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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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The importance of target binding kinetics for measuring target binding affinity in drug discovery: a case study from a CRF1 receptor antagonist program. Drug Discov Today 2020; 25:7-14. [DOI: 10.1016/j.drudis.2019.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/16/2019] [Accepted: 09/13/2019] [Indexed: 12/28/2022]
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3
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Georgi V, Dubrovskiy A, Steigele S, Fernández-Montalván AE. Considerations for improved performance of competition association assays analysed with the Motulsky-Mahan's "kinetics of competitive binding" model. Br J Pharmacol 2019; 176:4731-4744. [PMID: 31444916 PMCID: PMC7029771 DOI: 10.1111/bph.14841] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 06/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022] Open
Abstract
Background and Purpose Target engagement dynamics can influence drugs' pharmacological effects. Kinetic parameters for drug:target interactions are often quantified by evaluating competition association experiments—measuring simultaneous protein binding of labelled tracers and unlabelled test compounds over time—with Motulsky–Mahan's “kinetics of competitive binding” model. Despite recent technical improvements, the current assay formats impose practical limitations to this approach. This study aims at the characterisation, understanding and prevention of these experimental constraints, and associated analytical challenges. Experimental Approach Monte Carlo simulations were used to run virtual kinetic and equilibrium tracer binding and competition experiments in both normal and perturbed assay conditions. Data were fitted to standard equations derived from the mass action law (including Motulsky–Mahan's) and to extended versions aiming to cope with frequently observed deviations of the canonical traces. Results were compared to assess the precision and accuracy of these models and identify experimental factors influencing their performance. Key Results Key factors influencing the precision and accuracy of the Motulsky–Mahan model are the interplay between compound dissociation rates, measurement time and interval frequency, tracer concentration and binding kinetics and the relative abundance of equilibrium complexes in vehicle controls. Experimental results produced recommendations for better design of tracer characterisation experiments and new strategies to deal with systematic signal decay. Conclusions and Implications Our data advances our comprehension of the Motulsky–Mahan kinetics of competitive binding models and provides experimental design recommendations, data analysis tools, and general guidelines for its practical application to in vitro pharmacology and drug screening.
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Affiliation(s)
| | - Alexey Dubrovskiy
- Research and Development, Genedata AG, Basel, Switzerland.,Software Engineering, Google Inc., Zürich, Switzerland
| | | | - Amaury E Fernández-Montalván
- Drug Discovery, Pharmaceuticals, Bayer AG, Berlin, Germany.,Compound Screening, Institut de Recherches Servier, Croissy-sur-Seine, France
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Janczak CM, Calderon IAC, Noviana E, Hadvani P, Lee JR, Aspinwall CA. Hybrid Nanoparticle Platform for Nanoscale Scintillation Proximity Assay. ACS APPLIED NANO MATERIALS 2019; 2:1259-1266. [PMID: 34316544 PMCID: PMC8313019 DOI: 10.1021/acsanm.8b02136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
β-particle emitting radionuclides, such as 3H, 14C, 32P, 33P, and 35S, are important molecular labels due to their small size and the prevalence of these atoms in biomolecules but are challenging to selectively detect and quantify within aqueous biological samples and systems. Here, we present a core-shell nanoparticle-based scintillation proximity assay platform (nanoSPA) for the separation-free, selective detection of radiolabeled analytes. nanoSPA is prepared by incorporating scintillant fluorophores into polystyrene core particles and encapsulating the scintillant-doped cores within functionalized silica shells. The functionalized surface enables covalent attachment of specific binding moieties such as small molecules, proteins, or DNA that can be used for analyte-specific detection. nanoSPA was demonstrated for detection of 3H-labeled analytes, the most difficult biologically relevant β-emitter to measure due to the low energy β-particle emission, using three model assays that represent covalent and non-covalent binding systems that necessitate selectivity over competing 3H-labeled species. In each model, nmol quantities of target were detected directly in aqueous solution without separation from unbound 3H-labeled analyte. The nanoSPA platform facilitated measurement of 3H-labeled analytes directly in bulk aqueous samples without surfactants or other agents used to aid particle dispersal. Selectivity for bound 3H-analytes over unbound 3H analytes was enhanced up to 30-fold when the labeled species was covalently bound to nanoSPA, and 4- and 8-fold for two non-covalent binding assays using nanoSPA. The small size and enhanced selectivity of nanoSPA should enable new applications compared to the commonly used microSPA platform, including the potential for separation-free, analyte-specific cellular or intracellular detection.
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Affiliation(s)
- Colleen M. Janczak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson 85721-00041, United States
| | - Isen A. C. Calderon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson 85721-00041, United States
| | - Eka Noviana
- Department of Chemistry and Biochemistry, University of Arizona, Tucson 85721-00041, United States
| | - Priyanka Hadvani
- Department of Chemistry and Biochemistry, University of Arizona, Tucson 85721-00041, United States
| | - Joo Ryung Lee
- Department of Chemistry and Biochemistry, University of Arizona, Tucson 85721-00041, United States
| | - Craig A. Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson 85721-00041, United States
- BIO5 Institute, University of Arizona, Tucson 85721-00041, United States
- Department of Biomedical Engineering, University of Arizona, Tucson 85721-00041, United States
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Zeilinger M, Pichler F, Nics L, Wadsak W, Spreitzer H, Hacker M, Mitterhauser M. New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. EJNMMI Res 2017; 7:22. [PMID: 28271461 PMCID: PMC5340791 DOI: 10.1186/s13550-016-0249-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/15/2016] [Indexed: 12/02/2022] Open
Abstract
Background Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A3R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the Ki of eight different A3R antagonists, using CHO-K1 cells stably expressing the hA3R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants kon and koff, as well as the dedicated Kd of the A3R agonist [125I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Results Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A3R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Conclusions Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.
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Affiliation(s)
- Markus Zeilinger
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Faculty of Engineering, University of Applied Sciences Wiener Neustadt, Wiener Neustadt, Austria
| | - Florian Pichler
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Faculty of Engineering, University of Applied Sciences Wiener Neustadt, Wiener Neustadt, Austria
| | - Lukas Nics
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Wolfgang Wadsak
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Department of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Helmut Spreitzer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Marcus Hacker
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Markus Mitterhauser
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Radiopharmacy and Experimental Nuclear Medicine, Waehringer Guertel 18-20, 1090, Vienna, Austria. .,Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria. .,Ludwig Boltzmann Institute for Applied Diagnostics, Vienna, Austria.
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Bernetti M, Cavalli A, Mollica L. Protein-ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling. MEDCHEMCOMM 2017; 8:534-550. [PMID: 30108770 PMCID: PMC6072069 DOI: 10.1039/c6md00581k] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/25/2017] [Indexed: 12/14/2022]
Abstract
In the last three decades, protein and nucleic acid structure determination and comprehension of the mechanisms, leading to their physiological and pathological functions, have become a cornerstone of biomedical sciences. A deep understanding of the principles governing the fates of cells and tissue at the molecular level has been gained over the years, offering a solid basis for the rational design of drugs aimed at the pharmacological treatment of numerous diseases. Historically, affinity indicators (i.e. Kd and IC50/EC50) have been assumed to be valid indicators of the in vivo efficacy of a drug. However, recent studies pointed out that the kinetics of the drug-receptor binding process could be as important or even more important than affinity in determining the drug efficacy. This eventually led to a growing interest in the characterisation and prediction of the rate constants of protein-ligand association and dissociation. For instance, a drug with a longer residence time can kinetically select a given receptor over another, even if the affinity for both receptors is comparable, thus increasing its therapeutic index. Therefore, understanding the molecular features underlying binding and unbinding processes is of central interest towards the rational control of drug binding kinetics. In this review, we report the theoretical framework behind protein-ligand association and highlight the latest advances in the experimental and computational approaches exploited to investigate the binding kinetics.
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Affiliation(s)
- M Bernetti
- Department of Pharmacy and Biotechnology , University of Bologna , via Belmeloro 6 , 40126 Bologna , Italy
- CompuNet , Istituto Italiano di Tecnologia , via Morego 30 , 16163 Genova , Italy .
| | - A Cavalli
- Department of Pharmacy and Biotechnology , University of Bologna , via Belmeloro 6 , 40126 Bologna , Italy
- CompuNet , Istituto Italiano di Tecnologia , via Morego 30 , 16163 Genova , Italy .
| | - L Mollica
- CompuNet , Istituto Italiano di Tecnologia , via Morego 30 , 16163 Genova , Italy .
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7
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Dynamics of ligand binding to GPCR: Residence time of melanocortins and its modulation. Pharmacol Res 2016; 113:747-753. [DOI: 10.1016/j.phrs.2016.05.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/22/2016] [Accepted: 05/27/2016] [Indexed: 01/06/2023]
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8
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Abstract
Radioligand binding assays provide sensitive and quantitative information about guanine nucleotide protein G protein-coupled receptor (GPCR) expression and affinity for a wide variety of ligands, making them essential for drug structure-activity studies and basic GPCR research. Three basic radioligand binding protocols, saturation, indirect (competition, displacement, or modulation), and kinetic binding assays, are used to assess GPCR expression (Bmax), equilibrium dissociation constants for radioligands (Kd) and nonradioactive ligands (Ki), association and dissociation rates, and to distinguish competitive and allosteric mechanisms of GPCR-ligand interactions. Nonspecific radioligand binding may be mitigated by appropriate choices of reaction conditions. Radioligand depletion (bound radioactivity >10% of total radioligand), which compromises accuracy of Kd and Ki measurements, can be limited by adjusting receptor concentration and appropriate radioligand choice. Accurate Kd and Ki values in saturation and indirect binding assays depend on binding equilibrium. Equilibration time for high-affinity ligands, with slow dissociation rates, may require much extended incubation times or increased incubation temperature.
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Affiliation(s)
- Colleen A Flanagan
- School of Physiology and Medical Research Council Receptor Biology Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Wits Parktown, Johannesburg, South Africa.
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Nederpelt I, Georgi V, Schiele F, Nowak‐Reppel K, Fernández‐Montalván AE, IJzerman AP, Heitman LH. Characterization of 12 GnRH peptide agonists - a kinetic perspective. Br J Pharmacol 2016; 173:128-41. [PMID: 26398856 PMCID: PMC4813373 DOI: 10.1111/bph.13342] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND AND PURPOSE Drug-target residence time is an important, yet often overlooked, parameter in drug discovery. Multiple studies have proposed an increased residence time to be beneficial for improved drug efficacy and/or longer duration of action. Currently, there are many drugs on the market targeting the gonadotropin-releasing hormone (GnRH) receptor for the treatment of hormone-dependent diseases. Surprisingly, the kinetic receptor-binding parameters of these analogues have not yet been reported. Therefore, this project focused on determining the receptor-binding kinetics of 12 GnRH peptide agonists, including many marketed drugs. EXPERIMENTAL APPROACH A novel radioligand-binding competition association assay was developed and optimized for the human GnRH receptor with the use of a radiolabelled peptide agonist, [(125) I]-triptorelin. In addition to radioligand-binding studies, a homogeneous time-resolved FRET Tag-lite™ method was developed as an alternative assay for the same purpose. KEY RESULTS Two novel competition association assays were successfully developed and applied to determine the kinetic receptor-binding characteristics of 12 high-affinity GnRH peptide agonists. Results obtained from both methods were highly correlated. Interestingly, the binding kinetics of the peptide agonists were more divergent than their affinities with residence times ranging from 5.6 min (goserelin) to 125 min (deslorelin). CONCLUSIONS AND IMPLICATIONS Our research provides new insights by incorporating kinetic, next to equilibrium, binding parameters in current research and development that can potentially improve future drug discovery targeting the GnRH receptor.
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Affiliation(s)
- Indira Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenThe Netherlands
| | - Victoria Georgi
- Global Drug Discovery, Lead Discovery BerlinBayer Healthcare PharmaceuticalsBerlinGermany
| | - Felix Schiele
- Global Drug Discovery, Lead Discovery BerlinBayer Healthcare PharmaceuticalsBerlinGermany
| | - Katrin Nowak‐Reppel
- Global Drug Discovery, Lead Discovery BerlinBayer Healthcare PharmaceuticalsBerlinGermany
| | | | - Adriaan P. IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenThe Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenThe Netherlands
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10
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Xia L, de Vries H, IJzerman AP, Heitman LH. Scintillation proximity assay (SPA) as a new approach to determine a ligand's kinetic profile. A case in point for the adenosine A1 receptor. Purinergic Signal 2015; 12:115-26. [PMID: 26647040 PMCID: PMC4749533 DOI: 10.1007/s11302-015-9485-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/19/2015] [Indexed: 01/11/2023] Open
Abstract
Scintillation proximity assay (SPA) is a radio-isotopic technology format used to measure a wide range of biological interactions, including drug-target binding affinity studies. The assay is homogeneous in nature, as it relies on a “mix and measure” format. It does not involve a filtration step to separate bound from free ligand as is the case in a traditional receptor-binding assay. For G protein-coupled receptors (GPCRs), it has been shown that optimal binding kinetics, next to a high affinity of a ligand, can result in more desirable pharmacological profiles. However, traditional techniques to assess kinetic parameters tend to be cumbersome and laborious. We thus aimed to evaluate whether SPA can be an alternative platform for real-time receptor-binding kinetic measurements on GPCRs. To do so, we first validated the SPA technology for equilibrium binding studies on a prototypic class A GPCR, the human adenosine A1 receptor (hA1R). Differently to classic kinetic studies, the SPA technology allowed us to study binding kinetic processes almost real time, which is impossible in the filtration assay. To demonstrate the reliability of this technology for kinetic purposes, we performed the so-called competition association experiments. The association and dissociation rate constants (kon and koff) of unlabeled hA1R ligands were reliably and quickly determined and agreed very well with the same parameters from a traditional filtration assay performed simultaneously. In conclusion, SPA is a very promising technique to determine the kinetic profile of the drug-target interaction. Its robustness and potential for high-throughput may render this technology a preferred choice for further kinetic studies.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Ad P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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Vauquelin G, Huber W, Swinney DC. Experimental Methods to Determine Binding Kinetics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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12
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Guo D, Hillger JM, IJzerman AP, Heitman LH. Drug-Target Residence Time-A Case for G Protein-Coupled Receptors. Med Res Rev 2014; 34:856-92. [DOI: 10.1002/med.21307] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research; Leiden University; P.O. Box 9502 2300 RA Leiden the Netherlands
| | - Julia M. Hillger
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research; Leiden University; P.O. Box 9502 2300 RA Leiden the Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research; Leiden University; P.O. Box 9502 2300 RA Leiden the Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research; Leiden University; P.O. Box 9502 2300 RA Leiden the Netherlands
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13
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Khawaja X, Dunlop J, Kowal D. Scintillation proximity assay in lead discovery. Expert Opin Drug Discov 2013; 3:1267-80. [PMID: 23496165 DOI: 10.1517/17460441.3.11.1267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Scintillation proximity assay (SPA) is a homogeneous scintillant bead-based platform for the measurement of biological processes and plays an important role in the identification of active chemical entities in drug discovery. OBJECTIVE The design and development of solid-phase SPA approaches are examined and compared with alternative non-radiometric fluorescence-based technologies. METHODS This review provides background on the principle of SPA and its application to biomolecular interactions from a variety of biological sources. CONCLUSION The SPA approach is well suited to the demands of commercial high volume automation and assay miniaturization for target-based high-throughput screening campaigns on synthetic and natural product libraries as well as for benchtop characterization and confirmation studies. In the near future, innovations in the way SPA and fluorescence-based screening strategies are multiplexed will improve our comprehensive understanding of cellular system biology and dramatically advance the lead discovery process for the treatment of complex target-related disorders.
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Affiliation(s)
- Xavier Khawaja
- Depression and Anxiety, Neuroscience Discovery Research, Wyeth Research, Princeton, NJ 08543, USA +1 732 274 4382 ; +1 732 274 4020 ;
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Guo D, van Dorp EJH, Mulder-Krieger T, van Veldhoven JPD, Brussee J, IJzerman AP, Heitman LH. Dual-Point Competition Association Assay. ACTA ACUST UNITED AC 2012; 18:309-20. [DOI: 10.1177/1087057112464776] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The concept of ligand-receptor binding kinetics is emerging as an important parameter in the early phase of drug discovery. Since the currently used kinetic assays are laborious and low throughput, we developed a method that enables fast and large format screening. It is a so-called dual-point competition association assay, which measures radioligand binding at two different time points in the absence or presence of unlabeled competitors. Specifically, this assay yields the kinetic rate index (KRI), which is a measure for the binding kinetics of the unlabeled ligands screened. As a prototypical drug target, the adenosine A1 receptor (A1R) was chosen for assay validation and optimization. A screen with 35 high-affinity A1R antagonists yielded seven compounds with a KRI value above 1.0, which indicated a relatively slow dissociation from the target. All other compounds had a KRI value below or equal to 1.0, predicting a relatively fast dissociation rate. Several compounds were selected for follow-up kinetic quantifications in classical kinetic assays and were shown to have kinetic rates that corresponded to their KRI values. The dual-point assay and KRI value may have general applicability at other G-protein-coupled receptors, as well as at drug targets from other protein families.
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Affiliation(s)
- Dong Guo
- Leiden University, Leiden, the Netherlands
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15
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Vauquelin G, Van Liefde I. Radioligand dissociation measurements: potential interference of rebinding and allosteric mechanisms and physiological relevance of the biological model systems. Expert Opin Drug Discov 2012; 7:583-95. [DOI: 10.1517/17460441.2012.687720] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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16
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Vauquelin G, Bostoen S, Vanderheyden P, Seeman P. Clozapine, atypical antipsychotics, and the benefits of fast-off D2 dopamine receptor antagonism. Naunyn Schmiedebergs Arch Pharmacol 2012; 385:337-72. [PMID: 22331262 DOI: 10.1007/s00210-012-0734-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/25/2012] [Indexed: 12/20/2022]
Abstract
Drug-receptor interactions are traditionally quantified in terms of affinity and efficacy, but there is increasing awareness that the drug-on-receptor residence time also affects clinical performance. While most interest has hitherto been focused on slow-dissociating drugs, D(2) dopamine receptor antagonists show less extrapyramidal side effects but still have excellent antipsychotic activity when they dissociate swiftly. Fast dissociation of clozapine, the prototype of the "atypical antipsychotics", has been evidenced by distinct radioligand binding approaches both on cell membranes and intact cells. The surmountable nature of clozapine in functional assays with fast-emerging responses like calcium transients is confirmatory. Potential advantages and pitfalls of the hitherto used techniques are discussed, and recommendations are given to obtain more precise dissociation rates for such drugs. Surmountable antagonism is necessary to allow sufficient D(2) receptor stimulation by endogenous dopamine in the striatum. Simulations are presented to find out whether this can be achieved during sub-second bursts in dopamine concentration or rather during much slower, activity-related increases thereof. While the antagonist's dissociation rate is important to distinguish between both mechanisms, this becomes much less so when contemplating time intervals between successive drug intakes, i.e., when pharmacokinetic considerations prevail. Attention is also drawn to the divergent residence times of hydrophobic antagonists like haloperidol when comparing radioligand binding data on cell membranes with those on intact cells and clinical data.
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Affiliation(s)
- Georges Vauquelin
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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17
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Vauquelin G. Determination of drug–receptor residence times by radioligand binding and functional assays: experimental strategies and physiological relevance. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20015e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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Packeu A, Wennerberg M, Balendran A, Vauquelin G. Estimation of the dissociation rate of unlabelled ligand-receptor complexes by a 'two-step' competition binding approach. Br J Pharmacol 2011; 161:1311-28. [PMID: 20946109 DOI: 10.1111/j.1476-5381.2010.00931.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE Because the in vivo effectiveness of ligands may also be determined by the rate by which they dissociate from their target receptors, drug candidates are being increasingly screened for this kinetic property. The dissociation rate of unlabelled ligand-receptor complexes can be estimated indirectly from their ability to slow the association of subsequently added radioligand molecules. EXPERIMENTAL APPROACH We used the 'two-step competition' binding approach consisting of pre-incubating the receptor preparation with a wide range of ligand concentrations, washing off free ligand molecules, adding radioligand and monitoring its receptor binding after a fixed time. Based on the rationale that binding of both ligands is mutually exclusive and that they bind according to the law of mass action to a single class of sites, the unlabelled ligand's dissociation rate can be estimated from the upward shift that the competition curve experiences after washing. KEY RESULTS The relevance of the 'two-step competition' approach was explored by computer simulations and by comparing the dissociation behaviour of unlabelled D(2) dopamine and CB(1) cannabinoid receptor antagonists in this and alternative approaches. Besides providing satisfactory estimations of dissociation rates, the method also detects the ability of the unlabelled ligand molecules to be released from 'sinks' such as the cell membrane. CONCLUSIONS AND IMPLICATIONS As the 'two-step competition' requires rapid intermediate washing steps and needs radioligand binding to be measured at only one time point, this approach is particularly suited for binding studies on intact plated cells. LINKED ARTICLES This article is part of a themed section on Analytical Receptor Pharmacology in Drug Discovery. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2010.161.issue-6.
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Affiliation(s)
- A Packeu
- Department of Molecular and Biochemical Pharmacology, Free University of Brussels (VUB), Brussels, Belgium
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19
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Hulme EC, Trevethick MA. Ligand binding assays at equilibrium: validation and interpretation. Br J Pharmacol 2011; 161:1219-37. [PMID: 20132208 DOI: 10.1111/j.1476-5381.2009.00604.x] [Citation(s) in RCA: 431] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The focus of this review paper is factors affecting data interpretation in ligand binding assays under equilibrium conditions. Protocols for determining K(d) (the equilibrium dissociation constant) and K(dA) (the equilibrium inhibitor constant) for receptor ligands are discussed. The basic theory describing the interaction of a radiotracer and an unlabelled competitor ligand with a receptor is developed. Inappropriate experimental design may result in ligand depletion and non-attainment of equilibrium, distorting the calculation of K(d) and K(dA) . Strategies, both theoretical and practical, will be given to avoid and correct such errors, thus leading to the determination of reliable values for these constants. In determining K(dA) from competition binding studies, two additional concepts are discussed. First, the necessity to measure an adequate specific binding signal from the bound radiotracer ligand limits the range of affinity constants that can be measured: a particular set of assay conditions may lead to an upper limit on the apparent affinity of unlabelled ligands. Second, an extension of the basic assay methodology can indicate whether the interaction between the tracer and a test ligand is mediated by a competitive or an allosteric mechanism. Finally, the review ends with a discussion of two factors that are often overlooked: buffer composition and the temperature at which the assay is conducted, and the impact these can have on affinity measurements and the understanding of drug interactions.
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Affiliation(s)
- Edward C Hulme
- Division of Physical Biochemistry, MRC National Institute for Medical Research, Mill Hill, London, UK.
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20
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Liu Y, Gong W, Breinholt J, Norskov-Lauritsen L, Zhang J, Ma Q, Chen J, Panina S, Guo W, Li T, Zhang J, Kong M, Liu Z, Mao J, Christensen L, Hu S, Wang L. Discovery of the improved antagonistic prolactin variants by library screening. Protein Eng Des Sel 2011; 24:855-60. [DOI: 10.1093/protein/gzr047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Real-time, high-throughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay. J Immunol Methods 2010; 374:5-12. [PMID: 21044632 DOI: 10.1016/j.jim.2010.10.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 10/27/2010] [Indexed: 11/21/2022]
Abstract
Efficient presentation of peptide-MHC class I complexes to immune T cells depends upon stable peptide-MHC class I interactions. Theoretically, determining the rate of dissociation of a peptide-MHC class I complexes is straightforward; in practical terms, however, generating the accurate and closely timed data needed to determine the rate of dissociation is not simple. Ideally, one should use a homogenous assay involving an inexhaustible and label-free assay principle. Here, we present a homogenous, high-throughput peptide-MHC class I dissociation assay, which by and large fulfill these ideal requirements. To avoid labeling of the highly variable peptide, we labeled the invariant β2m and monitored its dissociation by a scintillation proximity assay, which has no separation steps and allows for real-time quantitative measurement of dissociation. Validating this work-around to create a virtually label-free assay, we showed that rates of peptide-MHC class I dissociation measured in this assay correlated well with rates of dissociation rates measured conventionally with labeled peptides. This assay can be used to measure the stability of any peptide-MHC class I combination, it is reproducible and it is well suited for high-throughput screening. To exemplify this, we screened a panel of 384 high-affinity peptides binding to the MHC class I molecule, HLA-A*02:01, and observed the rates of dissociation that ranged from 0.1h to 46h depending on the peptide used.
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22
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Vauquelin G. Rebinding: or why drugs may act longer in vivo than expected from their in vitro target residence time. Expert Opin Drug Discov 2010; 5:927-41. [PMID: 22823988 DOI: 10.1517/17460441.2010.512037] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
IMPORTANCE OF THE FIELD It is well established that the in vivo duration of drug action not only depends on macroscopic pharmacokinetic properties like its plasma half-life, but also on the residence time of the drug-target complexes. However, drug 'rebinding' (i.e., the consecutive binding of dissociated drug molecules to the original target and/or targets nearby) can be influential in vivo as well. AREAS COVERED IN THIS REVIEW Information about rebinding is available since the 1980s but it is dispersed in the life sciences literature. This review compiles this information. In this respect, neurochemists and biopohysicians advance the same equations to describe drug rebinding. WHAT THE READER WILL GAIN The rebinding mechanism is explained according to the prevailing viewpoint in different life science disciplines. There is a general consensus that high target densities, high association rates and local phenomena that hinder the diffusion of free drug molecules away from their target all promote rebinding. TAKE HOME MESSAGE Simulations presented here for the first time suggest that rebinding may increase the duration and even the constancy of the drug's clinical action. Intact cell radioligand dissociation and related ex vivo experiments offer useful indications about a drug's aptitude to experience target rebinding.
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Affiliation(s)
- Georges Vauquelin
- Free University Brussels (VUB), Department of Molecular and Biochemical Pharmacology, Building E.5.10, Pleinlaan 2, B-1050 Brussels, Belgium +32 2 6291955 ; +32 2 6291358 ;
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23
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Malany S, Hernandez LM, Smith WF, Crowe PD, Hoare SRJ. Analytical method for simultaneously measuring ex vivo drug receptor occupancy and dissociation rate: application to (R)-dimethindene occupancy of central histamine H1 receptors. J Recept Signal Transduct Res 2009; 29:84-93. [PMID: 19308787 DOI: 10.1080/10799890902721339] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We introduce a novel experimental method to determine both the extent of ex vivo receptor occupancy of administered compound and its dissociation rate constant (k4). [Here, we reference k4 as the rate of offset of unlabeled ligand in convention with Motulsky and Mahan (1)]. We derived a kinetic rate equation based on the dissociation rate constant for an unlabeled compound competing for the same site as a labeled compound and describe a model to simulate fractional occupancy. To validate our model, we performed in vitro kinetics and ex vivo occupancy experiments in rat cortex with varying concentrations of (R)-dimethindene, a sedating antihistamine. Brain tissue was removed at various times post oral administration, and histamine H1 receptor ligand [3H]-doxepin binding to homogenates from drug-treated or vehicle-treated rats was measured at multiple time points at room temperature. Fractional occupancy and k4 for (R)-dimethindene binding to H1 receptors were calculated by using our proposed model. Rats dosed with 30 and 60 mg/kg (R)-dimethindene showed 42% and 67% occupancy of central H1 receptors, respectively. These results were comparable to occupancy data determined by equilibrium radioligand binding. In addition, drug k4 rate determined by using our ex vivo method was equivalent to k4 determined by in vitro competition kinetics (dissociation half-life t(1/2) approximately 30 min). The outlined method can be used to assess, by simulation and experiment, occupancy for compounds based on dissociation rate constants and contributes to current efforts in drug optimization to profile antagonist efficacy in terms of its kinetic drug-target binding parameters. Data described by the method may be analyzed with commercially available software. Suggested fitting procedures are given in the appendix.
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Affiliation(s)
- Siobhan Malany
- Division of Emerging New Technologies, Neurocrine Biosciences, San Diego, California, USA.
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24
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Chen C, Wu D, Guo Z, Xie Q, Reinhart GJ, Madan A, Wen J, Chen T, Huang CQ, Chen M, Chen Y, Tucci FC, Rowbottom M, Pontillo J, Zhu YF, Wade W, Saunders J, Bozigian H, Struthers RS. Discovery of Sodium R-(+)-4-{2-[5-(2-Fluoro-3-methoxyphenyl)-3-(2-fluoro-6-[trifluoromethyl]benzyl)-4-methyl-2,6-dioxo-3,6-dihydro-2H-pyrimidin-1-yl]-1-phenylethylamino}butyrate (Elagolix), a Potent and Orally Available Nonpeptide Antagonist of the Human Gonadotropin-Releasing Hormone Receptor. J Med Chem 2008; 51:7478-85. [DOI: 10.1021/jm8006454] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chen Chen
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Dongpei Wu
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Zhiqiang Guo
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Qiu Xie
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Greg J. Reinhart
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Ajay Madan
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Jenny Wen
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Takung Chen
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Charles Q. Huang
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Mi Chen
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Yongsheng Chen
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Fabio C. Tucci
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Martin Rowbottom
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Joseph Pontillo
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Yun-Fei Zhu
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Warren Wade
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - John Saunders
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Haig Bozigian
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - R. Scott Struthers
- Department of Medicinal Chemistry, Department of Endocrinology, and Department of Preclinical Development, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
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25
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Glickman JF, Schmid A, Ferrand S. Scintillation Proximity Assays in High-Throughput Screening. Assay Drug Dev Technol 2008; 6:433-55. [DOI: 10.1089/adt.2008.135] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Andres Schmid
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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26
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Betz SF, Zhu YF, Chen C, Struthers RS. Non-Peptide Gonadotropin-Releasing Hormone Receptor Antagonists. J Med Chem 2008; 51:3331-48. [DOI: 10.1021/jm701249f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephen F. Betz
- Endocrinology & Metabolism, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Yun-Fei Zhu
- Endocrinology & Metabolism, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - Chen Chen
- Endocrinology & Metabolism, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
| | - R. Scott Struthers
- Endocrinology & Metabolism, Neurocrine Biosciences, Inc., 12790 El Camino Real, San Diego, California 92130
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