mol.118.113373] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/19/2018] [Indexed: 11/22/2022] Open
Abstract
Receptor-binding affinity and ligand-receptor residence time are key parameters for the selection of drug candidates and are routinely determined using radioligand competition-binding assays. Recently, a novel bioluminescence resonance energy transfer (BRET) method utilizing a NanoLuc-fused receptor was introduced to detect fluorescent ligand binding. Moreover, this NanoBRET method gives the opportunity to follow fluorescent ligand binding on intact cells in real time, and therefore, results might better reflect in vivo conditions as compared with the routinely used cell homogenates or purified membrane fractions. In this study, a real-time NanoBRET-based binding assay was established and validated to detect binding of unlabeled ligands to the histamine H3 receptor (H3R) and histamine H4 receptor on intact cells. Obtained residence times of clinically tested H3R antagonists were reflected by their duration of H3R antagonism in a functional receptor recovery assay.
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Affiliation(s)
- Tamara A M Mocking
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Eléonore W E Verweij
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Henry F Vischer
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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30
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Doornbos ML, Vermond SC, Lavreysen H, Tresadern G, IJzerman AP, Heitman LH. Impact of allosteric modulation: Exploring the binding kinetics of glutamate and other orthosteric ligands of the metabotropic glutamate receptor 2. Biochem Pharmacol 2018; 155:356-365. [DOI: 10.1016/j.bcp.2018.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/14/2018] [Indexed: 01/22/2023]
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31
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De Benedetti PG, Fanelli F. Computational modeling approaches to quantitative structure-binding kinetics relationships in drug discovery. Drug Discov Today 2018; 23:1396-1406. [PMID: 29574212 DOI: 10.1016/j.drudis.2018.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/22/2018] [Accepted: 03/19/2018] [Indexed: 11/22/2022]
Abstract
Simple comparative correlation analyses and quantitative structure-kinetics relationship (QSKR) models highlight the interplay of kinetic rates and binding affinity as an essential feature in drug design and discovery. The choice of the molecular series, and their structural variations, used in QSKR modeling is fundamental to understanding the mechanistic implications of ligand and/or drug-target binding and/or unbinding processes. Here, we discuss the implications of linear correlations between kinetic rates and binding affinity constants and the relevance of the computational approaches to QSKR modeling.
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Affiliation(s)
- Pier G De Benedetti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy.
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
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32
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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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33
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Hoare SRJ, Pierre N, Moya AG, Larson B. Kinetic operational models of agonism for G-protein-coupled receptors. J Theor Biol 2018; 446:168-204. [PMID: 29486201 DOI: 10.1016/j.jtbi.2018.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 01/06/2023]
Abstract
The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, kτ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter kτ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics.
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Affiliation(s)
- Samuel R J Hoare
- Pharmechanics, LLC, 14 Sunnyside Drive South, Owego NY 13827, USA.
| | | | | | - Brad Larson
- BioTek Instruments, Inc, 100 Tigan Street, Winooski, VT 05404, USA
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34
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Tang Z, Chang CEA. Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition. J Chem Theory Comput 2018; 14:303-318. [PMID: 29149564 PMCID: PMC5920803 DOI: 10.1021/acs.jctc.7b00899] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-time-scale molecular dynamics (MD) simulations, postanalysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, ΔH, ΔS, and ΔG using GAFF-CD and q4MD-CD force fields for β-CD could be compared with experimental data directly and agreed reasonably with experiment findings. In addition, our study further interprets experiments. Both force fields resulted in similar computed ΔG from independently computed kinetics rates, ΔG = -RT ln(kon·C0/koff), and thermodynamics properties, ΔG = ΔH - TΔS. The water entropy calculations show that the entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of nonpolar attractions between solutes and β-CD as well. Water molecules play a crucial role in guest binding to β-CD. However, collective water/β-CD motions could contribute to different computed kon and ΔH values by different force fields, mainly because the parameters of β-CD provide different motions of β-CD, hydrogen-bond networks of water molecules in the cavity of free β-CD, and strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driving force of binding. The study deepens our understanding of ligand-receptor recognition and suggests strategies for force field parametrization for accurately modeling molecular systems.
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Affiliation(s)
- Zhiye Tang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, California 92521, United States
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35
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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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36
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Sykes DA, Charlton SJ. Single Step Determination of Unlabeled Compound Kinetics Using a Competition Association Binding Method Employing Time-Resolved FRET. Methods Mol Biol 2018; 1824:177-194. [PMID: 30039407 DOI: 10.1007/978-1-4939-8630-9_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The competition association binding method allows the characterization of the kinetics of unlabeled compounds and the calculation of receptor-drug affinity (K d). The K d value is defined as the ratio of the dissociation constant (or k off) of the receptor-bound ligand to its association rate constant (or k on) for a system at equilibrium. Traditionally, competition association binding experiments have been carried out using radiometric detection methods with limited assay throughput. Here we describe a novel method for the determination of unlabeled compound kinetics using the technique of time-resolved fluorescence resonance energy transfer (TR-FRET) performed at physiological temperature and sodium ion concentration. Based on a traditional screening format (10-point curves), up to 28 compounds can be tested on a single 384-well plate by this method.
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Affiliation(s)
- David A Sykes
- School of Life Science, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Steven J Charlton
- School of Life Science, Queen's Medical Centre, University of Nottingham, Nottingham, UK.
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37
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Ramos I, Aparici M, Letosa M, Puig C, Gavaldà A, Huerta JM, Espinosa S, Vilella D, Miralpeix M. Abediterol (LAS100977), an inhaled long-acting β 2-adrenoceptor agonist, has a fast association rate and long residence time at receptor. Eur J Pharmacol 2017; 819:89-97. [PMID: 29183838 DOI: 10.1016/j.ejphar.2017.11.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 12/28/2022]
Abstract
This study describes the association rate and residence time of abediterol, a novel long-acting β2-adrenoceptor agonist (LABA) in Phase II development for treatment of asthma and COPD, in comparison with indacaterol, olodaterol, vilanterol and salmeterol, for both human β1- and β2-adrenoceptors. Abediterol association and dissociation rates were monitored directly by using its tritiated form. Moreover, association was determined indirectly using experimental Ki and koff obtained from assays performed with unlabelled compound. Dissociation was also studied indirectly by measuring the association rate of 3H-CGP12177 to beta adrenoceptors previously occupied by unlabelled compounds. Abediterol shows a fast association for the β2-adrenoceptor (kon 1.4 × 107 ± 1.8 × 106M-1min-1) while its dissociation rate is between 30 and 64 times slower than that of the reference LABA compounds tested, with a residence time of 91.3 ± 13.3min (measured directly) and 185.5 ± 7.5min (measured indirectly). Abediterol shows kinetic selectivity for the β2- over the β1-adrenoceptor, with a dissociation rate from the β1-adrenoceptor similar to the other LABA compounds tested. In conclusion, abediterol is a potent LABA with a fast association rate and a long residence time at β2-adrenoceptors. These data are in agreement with the onset and duration of action of abediterol shown in humans.
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Affiliation(s)
- Israel Ramos
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain.
| | - Mònica Aparici
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Maria Letosa
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Carlos Puig
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Amadeu Gavaldà
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Josep Maria Huerta
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Sonia Espinosa
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Dolors Vilella
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
| | - Montserrat Miralpeix
- Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain
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38
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Pronin AN, Wang Q, Slepak VZ. Teaching an Old Drug New Tricks: Agonism, Antagonism, and Biased Signaling of Pilocarpine through M3 Muscarinic Acetylcholine Receptor. Mol Pharmacol 2017; 92:601-612. [PMID: 28893976 DOI: 10.1124/mol.117.109678] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/06/2017] [Indexed: 12/27/2022] Open
Abstract
Pilocarpine is a prototypical drug used to treat glaucoma and dry mouth and is classified as either a full or partial muscarinic agonist. Here, we report several unexpected results pertaining to its interaction with muscarinic M3 receptor (M3R). We found that pilocarpine was 1000 times less potent in stimulating mouse-eye pupil constriction than muscarinic agonists oxotremorin-M (Oxo-M) or carbachol (CCh), although all three ligands have similar Kd values for M3R. In contrast to CCh or Oxo-M, pilocarpine does not induce Ca2+ mobilization via endogenous M3R in human embryonic kidney cell line 293T (HEK293T) or mouse insulinoma (MIN6) cells. Pilocarpine also fails to stimulate insulin secretion and, instead, antagonizes the insulinotropic effect of Oxo-M and CCh-induced Ca2+ upregulation; however, in HEK293T or Chinese hamster ovary-K1 cells overexpressing M3R, pilocarpine induces Ca2+ transients like those recorded with another cognate G protein-coupled muscarinic receptor, M1R. Stimulation of cells overexpressing M1R or M3R with CCh resulted in a similar reduction in phosphatidylinositol 4,5-bisphosphate (PIP2). In contrast to CCh, pilocarpine stimulated PIP2 hydrolysis only in cells overexpressing M1R but not M3R. Moreover, pilocarpine blocked CCh-stimulated PIP2 hydrolysis in M3R-overexpressing cells, thus, it acted as an antagonist. Pilocarpine activates extracellular regulated kinase 1/2 in MIN6 cells. The stimulatory effect on extracellular regulated kinase (ERK1/2) was blocked by the Src family kinase inhibitor PP2, indicating that the action of pilocarpine on endogenous M3R is biased toward β-arrestin. Taken together, our findings show that pilocarpine can act as either an agonist or antagonist of M3R, depending on the cell type, expression level, and signaling pathway downstream of this receptor.
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Affiliation(s)
- Alexey N Pronin
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
| | - Qiang Wang
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
| | - Vladlen Z Slepak
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
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A kinetic view of GPCR allostery and biased agonism. Nat Chem Biol 2017; 13:929-937. [DOI: 10.1038/nchembio.2431] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/31/2017] [Indexed: 12/21/2022]
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Doornbos MLJ, Cid JM, Haubrich J, Nunes A, van de Sande JW, Vermond SC, Mulder-Krieger T, Trabanco AA, Ahnaou A, Drinkenburg WH, Lavreysen H, Heitman LH, IJzerman AP, Tresadern G. Discovery and Kinetic Profiling of 7-Aryl-1,2,4-triazolo[4,3-a]pyridines: Positive Allosteric Modulators of the Metabotropic Glutamate Receptor 2. J Med Chem 2017; 60:6704-6720. [DOI: 10.1021/acs.jmedchem.7b00669] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Maarten L. J. Doornbos
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - José María Cid
- Janssen Research and Development, Calle Jarama 75A, 45007, Toledo, Spain
| | - Jordi Haubrich
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Alexandro Nunes
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Jasper W. van de Sande
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Sophie C. Vermond
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Thea Mulder-Krieger
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Andrés A. Trabanco
- Janssen Research and Development, Calle Jarama 75A, 45007, Toledo, Spain
| | - Abdellah Ahnaou
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Hilde Lavreysen
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, 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
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Martella A, Sijben H, Rufer AC, Grether U, Fingerle J, Ullmer C, Hartung T, IJzerman AP, van der Stelt M, Heitman LH. A Novel Selective Inverse Agonist of the CB2 Receptor as a Radiolabeled Tool Compound for Kinetic Binding Studies. Mol Pharmacol 2017; 92:389-400. [DOI: 10.1124/mol.117.108605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/21/2017] [Indexed: 01/14/2023] Open
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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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Callegari D, Lodola A, Pala D, Rivara S, Mor M, Rizzi A, Capelli AM. Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8. J Chem Inf Model 2017; 57:159-169. [DOI: 10.1021/acs.jcim.6b00679] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Donatella Callegari
- Dipartimento
di Farmacia, Università degli Studi di Parma, Viale delle
scienze 27/A, 43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Farmacia, Università degli Studi di Parma, Viale delle
scienze 27/A, 43124 Parma, Italy
| | - Daniele Pala
- Dipartimento
di Farmacia, Università degli Studi di Parma, Viale delle
scienze 27/A, 43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento
di Farmacia, Università degli Studi di Parma, Viale delle
scienze 27/A, 43124 Parma, Italy
| | - Marco Mor
- Dipartimento
di Farmacia, Università degli Studi di Parma, Viale delle
scienze 27/A, 43124 Parma, Italy
| | - Andrea Rizzi
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Anna Maria Capelli
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
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Riddy DM, Cook AE, Diepenhorst NA, Bosnyak S, Brady R, Mannoury la Cour C, Mocaer E, Summers RJ, Charman WN, Sexton PM, Christopoulos A, Langmead CJ. Isoform-Specific Biased Agonism of Histamine H3 Receptor Agonists. Mol Pharmacol 2016; 91:87-99. [PMID: 27864425 DOI: 10.1124/mol.116.106153] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/17/2016] [Indexed: 12/11/2022] Open
Abstract
The human histamine H3 receptor (hH3R) is subject to extensive gene splicing that gives rise to a large number of functional and nonfunctional isoforms. Despite the general acceptance that G protein-coupled receptors can adopt different ligand-induced conformations that give rise to biased signaling, this has not been studied for the H3R; further, it is unknown whether splice variants of the same receptor engender the same or differential biased signaling. Herein, we profiled the pharmacology of histamine receptor agonists at the two most abundant hH3R splice variants (hH3R445 and hH3R365) across seven signaling endpoints. Both isoforms engender biased signaling, notably for 4-[3-(benzyloxy)propyl]-1H-imidazole (proxyfan) [e.g., strong bias toward phosphorylation of glycogen synthase kinase 3β (GSK3β) via the full-length receptor] and its congener 3-(1H-imidazol-4-yl)propyl-(4-iodophenyl)-methyl ether (iodoproxyfan), which are strongly consistent with the former's designation as a "protean" agonist. The 80 amino acid IL3 deleted isoform hH3R365 is more permissive in its signaling than hH3R445: 2-(1H-imidazol-5-yl)ethyl imidothiocarbamate (imetit), proxyfan, and iodoproxyfan were all markedly biased away from calcium signaling, and principal component analysis of the full data set revealed divergent profiles for all five agonists. However, most interesting was the identification of differential biased signaling between the two isoforms. Strikingly, hH3R365 was completely unable to stimulate GSK3β phosphorylation, an endpoint robustly activated by the full-length receptor. To the best of our knowledge, this is the first quantitative example of differential biased signaling via isoforms of the same G protein-coupled receptor that are simultaneously expressed in vivo and gives rise to the possibility of selective pharmacological targeting of individual receptor splice variants.
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Affiliation(s)
- Darren M Riddy
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Anna E Cook
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Natalie A Diepenhorst
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Sanja Bosnyak
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Ryan Brady
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Clotilde Mannoury la Cour
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Elisabeth Mocaer
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Roger J Summers
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - William N Charman
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
| | - Christopher J Langmead
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (D.M.R., A.E.C., N.A.D., S.B., R.B., R.J.S., W.N.C., P.M.S., A.C., C.J.L.); and Institut de Recherches Internationales Servier, Suresnes, France (C.M.C., E.M.)
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45
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de Witte WE, Danhof M, van der Graaf PH, de Lange EC. In vivo Target Residence Time and Kinetic Selectivity: The Association Rate Constant as Determinant. Trends Pharmacol Sci 2016; 37:831-842. [DOI: 10.1016/j.tips.2016.06.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/13/2016] [Accepted: 06/15/2016] [Indexed: 12/16/2022]
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McNeely PM, Naranjo AN, Forsten-Williams K, Robinson AS. A 2AR Binding Kinetics in the Ligand Depletion Regime. SLAS DISCOVERY 2016; 22:166-175. [PMID: 27577981 DOI: 10.1177/1087057116667256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A2A receptor (A2AR) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.
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Affiliation(s)
- Patrick M McNeely
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Andrea N Naranjo
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | | | - Anne Skaja Robinson
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.,2 Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
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Nederpelt I, Bleeker D, Tuijt B, IJzerman AP, Heitman LH. Kinetic binding and activation profiles of endogenous tachykinins targeting the NK1 receptor. Biochem Pharmacol 2016; 118:88-95. [PMID: 27501920 DOI: 10.1016/j.bcp.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023]
Abstract
Ligand-receptor binding kinetics (i.e. association and dissociation rates) are emerging as important parameters for drug efficacy in vivo. Awareness of the kinetic behavior of endogenous ligands is pivotal, as drugs often have to compete with those. The binding kinetics of neurokinin 1 (NK1) receptor antagonists have been widely investigated while binding kinetics of endogenous tachykinins have hardly been reported, if at all. Therefore, the aim of this research was to investigate the binding kinetics of endogenous tachykinins and derivatives thereof and their role in the activation of the NK1 receptor. We determined the binding kinetics of seven tachykinins targeting the NK1 receptor. Dissociation rate constants (koff) ranged from 0.026±0.0029min-1 (Sar9,Met(O2)11-SP) to 0.21±0.015min-1 (septide). Association rate constants (kon) were more diverse: substance P (SP) associated the fastest with a kon value of 0.24±0.046nM-1min-1 while neurokinin A (NKA) had the slowest association rate constant of 0.001±0.0002nM-1min-1. Kinetic binding parameters were highly correlated with potency and maximal response values determined in label-free impedance-based experiments on U-251 MG cells. Our research demonstrates large variations in binding kinetics of tachykinins which correlate to receptor activation. These findings provide new insights into the ligand-receptor interactions of tachykinins and underline the importance of measuring binding kinetics of both drug candidates and competing endogenous ligands.
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Affiliation(s)
- I Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - D Bleeker
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - B Tuijt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - A P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - L 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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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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Baltos JA, Paoletta S, Nguyen ATN, Gregory KJ, Tosh DK, Christopoulos A, Jacobson KA, May LT. Structure-Activity Analysis of Biased Agonism at the Human Adenosine A3 Receptor. Mol Pharmacol 2016; 90:12-22. [PMID: 27136943 DOI: 10.1124/mol.116.103283] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/29/2016] [Indexed: 02/06/2023] Open
Abstract
Biased agonism at G protein-coupled receptors (GPCRs) has significant implications for current drug discovery, but molecular determinants that govern ligand bias remain largely unknown. The adenosine A3 GPCR (A3AR) is a potential therapeutic target for various conditions, including cancer, inflammation, and ischemia, but for which biased agonism remains largely unexplored. We now report the generation of bias "fingerprints" for prototypical ribose containing A3AR agonists and rigidified (N)-methanocarba 5'-N-methyluronamide nucleoside derivatives with regard to their ability to mediate different signaling pathways. Relative to the reference prototypical agonist IB-MECA, (N)-methanocarba 5'-N-methyluronamide nucleoside derivatives with significant N(6) or C2 modifications, including elongated aryl-ethynyl groups, exhibited biased agonism. Significant positive correlation was observed between the C2 substituent length (in Å) and bias toward cell survival. Molecular modeling suggests that extended C2 substituents on (N)-methanocarba 5'-N-methyluronamide nucleosides promote a progressive outward shift of the A3AR transmembrane domain 2, which may contribute to the subset of A3AR conformations stabilized on biased agonist binding.
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Affiliation(s)
- Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Silvia Paoletta
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Anh T N Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Karen J Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Dilip K Tosh
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Kenneth A Jacobson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
| | - Lauren T May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (J.-A.B., A.T.N.N., K.J.G., A.C., L.T.M); and Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland (S.P., D.K.T., K.A.J)
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Santini G, Mores N, Malerba M, Mondino C, Macis G, Montuschi P. Investigational prostaglandin D2 receptor antagonists for airway inflammation. Expert Opin Investig Drugs 2016; 25:639-52. [PMID: 27094922 DOI: 10.1080/13543784.2016.1175434] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION By activating DP1 and DP2 receptors on immune and non-immune cells, prostaglandin D2 (PGD2), a major metabolic product of cyclo-oxygenase pathway released after IgE-mediated mast cell activation, has pro-inflammatory effects, which are relevant to the pathophysiology of allergic airway disease. At least 15 selective, orally active, DP2 receptor antagonists and one DP1 receptor antagonist (asapiprant) are under development for asthma and/or allergic rhinitis. AREAS COVERED In this review, the authors cover the pharmacology of PGD2 and PGD2 receptor antagonists and look at the preclinical, phase I and phase II studies with selective DP1 and DP2 receptor antagonists. EXPERT OPINION Future research should aim to develop once daily compounds and increase the drug clinical potency which, apart from OC000459 and ADC-3680, seems to be relatively low. Further research and development of DP2 receptor antagonists is warranted, particularly in patients with severe uncontrolled asthma, whose management is a top priority. Pediatric studies, which are not available, are required for assessing the efficacy and safety of this novel drug class in children with asthma and allergic rhinitis. Studies on the efficacy of DP2 receptor antagonists in various asthma phenotypes including: smokers, obese subjects, early vs late asthma onset, fixed vs reversible airflow limitation, are required for establishing their pharmacotherapeutic role.
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Affiliation(s)
- Giuseppe Santini
- a Department of Pharmacology, Faculty of Medicine , Catholic University of the Sacred Heart , Rome , Italy
| | - Nadia Mores
- a Department of Pharmacology, Faculty of Medicine , Catholic University of the Sacred Heart , Rome , Italy
| | - Mario Malerba
- b Department of Internal Medicine , University of Brescia , Brescia , Italy
| | - Chiara Mondino
- c Department of Allergology , 'Bellinzona e Valli' Hospital , Bellinzona , Switzerland
| | - Giuseppe Macis
- d Department of Radiological Sciences, Faculty of Medicine , Catholic University of the Sacred Heart , Rome , Italy
| | - Paolo Montuschi
- a Department of Pharmacology, Faculty of Medicine , Catholic University of the Sacred Heart , Rome , Italy
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