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Kesler V, Fu K, Chen Y, Park CH, Eisenstein M, Murmann B, Soh HT. Tailoring electrode surface charge to achieve discrimination and quantification of chemically similar small molecules with electrochemical aptamers. ADVANCED FUNCTIONAL MATERIALS 2023; 33:2208534. [PMID: 36819738 PMCID: PMC9937077 DOI: 10.1002/adfm.202208534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 06/18/2023]
Abstract
Electrochemical biosensors based on structure-switching aptamers offer many advantages because they can operate directly in complex samples and offer the potential to integrate with miniaturized electronics. Unfortunately, these biosensors often suffer from cross-reactivity problems when measuring a target in samples containing other chemically similar molecules, such as precursors or metabolites. While some progress has been made in selecting highly specific aptamers, the discovery of these reagents remains slow and costly. In this work, we demonstrate a novel strategy to distinguish molecules with miniscule difference in chemical composition (such as a single hydroxyl group) - with cross reactive aptamer probes - by tuning the charge state of the surface on which the aptamer probes are immobilized. As an exemplar, we show that our strategy can distinguish between DOX and many structurally similar analytes, including its primary metabolite doxorubicinol (DOXol). We then demonstrate the ability to accurately quantify mixtures of these two molecules based on their differential response to sensors with different surface-charge properties. We believe this methodology is general and can be extended to a broad range of applications.
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Affiliation(s)
- Vladimir Kesler
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Kaiyu Fu
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Yihang Chen
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Chan Ho Park
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Boris Murmann
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - H. Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Wang Y, Zheng Y, Zhou R, Ma M. Kinetic studies on soluble sugar profile in rice during storage: Derivation using the Laplace transform. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2021.102915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhao X, Wei L, Pang G, Xie J. A Novel GABA
B
R1a Receptor Electrochemical Biosensor Based on Gold Nanoparticles Chitosan‐horseradish Peroxidase. ELECTROANAL 2021. [DOI: 10.1002/elan.202060594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Xiaotong Zhao
- Biotechnology & food Science College Tianjin University of Commerce Tianjin 300134 PR China
| | - Lihui Wei
- Biotechnology & food Science College Tianjin University of Commerce Tianjin 300134 PR China
| | - Guangchang Pang
- Biotechnology & food Science College Tianjin University of Commerce Tianjin 300134 PR China
| | - Junbo Xie
- School of Chinese Materia Medica Tianjin University of Traditional Chinese Medicine Tianjin 301617 PR China
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Thevendran R, Navien TN, Meng X, Wen K, Lin Q, Sarah S, Tang TH, Citartan M. Mathematical approaches in estimating aptamer-target binding affinity. Anal Biochem 2020; 600:113742. [PMID: 32315616 DOI: 10.1016/j.ab.2020.113742] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/25/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Mathematical models ranging from one-site binding to multiple aptameric binding site-based models are explained in detail. Models applied in several different approaches of affinity measurements such as thermodynamics and kinetic analysis, including cooperativity and competitive-assay based mathematical models have been elaborately discussed. Mathematical models incorporating factors that could potentially affect affinity measurements are also further scrutinized.
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Affiliation(s)
- Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Xin Meng
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Kechun Wen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Shigdar Sarah
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria, 3216, Australia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia; Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States.
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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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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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