1
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Khiar-Fernández N, Zian D, Vázquez-Villa H, Martínez RF, Escobar-Peña A, Foronda-Sainz R, Ray M, Puigdomenech-Poch M, Cincilla G, Sánchez-Martínez M, Kihara Y, Chun J, López-Vales R, López-Rodríguez ML, Ortega-Gutiérrez S. Novel Antagonist of the Type 2 Lysophosphatidic Acid Receptor (LPA 2), UCM-14216, Ameliorates Spinal Cord Injury in Mice. J Med Chem 2022; 65:10956-10974. [PMID: 35948083 PMCID: PMC9421655 DOI: 10.1021/acs.jmedchem.2c00046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Spinal cord injuries (SCIs) irreversibly disrupt spinal
connectivity,
leading to permanent neurological disabilities. Current medical treatments
for reducing the secondary damage that follows the initial injury
are limited to surgical decompression and anti-inflammatory drugs,
so there is a pressing need for new therapeutic strategies. Inhibition
of the type 2 lysophosphatidic acid receptor (LPA2) has
recently emerged as a new potential pharmacological approach to decrease
SCI-associated damage. Toward validating this receptor as a target
in SCI, we have developed a new series of LPA2 antagonists,
among which compound 54 (UCM-14216) stands out as a potent
and selective LPA2 receptor antagonist (Emax = 90%, IC50 = 1.9 μM, KD = 1.3 nM; inactive at LPA1,3–6 receptors).
This compound shows efficacy in an in vivo mouse model of SCI in an
LPA2-dependent manner, confirming the potential of LPA2 inhibition for providing a new alternative for treating SCI.
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Affiliation(s)
- Nora Khiar-Fernández
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Debora Zian
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - R Fernando Martínez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Andrea Escobar-Peña
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Román Foronda-Sainz
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Manisha Ray
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maria Puigdomenech-Poch
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, BarcelonaE-08193, Spain
| | - Giovanni Cincilla
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, Barcelona E-08028, Spain
| | - Melchor Sánchez-Martínez
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, Barcelona E-08028, Spain.,Burua Scientific, Sant Pere de Ribes E-08810, Spain
| | - Yasuyuki Kihara
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jerold Chun
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rubèn López-Vales
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, BarcelonaE-08193, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
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2
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Kerschbaumer NM, Fochler LI, Reichenspurner M, Rieger S, Fedoruk M, Feldmann J, Lohmüller T. Twisted light Michelson interferometer for high precision refractive index measurements. OPTICS EXPRESS 2022; 30:29722-29734. [PMID: 36299140 DOI: 10.1364/oe.462782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/07/2022] [Indexed: 06/16/2023]
Abstract
Using orbital angular momentum beams in a Michelson interferometer opens the possibility for non-invasive measurements of refractive index changes down to 10-6 refractive index units. We demonstrate the application of a twisted light interferometer to directly measure the concentration of NaCl and glucose solutions label-free and in situ and to monitor temperature differences in the mK-µK range. From these measurements we can extract a correlation of the refractive index to concentration and to temperature from a liquid sample which is in good agreement with literature. Applying this type of twisted light interferometry yields a novel, robust, and easily implementable method for in situ monitoring of concentration and temperature changes in microfluidic samples.
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3
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Mulkerns NMC, Hoffmann WH, Lindsay ID, Gersen H. An Analysis of Semicircular Channel Backscattering Interferometry through Ray Tracing Simulations. SENSORS 2022; 22:s22114301. [PMID: 35684929 PMCID: PMC9185450 DOI: 10.3390/s22114301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023]
Abstract
Recent backscattering interferometry studies utilise a single channel microfluidic system, typically approximately semicircular in cross-section. Here, we present a complete ray tracing model for on-chip backscattering interferometry with a semicircular cross-section, including the dependence upon polarisation and angle of incidence. The full model is validated and utilised to calculate the expected fringe patterns and sensitivities observed under both normal and oblique angles of incidence. Comparison with experimental data from approximately semicircular channels using the parameters stated shows that they cannot be explained using a semicircular geometry. The disagreement does not impact on the validity of the experimental data, but highlights that the optical mechanisms behind the various modalities of backscattering interferometry would benefit from clarification. From the analysis presented here, we conclude that for reasons of ease of analysis, data quality, and sensitivity for a given radius, capillary-based backscattering interferometry affords numerous benefits over on-chip backscattering interferometry.
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Affiliation(s)
- Niall M. C. Mulkerns
- H. H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK; (N.M.C.M.); (W.H.H.); (I.D.L.)
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol BS8 1TL, UK
| | - William H. Hoffmann
- H. H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK; (N.M.C.M.); (W.H.H.); (I.D.L.)
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol BS8 1TL, UK
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Ian D. Lindsay
- H. H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK; (N.M.C.M.); (W.H.H.); (I.D.L.)
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol BS8 1TL, UK
| | - Henkjan Gersen
- H. H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK; (N.M.C.M.); (W.H.H.); (I.D.L.)
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol BS8 1TL, UK
- Correspondence:
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4
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Shedding Light on Capillary-Based Backscattering Interferometry. SENSORS 2022; 22:s22062157. [PMID: 35336326 PMCID: PMC8949530 DOI: 10.3390/s22062157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 02/05/2023]
Abstract
Capillary-based backscattering interferometry has been used extensively as a tool to measure molecular binding via interferometric refractive index sensing. Previous studies have analysed the fringe patterns created in the backscatter direction. However, polarisation effects, spatial chirps in the fringe pattern and the practical impact of various approximations, and assumptions in existing models are yet to be fully explored. Here, two independent ray tracing approaches are applied, analysed, contrasted, compared to experimental data, and improved upon by introducing explicit polarisation dependence. In doing so, the significance of the inner diameter, outer diameter, and material of the capillary to the resulting fringe pattern and subsequent analysis are elucidated for the first time. The inner diameter is shown to dictate the fringe pattern seen, and therefore, the effectiveness of any dechirping algorithm, demonstrating that current dechirping methods are only valid for a subset of capillary dimensions. Potential improvements are suggested in order to guide further research, increase sensitivity, and promote wider applicability.
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5
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Eder C, Briesen H. Interferometric Probing of Physical and Chemical Properties of Solutions: Noncontact Investigation of Liquids. Annu Rev Chem Biomol Eng 2022; 13:99-121. [PMID: 35300516 DOI: 10.1146/annurev-chembioeng-092220-123822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interferometry is a highly versatile tool for probing physical and chemical phenomena. In addition to the benefit of noncontact investigations, even spatially resolved information can be obtained by choosing a suitable setup. This review presents the evolution of the various setups that have evolved since the first interferometers were developed in the mid-nineteenth century and highlights the benefits, limitations, and typical areas of application. This review focuses on interferometry based on electromagnetic waves in the near-infrared and visible range applied to liquid samples, categorizes the chemical/physical properties (e.g., pressure, temperature, composition) and phenomena (e.g., evaporation, crystal growth, diffusion, thermophoresis) that can be assessed, and presents a comprehensive literature review of specific existing applications. Finally, it discusses some fundamental open questions with respect to geometric considerations and overlapping effects. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Cornelia Eder
- Process Systems Engineering, Technical University of Munich, Freising, Germany;
| | - Heiko Briesen
- Process Systems Engineering, Technical University of Munich, Freising, Germany;
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6
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Abbas S, Koch KW. Label-free Quantification of Direct Protein-protein Interactions with Backscattering Interferometry. Bio Protoc 2021; 11:e4256. [PMID: 35087916 DOI: 10.21769/bioprotoc.4256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
The functional performance of a cell depends on how macromolecules, in particular proteins, come together in a precise orientation, how they assemble into protein complexes and interact with each other. In order to study protein-protein interactions at a molecular level, a variety of methods to investigate these binding processes yield affinity constants and/or the identification of binding regions. There are several well-established biophysical techniques for biomolecular interaction studies, such as fluorescence spectroscopy and surface plasmon resonance. Although these techniques have been proven to be efficient, they either need labeling or immobilization of one interaction partner. Backscattering interferometry (BSI) is a label-free detection method, which allows label- and immobilization-free interaction analysis under physiologically relevant conditions with high sensitivity and in small volumes. We used BSI to measure the interaction of the neuronal calcium sensor recoverin with its target G protein-coupled receptor kinase 1 (GRK1) as a model system. Increasing concentrations of purified recoverin were mixed with a specific concentration of a GRK1 fusion protein. In this protocol, we provide a full description of the instrumental setup, data acquisition, and evaluation. Equilibrium dissociation constants of recoverin-GRK1 interaction determined by the BSI instrumental setup are in full agreement with affinity constants obtained by different methods as described in the literature.
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Affiliation(s)
- Seher Abbas
- Department of Neuroscience, University of Oldenburg, Oldenburg D-26129, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, University of Oldenburg, Oldenburg D-26129, Germany
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7
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Jiang D, Zhao X, Liu YN, Chen HB, Lv WL, Qian C, Liu XW. Label-Free Probing of Molecule Binding Kinetics Using Single-Particle Interferometric Imaging. Anal Chem 2021; 93:7965-7969. [PMID: 34029055 DOI: 10.1021/acs.analchem.1c00828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Probing molecular interactions is critical for screening drugs, detecting pollutants, and understanding biological processes at the molecular level, but these interactions are difficult to detect, especially for small molecules. A label-free optical imaging technology that can detect molecule binding kinetics is presented, in which free-moving particles are driven into oscillations with an alternating electrical field and the interferometric scattering patterns of the particles are imaged via an optical imaging method. By tracking the charge-sensitive variations in the oscillation amplitude with sub-nanometer precision, the small molecules and metal ions binding to the surface as well as protein-protein binding kinetics were measured. The capability of the label-free measurement of molecular interactions can provide a promising platform for screening small-molecule drugs, probing conformational changes in proteins, and detecting environmental pollutants.
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Affiliation(s)
- Di Jiang
- Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Xiaona Zhao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Hefei National Laboratory for Physical Sciences at the Microscale, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yi-Nan Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Hefei National Laboratory for Physical Sciences at the Microscale, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Hai-Bo Chen
- Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Wen-Li Lv
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Hefei National Laboratory for Physical Sciences at the Microscale, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Chen Qian
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Hefei National Laboratory for Physical Sciences at the Microscale, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xian-Wei Liu
- Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China.,Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Hefei National Laboratory for Physical Sciences at the Microscale, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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8
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Liang R, Ma G, Jing W, Wang Y, Yang Y, Tao N, Wang S. Charge-Sensitive Optical Detection of Small Molecule Binding Kinetics in Normal Ionic Strength Buffer. ACS Sens 2021; 6:364-370. [PMID: 32842724 DOI: 10.1021/acssensors.0c01063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most label-free detection technologies detect the masses of molecules, and their sensitivities thus decrease with molecular weight, making it challenging to detect small molecules. To address this need, we have developed a charge-sensitive optical detection (CSOD) technique, which detects the charge rather than the mass of a molecule with an optical fiber. However, the effective charge of a molecule decreases with the buffer ionic strength. For this reason, the previous CSOD works with diluted buffers, which could affect the measured molecular binding kinetics. Here, we show a technique capable of detecting molecular binding kinetics in normal ionic strength buffers. An H-shaped sample well was developed to increase the current density at the sensing area to compensate the signal loss due to ionic screening at normal ionic strength buffer, while keeping the current density low at the electrodes to minimize the electrode reaction. In addition, agarose gels were used to cover the electrodes to prevent electrode reaction generated bubbles from entering the sensing area. With this new design, we have measured the binding kinetics between G-protein-coupled receptors (GPCRs) and their small molecule ligands in normal buffer. We found that the affinities measured in normal buffer are stronger than those measured in diluted buffer, likely due to the stronger electrostatic repulsion force between the same charged ligands and receptors in the diluted buffer.
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9
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Crump GM, Zhou J, Mashayekh S, Grimes CL. Revisiting peptidoglycan sensing: interactions with host immunity and beyond. Chem Commun (Camb) 2020; 56:13313-13322. [PMID: 33057506 PMCID: PMC7642115 DOI: 10.1039/d0cc02605k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interaction between host immunity and bacterial cells plays a pivotal role in a variety of human diseases. The bacterial cell wall component peptidoglycan (PG) is known to stimulate an immune response, which makes PG a distinctive recognition element for unveiling these complicated molecular interactions. Pattern recognition receptor (PRR) proteins are among the critical components of this system that initially recognize molecular patterns associated with microorganisms such as bacteria and fungi. These molecular patterns are mostly embedded in the bacterial or fungal cell wall structure and can be released and presented to the immune system in various situations. Nonetheless, detailed knowledge of this recognition is limited due to the diversity among the PG polymer and its fragments; the subsequent responses by multiple hosts add more complexity. Here, we discuss how our understanding of the role and molecular mechanisms of the well-studied PRR, the NOD-like receptors (NLRs), in the human immune system has evolved in recent years. We highlight the instances of other classes of proteins with similar behavior in the recognition of PG that have been identified in other microorganisms such as yeasts. These proteins are particularly interesting because a network of cellular interactions exists between human host cells, bacteria and yeast as a part of the normal human flora. To support our understanding of these interactions, we provide insight into the chemist's toolbox of peptidoglycan probes that aid in the investigations of the behaviors of these proteins and other biological contexts relevant to the sensing and recognition of peptidoglycan. The importance of these interactions in human health for the development of biomarkers and biotherapy is highlighted.
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Affiliation(s)
- Geneva Maddison Crump
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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10
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Kammer M, Kussrow AK, Olmsted IR, Jackson GW, Bornhop DJ. Free Solution Assay Signal Modulation in Variable-Stem-Length Hairpin Aptamers. ACS OMEGA 2020; 5:11308-11313. [PMID: 32478218 PMCID: PMC7254501 DOI: 10.1021/acsomega.9b04341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Interferometric measurements of free solution assays (FSAs) quantify changes in molecular conformation and hydration upon binding. Here, we demonstrate that aptamer probes designed to undergo varying levels of conformational change upon binding produce corresponding variations in FSA signals. A series of hairpin aptamers were synthesized for the small molecule (tenofovir) with identical loop regions that contain the binding pocket, with between 2 and 10 self-associating base pairings in the stem region. Aptamers selected for tenofovir showed a decrease in the FSA signal and binding affinity (increase in K D) with increasing stem length. Thermodynamic calculations of the Gibbs free energy (ΔG) reported a decrease in ΔG with respect to a corresponding increase in the aptamer stem length. Collectively, these observations provide an expanded understanding of FSA and demonstrate the potential for the rational design of label-free aptamer beacons using FSA as readout.
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Affiliation(s)
- Michael
N. Kammer
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - George W. Jackson
- Base
Pair Biotechnologies, Inc., Pearland, Texas 77584, United States
| | - Darryl J. Bornhop
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
University Institute of Chemical Biology, Nashville, Tennessee 37232-6304, United States
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11
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Gauglitz G. Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects. Anal Bioanal Chem 2020; 412:3317-3349. [PMID: 32313998 PMCID: PMC7214504 DOI: 10.1007/s00216-020-02581-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022]
Abstract
Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.
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Affiliation(s)
- Günter Gauglitz
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
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12
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Wang Y, Guo W, Yang Q, Su B. Electrochemiluminescence Self-Interference Spectroscopy with Vertical Nanoscale Resolution. J Am Chem Soc 2020; 142:1222-1226. [DOI: 10.1021/jacs.9b12833] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yafeng Wang
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Weiliang Guo
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qian Yang
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Bin Su
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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13
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Wan Y, Zhao J, He J, Lou X. Nano-Affi: a solution-phase, label-free, colorimetric aptamer affinity assay based on binding-inhibited aggregation of gold nanoparticles. Analyst 2020; 145:4276-4282. [DOI: 10.1039/d0an00827c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ideal way to assess aptamer affinity is when both aptamer and target are in a native state, without the unpredictable interference associated with labelling and surface immobilization.
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Affiliation(s)
- Yuan Wan
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Jiaxing Zhao
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing
- China
| | - Xinhui Lou
- Department of Chemistry
- Capital Normal University
- Beijing
- China
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14
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Wang Y, Yang Q, Su B. Spatially resolved electrochemistry enabled by thin-film optical interference. Chem Commun (Camb) 2020; 56:12359-12362. [DOI: 10.1039/d0cc05265e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical reactions occurring on the local surface can be spatially resolved by successive interferometric imaging of the nanochannel membrane coated electrode.
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Affiliation(s)
- Yafeng Wang
- Institute of Analytical Chemistry
- Department of Chemistry
- Zhejiang University
- Hangzhou 310058
- China
| | - Qian Yang
- Institute of Analytical Chemistry
- Department of Chemistry
- Zhejiang University
- Hangzhou 310058
- China
| | - Bin Su
- Institute of Analytical Chemistry
- Department of Chemistry
- Zhejiang University
- Hangzhou 310058
- China
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15
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González-Gil I, Zian D, Vázquez-Villa H, Hernández-Torres G, Martínez RF, Khiar-Fernández N, Rivera R, Kihara Y, Devesa I, Mathivanan S, Del Valle CR, Zambrana-Infantes E, Puigdomenech M, Cincilla G, Sanchez-Martinez M, Rodríguez de Fonseca F, Ferrer-Montiel AV, Chun J, López-Vales R, López-Rodríguez ML, Ortega-Gutiérrez S. A Novel Agonist of the Type 1 Lysophosphatidic Acid Receptor (LPA 1), UCM-05194, Shows Efficacy in Neuropathic Pain Amelioration. J Med Chem 2019; 63:2372-2390. [PMID: 31790581 DOI: 10.1021/acs.jmedchem.9b01287] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neuropathic pain (NP) is a complex chronic pain state with a prevalence of almost 10% in the general population. Pharmacological options for NP are limited and weakly effective, so there is a need to develop more efficacious NP attenuating drugs. Activation of the type 1 lysophosphatidic acid (LPA1) receptor is a crucial factor in the initiation of NP. Hence, it is conceivable that a functional antagonism strategy could lead to NP mitigation. Here we describe a new series of LPA1 agonists among which derivative (S)-17 (UCM-05194) stands out as the most potent and selective LPA1 receptor agonist described so far (Emax = 118%, EC50 = 0.24 μM, KD = 19.6 nM; inactive at autotaxin and LPA2-6 receptors). This compound induces characteristic LPA1-mediated cellular effects and prompts the internalization of the receptor leading to its functional inactivation in primary sensory neurons and to an efficacious attenuation of the pain perception in an in vivo model of NP.
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Affiliation(s)
- Inés González-Gil
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Debora Zian
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Gloria Hernández-Torres
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - R Fernando Martínez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Nora Khiar-Fernández
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Isabel Devesa
- IDiBE, Universidad Miguel Hernández de Elche, E-03202 Alicante, Spain
| | | | - Cristina Rosell Del Valle
- Instituto de Investigación Biomédica de Málaga, UGC Salud Mental, Universidad de Málaga, Hospital Universitario Regional de Málaga, E-29010 Málaga, Spain
| | - Emma Zambrana-Infantes
- Instituto de Investigación Biomédica de Málaga, UGC Salud Mental, Universidad de Málaga, Hospital Universitario Regional de Málaga, E-29010 Málaga, Spain
| | - María Puigdomenech
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - Giovanni Cincilla
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, E-08028 Barcelona, Spain
| | | | - Fernando Rodríguez de Fonseca
- Instituto de Investigación Biomédica de Málaga, UGC Salud Mental, Universidad de Málaga, Hospital Universitario Regional de Málaga, E-29010 Málaga, Spain.,Departamento de Psicobiología, Facultad de Psicología, Universidad Complutense de Madrid, Pozuelo de Alarcón, E-28223 Madrid, Spain
| | | | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rubén López-Vales
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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16
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Abbas S, Marino V, Dell’Orco D, Koch KW. Molecular Recognition of Rhodopsin Kinase GRK1 and Recoverin Is Tuned by Switching Intra- and Intermolecular Electrostatic Interactions. Biochemistry 2019; 58:4374-4385. [DOI: 10.1021/acs.biochem.9b00846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Seher Abbas
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
| | - Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Daniele Dell’Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
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17
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Kammer MN, Kussrow A, Gandhi I, Drabek R, Batchelor RH, Jackson GW, Bornhop DJ. Quantification of Opioids in Urine Using an Aptamer-Based Free-Solution Assay. Anal Chem 2019; 91:10582-10588. [PMID: 31314489 DOI: 10.1021/acs.analchem.9b01638] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The opioid epidemic continues in the United States. Many have been impacted by this epidemic, including neonates who exhibit Neonatal Abstinence Syndrome (NAS). Opioid diagnosis and NAS can be negatively impacted by limited testing options outside the hospital, due to poor assay performance, false-negatives, rapid drug clearance rates, and difficulty in obtaining enough specimen for testing. Here we report a small volume urine assay for oxycodone, hydrocodone, fentanyl, noroxycodone, norhydrocodone, and norfentanyl with excellent LODs and LOQs. The free-solution assay (FSA), coupled with high affinity DNA aptamer probes and a compensated interferometric reader (CIR), represents a potential solution for quantifying opioids rapidly, at high sensitivity, and noninvasively on small sample volumes. The mix-and-read test is 5- to 275-fold and 50- to 1250-fold more sensitive than LC-MS/MS and immunoassays, respectively. Using FSA, oxycodone, hydrocodone, fentanyl, and their urinary metabolites were quantified using 10 μL of urine at 28-81 pg/mL, with >95% specificity and excellent accuracy in ∼1 h. The assay sensitivity, small sample size requirement, and speed could enable opioid screening, particularly for neonates, and points to the potential for pharmacokinetic tracking.
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Affiliation(s)
- Michael N Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Ilavarasi Gandhi
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Rafal Drabek
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Robert H Batchelor
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - George W Jackson
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
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18
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Leclercq L, Saetear P, Rolland-Sabaté A, Biron JP, Chamieh J, Cipelletti L, Bornhop DJ, Cottet H. Size-Based Characterization of Polysaccharides by Taylor Dispersion Analysis with Photochemical Oxidation or Backscattering Interferometry Detections. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Laurent Leclercq
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
| | - Phoonthawee Saetear
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
- Department of Chemistry and the Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Agnès Rolland-Sabaté
- UR1268 Biopolymères Interactions Assemblages, INRA, F-44300 Nantes, France
- UMR0408 Sécurité et Qualité des Produits d’Origine Végétale, INRA, Université Avignon, F-84000 Avignon, France
| | | | - Joseph Chamieh
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
| | - Luca Cipelletti
- L2C, Université de Montpellier, CNRS, Montpellier 34095, France
| | | | - Hervé Cottet
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
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19
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Rectangular plasmonic interferometer for high sensitive glycerol sensor. Sci Rep 2019; 9:1378. [PMID: 30718632 PMCID: PMC6361946 DOI: 10.1038/s41598-018-37499-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
A novel plasmonic interferometric sensor intended for application to biochemical sensing has been investigated experimentally and theoretically. The sensor was included a slit surrounded by rectangular grooves using a thick gold film. A three-dimensional finite difference time-domain commercial software package was applied to simulate the structure. The Focused ion beam milling has been used as a mean to fabricate series of rectangular plasmonic interferometer with varying slit-groove distance L. Oscillation behavior is shown by transmission spectra in a broadband wavelength range between 400 nm and 800 nm in the distance between slit and grooves. Red-shifted interference spectrum is the result of increasing refractive indices. The proposed structure is functional from visible to near-infrared wavelength range and yields a sensitivity of 4923 nm/RIU and a figure of merit as high as 214 at 729 nm wavelength. In conclusion, this study indicates the possibility of fabricating a low cost, compact, and real-time high-throughput plasmonic interferometer.
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20
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Real-Time Interferometric Refractive Index Change Measurement for the Direct Detection of Enzymatic Reactions and the Determination of Enzyme Kinetics. SENSORS 2019; 19:s19030539. [PMID: 30696020 PMCID: PMC6387378 DOI: 10.3390/s19030539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 12/03/2022]
Abstract
Back scatter interferometry (BSI) is a sensitive method for detecting changes in the bulk refractive index of a solution in a microfluidic system. Here we demonstrate that BSI can be used to directly detect enzymatic reactions and, for the first time, derive kinetic parameters. While many methods in biomedical assays rely on detectable biproducts to produce a signal, direct detection is possible if the substrate or the product exert distinct differences in their specific refractive index so that the total refractive index changes during the enzymatic reaction. In this study, both the conversion of glucose to glucose-6-phosphate, catalyzed by hexokinase, and the conversion of adenosine-triphosphate to adenosine di-phosphate and mono-phosphate, catalyzed by apyrase, were monitored by BSI. When adding hexokinase to glucose solutions containing adenosine-triphosphate, the conversion can be directly followed by BSI, which shows the increasing refractive index and a final plateau corresponding to the particular concentration. From the initial reaction velocities, KM was found to be 0.33 mM using Michaelis–Menten kinetics. The experiments with apyrase indicate that the refractive index also depends on the presence of various ions that must be taken into account when using this technique. This study clearly demonstrates that measuring changes in the refractive index can be used for the direct determination of substrate concentrations and enzyme kinetics.
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21
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Mizuno H, Kihara Y, Kussrow A, Chen A, Ray M, Rivera R, Bornhop DJ, Chun J. Lysophospholipid G protein-coupled receptor binding parameters as determined by backscattering interferometry. J Lipid Res 2019; 60:212-217. [PMID: 30463988 PMCID: PMC6314248 DOI: 10.1194/jlr.d089938] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/13/2018] [Indexed: 12/23/2022] Open
Abstract
Lysophosphatidic acid (LPA) activates cognate G protein-coupled receptors (GPCRs) to initiate biological signaling cascades. Lysophospholipid (LP) receptor binding properties remain incompletely assessed because of difficulties with ligand lipophilicity and lipid "stickiness." These inherent attributes produce high levels of nonspecific binding within cell-membrane preparations used to assess GPCRs, as has been shown in classical binding assays using radiolabeled ligands, making accurate measurements of lipid binding kinetics difficult to achieve. Backscattering interferometry (BSI) is an optical technology that measures molecular binding interactions by reporting changes in the refractive index of a solution after binding events. Here, we report the use of BSI to assess LPA1 for its ability to bind to naturally occurring lipids and a synthetic LPA1 antagonist (ONO-9780307), under both primary- and competition-binding conditions. Assessment of 12 different lipids demonstrated that the known LP ligand, 1-oleoyl-LPA, as well as an endocannabinoid metabolite, anandamide phosphate, are specific ligands for LPA1, whereas other LPs tested were not. Newly determined dissociation constants (Kd values) for orthosteric lipid ligands approximated 10-9 M, substantially lower (i.e., with higher affinity) than measured Kd values in classical binding or cell-based assays. These results demonstrate that BSI may have particular utility in assessing binding interactions between lipid receptors and their lipid ligands and could provide new screening approaches for lipid receptor identification and drug discovery.
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Affiliation(s)
- Hirotaka Mizuno
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
- Discovery Technology Research Laboratories, Ono Pharmaceutical Co., Ltd., Osaka 618-8585, Japan
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Amanda Kussrow
- Department of Chemistry Vanderbilt University, Nashville, TN 37235
- Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Allison Chen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Manisha Ray
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Darryl J Bornhop
- Department of Chemistry Vanderbilt University, Nashville, TN 37235
- Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
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22
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Kammer MN, Kussrow AK, Olmsted IR, Bornhop DJ. A Highly Compensated Interferometer for Biochemical Analysis. ACS Sens 2018; 3:1546-1552. [PMID: 29984991 DOI: 10.1021/acssensors.8b00361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here we report an improved interferometric sensing approach that facilitates high sensitivity nanovolume refractive index (RI) measurements and molecular interaction assays without a temperature controller. The compensated backscattering interferometer (CBSI) is based on a helium-neon (He-Ne) laser, a microfluidic chip, and a CCD array. The CBSI enables simultaneous differential RI measurements within nanoliter volumes, at a compensation level of ca. 5 × 10-8 RIU in the presence of large thermal perturbations (8 °C). This level of d n/d T compensation is enabled by elongating the laser beam along the central axis of the microfluidic channel and measuring the difference in positional shift of interference patterns from two adjacent regions of the channel. By separating two solutions by an air gap or oil droplet, CBSI can discriminate the difference in RI for the sample and reference at a detection limit of 7 × 10-7 RIU in the absence of electronic filtering. At this level of ΔRI sensitivity, it is possible to perform label-free, free-solution biochemical assays at the 10s of nM level without the typical high-resolution temperature control needed in conventional interferometers. Here we illustrate the effective use of CBSI by quantifying the binding affinities for mannose-concanavalin A and Ca2+-recoverin interactions.
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Affiliation(s)
- Michael N. Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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23
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Dunn RC. Wavelength Modulated Back-Scatter Interferometry for Universal, On-Column Refractive Index Detection in Picoliter Volumes. Anal Chem 2018; 90:6789-6795. [PMID: 29762009 DOI: 10.1021/acs.analchem.8b00771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wavelength-modulated back scatter interferometry (M-BSI) is shown to improve the detection metrics for refractive index (RI) sensing in microseparations. In M-BSI, the output of a tunable diode laser is focused into the detection zone of a separation channel as the excitation wavelength is rapidly modulated. This spatially modulates the observed interference pattern, which is measured in the backscattered direction. Phase-sensitive detection using a split photodiode detector aligned on one fringe of the interference pattern is used to monitor RI changes as analytes are separated. Using sucrose standards, we report a detection limit of 700 μg/L in a 75 μm i.d. capillary at the 3σ level, corresponding to a detection volume of 90 pL. To validate the approach for electrophoretic separations, Na+ and Li+ were separated and detected with M-BSI and indirect-UV absorbance on the same capillary. A 4 mg/L NaCl and LiCl mixture leads to comparable separation efficiencies in the two detection schemes, with better signal-to-noise in the M-BSI detection, but less baseline stability. The latter arises in part from Joule heating, which influences RI measurements through the thermo-optic properties of the run buffer. To reduce this effect, a 25 μm i.d. capillary combined with active temperature control was used to detect the separation of sucrose, glucose, and lactose with M-BSI. The lack of suitable UV chromophores makes these analytes challenging to detect directly in ultrasmall volumes. Using a 55 mM NaOH run buffer, M-BSI is shown to detect the separation of a mixture of 174 mg/L sucrose, 97 mg/L glucose, and 172 mg/L lactose in a 15 pL detection volume. The universal on-column detection in ultrasmall volumes adds new capabilities for microanalysis platforms, while potentially reducing the footprint and costs of these systems.
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Affiliation(s)
- Robert C Dunn
- Ralph N. Adams Institute for Bioanalytical Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
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24
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Wimberg H, Janssen-Bienhold U, Koch KW. Control of the Nucleotide Cycle in Photoreceptor Cell Extracts by Retinal Degeneration Protein 3. Front Mol Neurosci 2018. [PMID: 29515371 PMCID: PMC5826319 DOI: 10.3389/fnmol.2018.00052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retinal degeneration protein 3 (RD3) is crucial for photoreceptor cell survival and linked to Leber Congenital Amaurosis type 12 (LCA12), a hereditary retinal disease in humans. RD3 inhibits photoreceptor guanylate cyclases GC-E and GC-F and is involved in transport of GCs from the inner to the outer segments. Otherwise, its role in photoreceptor physiology is poorly understood. Here, we describe a new function of RD3. Purified RD3 evoked an increase in guanylate kinase activity, an enzyme that is involved in the nucleotide cycle in photoreceptors. We demonstrate a direct interaction between guanylate kinase and RD3 using back-scattering interferometry and show by immunohistochemistry of mouse retina sections that RD3 and guanylate kinase co-localize in photoreceptor inner segments and to a lesser extent in the outer plexiform layer. Our findings point toward a more complex function of RD3 in photoreceptors. The RD3 – guanylate kinase interaction may also play a role in other cellular systems, while the GC – RD3 interaction is exclusive to photoreceptors.
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Affiliation(s)
- Hanna Wimberg
- Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Ulrike Janssen-Bienhold
- Department of Neuroscience, Visual Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
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25
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Kammer MN, Kussrow AK, Bornhop DJ. Longitudinal pixel averaging for improved compensation in backscattering interferometry. OPTICS LETTERS 2018; 43:482-485. [PMID: 29400820 DOI: 10.1364/ol.43.000482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Longitudinal averaging of the interference pattern in a compensated backscattering interferometer provides improved compensation for temperature induced refractive index perturbations. Fringe pattern likeness between two discrete detection regions of an off-the-shelf microfluidic chip illuminated by an inexpensive diode laser scales with interrogation length. Averaging the intensity distribution along a 2.75 mm length of the channel results in a 750-fold reduction in sensitivity to temperature and a baseline noise level of 3×10-8 refractive index units (RIU). These observations enable nanoliter-volume interferometric measurements at a level of 10-7 RIU in the presence of a 2°C temperature variation without the need for temperature control.
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26
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Cardarelli RA, Jones K, Pisella LI, Wobst HJ, McWilliams LJ, Sharpe PM, Burnham MP, Baker DJ, Chudotvorova I, Guyot J, Silayeva L, Morrow DH, Dekker N, Zicha S, Davies PA, Holenz J, Duggan ME, Dunlop J, Mather RJ, Wang Q, Medina I, Brandon NJ, Deeb TZ, Moss SJ. The small molecule CLP257 does not modify activity of the K +-Cl - co-transporter KCC2 but does potentiate GABA A receptor activity. Nat Med 2017; 23:1394-1396. [PMID: 29216042 PMCID: PMC7371006 DOI: 10.1038/nm.4442] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ross A Cardarelli
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
| | - Karen Jones
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Alderley Park, UK
| | - Lucie I Pisella
- INMED, INSERM, Unité 901, Marseille, France
- Aix-Marseille Université, UMR 901, Marseille, France
| | - Heike J Wobst
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | | | - Paul M Sharpe
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Alderley Park, UK
| | - Matthew P Burnham
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Alderley Park, UK
| | - David J Baker
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ilona Chudotvorova
- INMED, INSERM, Unité 901, Marseille, France
- Aix-Marseille Université, UMR 901, Marseille, France
| | - Justine Guyot
- INMED, INSERM, Unité 901, Marseille, France
- Aix-Marseille Université, UMR 901, Marseille, France
| | - Liliya Silayeva
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
| | - Danielle H Morrow
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Niek Dekker
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Stephen Zicha
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Paul A Davies
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Jörg Holenz
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Mark E Duggan
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - John Dunlop
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Robert J Mather
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Qi Wang
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Igor Medina
- INMED, INSERM, Unité 901, Marseille, France
- Aix-Marseille Université, UMR 901, Marseille, France
| | - Nicholas J Brandon
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
- Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Tarek Z Deeb
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
| | - Stephen J Moss
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Boston, Massachusetts, USA
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts, USA
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
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27
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Abstract
Perhaps because they are such commonly used tools, many researchers view antibodies one-dimensionally: Antibody Y binds antigen X. Although few techniques require a comprehensive understanding of any particular antibody's characteristics, well-executed experiments do require a basic appreciation of what is known and, equally as important, what is not known about the antibody being used. Ignorance of the relevant antibody characteristics critical for a particular assay can easily lead to loss of precious resources (time, money, and limiting amounts of sample) and, in worst-case scenarios, erroneous conclusions. Here, we describe various antibody characteristics to provide a more well-rounded perspective of these critical reagents. With this information, it will be easier to make informed decisions on how best to choose and use the available antibodies, as well as knowing when it is essential and how to determine a particular as yet-undefined characteristic.
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28
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Retzlaff CL, Kussrow A, Schorkopf T, Saetear P, Bornhop DJ, Hardaway JA, Sturgeon SM, Wright J, Blakely RD. Metallo-β-lactamase Domain-Containing Protein 1 (MBLAC1) Is a Specific, High-Affinity Target for the Glutamate Transporter Inducer Ceftriaxone. ACS Chem Neurosci 2017; 8:2132-2138. [PMID: 28783953 DOI: 10.1021/acschemneuro.7b00232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ceftriaxone, a β-lactam antibiotic, has been reported to act independently of its antimicrobial actions to normalize perturbed central nervous system glutamate levels, principally by elevating expression of glial glutamate transporters. Identification of a specific, high-affinity target for ceftriaxone could significantly impact therapeutic development for multiple brain disorders, ranging from neurodegenerative disorders to addiction. Recently, we identified a glial-expressed Caenorhabditis elegans gene, swip-10, that encodes a metallo-β-lactamase domain-containing protein, and limits glutamate-dependent changes in dopamine neuron excitability. Bioinformatic analyses identified MBLAC1 as the likely mammalian orthologue of swip-10. Using cyanogen bromide immobilized ceftriaxone for affinity capture experiments and backscattering interferometry to monitor MBLAC1 binding of unmodified ceftriaxone, we obtained evidence for specific, high affinity (KD = 2.2 μM) binding of ceftriaxone to MBLAC1. We discuss our findings with respect to MBLAC1 as a potentially exclusive, high-affinity binding partner of ceftriaxone in the CNS, and the path forward in the development of novel, MBLAC1-based therapeutics.
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Affiliation(s)
- Cassandra L. Retzlaff
- Department
of Biomedical Science and Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
| | | | | | | | | | | | | | | | - Randy D. Blakely
- Department
of Biomedical Science and Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
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29
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Schaefer AK, Melnyk JE, Baksh MM, Lazor KM, Finn MG, Grimes CL. Membrane Association Dictates Ligand Specificity for the Innate Immune Receptor NOD2. ACS Chem Biol 2017; 12:2216-2224. [PMID: 28708377 PMCID: PMC5569645 DOI: 10.1021/acschembio.7b00469] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
The
human gut must regulate its immune response to resident and
pathogenic bacteria, numbering in the trillions. The peptidoglycan
component of the bacterial cell wall is a dense and rigid structure
that consists of polymeric carbohydrates and highly cross-linked peptides
which offers protection from the host and surrounding environment.
Nucleotide-binding oligomerization domain-containing protein 2 (NOD2),
a human membrane-associated innate immune receptor found in the gut
epithelium and mutated in an estimated 30% of Crohn’s disease
patients, binds to peptidoglycan fragments and initiates an immune
response. Using a combination of chemical synthesis, advanced analytical
assays, and protein biochemistry, we tested the binding of a variety
of synthetic peptidoglycan fragments to wild-type (WT)-NOD2. Only
when the protein was presented in the native membrane did binding
measurements correlate with a NOD2-dependent nuclear factor kappa-light-chain-enhancer
of activated B cells (NF-κB) response, supporting the hypothesis
that the native-membrane environment confers ligand specificity to
the NOD2 receptor for NF-κB signaling. While N-acetyl-muramyl dipeptide (MDP) has been thought to be the minimal
peptidoglycan fragment necessary to activate a NOD2-dependent immune
response, we found that fragments with and without the dipeptide moiety
are capable of binding and activating a NOD2-dependent
NF-κB response, suggesting that the carbohydrate moiety of the
peptidoglycan fragments is the minimal functional epitope. This work
highlights the necessity of studying NOD2-ligand binding in systems
that resemble the receptor’s natural environment, as the cellular
membrane and/or NOD2 interacting partners appear to play a crucial
role in ligand binding and in triggering an innate immune response.
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Affiliation(s)
- Amy K. Schaefer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - James E. Melnyk
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Michael M. Baksh
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Klare M. Lazor
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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30
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Saetear P, Chamieh J, Kammer MN, Manuel TJ, Biron JP, Bornhop DJ, Cottet H. Taylor Dispersion Analysis of Polysaccharides Using Backscattering Interferometry. Anal Chem 2017; 89:6710-6718. [DOI: 10.1021/acs.analchem.7b00946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Joseph Chamieh
- IBMM, Univ. Montpellier,
CNRS, ENSCM, Montpellier, France
| | - Michael N. Kammer
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- The
Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Thomas J. Manuel
- Department
of Agricultural and Biological Engineering, Mississippi State University, Starkville, Mississippi 39762, United States
| | | | - Darryl J. Bornhop
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- The
Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hervé Cottet
- IBMM, Univ. Montpellier,
CNRS, ENSCM, Montpellier, France
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31
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Baksh MM, Finn M. An experimental check of backscattering interferometry. SENSORS AND ACTUATORS. B, CHEMICAL 2017; 243:977-981. [PMID: 28529409 PMCID: PMC5433263 DOI: 10.1016/j.snb.2016.12.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Backscattering interferometry (BSI) was used to determine the association constants for four well-known biomolecular interactions: protein A + IgG, trypsin + antitrypsin, trypsin + p-aminobenzamidine, and antithrombin + heparin. Each gave well-defined binding curves and Kd values in close agreement with published findings obtained using other techniques. These results stand in direct contrast to the claims in a 2015 publication in this journal (Discussion of "Back Scattering Interferometry revisited-a theoretical and experimental investigation" Jørgensen, T.M.; Jepsen, S.T.; Sørensen, H.S.; di Gennaro, A.K.; Kristensen, S.R. Sensors and Actuators B 2015, 220, 1328-1337, doi: 10.1016/j.snb.2015.06.121), thus invalidating the claim that BSI is unable to make measurements of this kind. The experimental details are discussed, and several potential sources of error in the previous publication are identified. No comments are made here on the discussion of the theoretical aspects of the BSI technique.
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32
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Label-free quantification of calcium-sensor targeting to photoreceptor guanylate cyclase and rhodopsin kinase by backscattering interferometry. Sci Rep 2017; 7:45515. [PMID: 28361875 PMCID: PMC5374524 DOI: 10.1038/srep45515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/28/2017] [Indexed: 01/26/2023] Open
Abstract
Quantification of protein binding to membrane proteins is challenging and a limited set of methods is available to study such systems. Here we employed backscattering interferometry (BSI), a free-solution label-free method with high sensitivity, to quantify the interaction of neuronal Ca2+-Sensor proteins with their targets operating in phototransduction. We tested direct binding of guanylate cyclase–activating proteins (GCAP1 and GCAP2) to their membrane target guanylate cyclase 1. The regulatory mechanism of GCAPs including their binding interface in the target is unresolved. Here we used a label-free, free-solution assay method based on BSI to determine binding constants of GCAP1 and GCAP2 to the full-length membrane-bound guanylate cyclase type 1. GCAP1 and GCAP2 bound to different regions on the target guanylate cyclase with submicromolar affinity (apparent KD-values of 663 ± 121 nM and 231 ± 63 nM for Ca2+-free GCAP1 and GCAP2, respectively). A guanylate cyclase construct containing the juxta-membrane and kinase homology domain harbored an exclusive binding site for GCAP1 with similar affinities as the full-length protein, whereas GCAP2 did not bind to this region. We provide a model in which GCAP1 and GCAP2 do not share a single binding site to the target, thus cannot exchange upon fluctuating Ca2+ levels.
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33
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Sarimov RM, Matveyeva TA, Vasin AL, Binhi VN. Changes in the refractive index of a solution during proteolysis of bovine serum albumin with pepsin. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917020221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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34
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Gielen F, Butz M, Rees EJ, Erdelyi M, Moschetti T, Hyvönen M, Edel JB, Kaminski CF, Hollfelder F. Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets. Anal Chem 2017; 89:1092-1101. [PMID: 28192993 PMCID: PMC5287478 DOI: 10.1021/acs.analchem.6b02528] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fluorescence anisotropy measurements of reagents compartmentalized into individual nanoliter droplets are shown to yield high-resolution binding curves from which precise dissociation constants (Kd) for protein-peptide interactions can be inferred. With the current platform, four titrations can be obtained per minute (based on ∼100 data points each), with stoichiometries spanning more than 2 orders of magnitude and requiring only tens of microliters of reagents. In addition to affinity measurements with purified components, Kd values for unpurified proteins in crude cell lysates can be obtained without prior knowledge of the concentration of the expressed protein, so that protein purification can be avoided. Finally, we show how a competition assay can be set up to perform focused library screens, so that compound labeling is not required anymore. These data demonstrate the utility of droplet compartments for the quantitative characterization of biomolecular interactions and establish fluorescence anisotropy imaging as a quantitative technique in a miniaturized droplet format, which is shown to be as reliable as its macroscopic test tube equivalent.
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Affiliation(s)
- Fabrice Gielen
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.,Living Systems Institute, University of Exeter , Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Maren Butz
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Eric J Rees
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom
| | - Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom.,Department of Optics and Quantum Electronics, University of Szeged , Dom ter 9, Szeged, Hungary
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Joshua B Edel
- Department of Chemistry, Imperial College London , South Kensington, London, SW7 2AZ, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
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35
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Khan M, Park SY. Liquid crystal-based biosensor with backscattering interferometry: A quantitative approach. Biosens Bioelectron 2017; 87:976-983. [DOI: 10.1016/j.bios.2016.09.065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/11/2016] [Accepted: 09/19/2016] [Indexed: 11/28/2022]
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36
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Kim U, Song J, Ryu S, Kim S, Joo C. A Rapid and Chemical-free Hemoglobin Assay with Photothermal Angular Light Scattering. J Vis Exp 2016. [PMID: 28060269 DOI: 10.3791/55006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Photo-thermal angular light scattering (PT-AS) is a novel optical method for measuring the hemoglobin concentration ([Hb]) of blood samples. On the basis of the intrinsic photothermal response of hemoglobin molecules, the sensor enables high-sensitivity, chemical-free measurement of [Hb]. [Hb] detection capability with a limit of 0.12 g/dl over the range of 0.35 - 17.9 g/dl has been demonstrated previously. The method can be readily implemented using inexpensive consumer electronic devices such as a laser pointer and a webcam. The use of a micro-capillary tube as a blood container also enables the hemoglobin assay with a nanoliter-scale blood volume and a low operating cost. Here, detailed instructions for the PT-AS optical setup and signal processing procedures are presented. Experimental protocols and representative results for blood samples in anemic conditions ([Hb] = 5.3, 7.5, and 9.9 g/dl) are also provided, and the measurements are compared with those from a hematology analyzer. Its simplicity in implementation and operation should enable its wide adoption in clinical laboratories and resource-limited settings.
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Affiliation(s)
- Uihan Kim
- School of Mechanical Engineering, Yonsei University
| | - Jaewoo Song
- Department of Laboratory Medicine, Yonsei University
| | - Suho Ryu
- School of Mechanical Engineering, Yonsei University
| | - Soocheol Kim
- School of Mechanical Engineering, Yonsei University
| | - Chulmin Joo
- School of Mechanical Engineering, Yonsei University;
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37
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Wang M, Kussrow AK, Ocana MF, Chabot JR, Lepsy CS, Bornhop DJ, O'Hara DM. Physiologically relevant binding affinity quantification of monoclonal antibody PF-00547659 to mucosal addressin cell adhesion molecule for in vitro in vivo correlation. Br J Pharmacol 2016; 174:70-81. [PMID: 27760281 PMCID: PMC5221447 DOI: 10.1111/bph.13654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 12/29/2022] Open
Abstract
Background and Purpose A monoclonal antibody (PF‐00547659) against mucosal addressin cell adhesion molecule (MAdCAM), expressed as both soluble (sMAdCAM) and trans‐membrane (mMAdCAM) target forms, showed over 30‐fold difference in antibody‐target KD between in vitro (Biacore) and clinically derived (KD,in‐vivo) values. Back‐scattering interferometry (BSI) was applied to acquire physiologically relevant KD values which were used to establish in vitro and in vivo correlation (IVIVC). Experimental Approach BSI was applied to obtain KD values between PF‐00547659 and recombinant human MAdCAM in buffer or CHO cells and endogenous MAdCAM in human serum or colon tissue. CHO cells and tissue were minimally processed to yield homogenate containing membrane vesicles and soluble proteins. A series of binding affinities in serum with various dilution factors was used to estimate both KD,in‐vivo and target concentrations; MAdCAM concentrations were also measured using LC–MS/MS. Key Results BSI measurements revealed low KD values (higher affinity) for sMAdCAM in buffer and serum, yet a 20‐fold higher KD value (lower affinity) for mMAdCAM in CHO, mMAdCAM and sMAdCAM in tissue. BSI predicted KD,in‐vivo in serum was similar to clinically derived KD,in‐vivo, and the BSI‐estimated serum sMAdCAM concentration also matched the measured concentration by LC–MS/MS. Conclusions and Implications Our results successfully demonstrated that BSI measurements of physiologically relevant KD values can be used to establish IVIVC, for PF‐00547659 to MAdCAM despite the lack of correlation when using Biacore measured KD and accurately estimates endogenous target concentrations. The application of BSI would greatly enhance successful basic pharmacological research and drug development.
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Affiliation(s)
- Mengmeng Wang
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | - Amanda K Kussrow
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Jeffrey R Chabot
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | | | - Darryl J Bornhop
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Denise M O'Hara
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
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38
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Dell’Orco D, Koch KW. Fingerprints of Calcium-Binding Protein Conformational Dynamics Monitored by Surface Plasmon Resonance. ACS Chem Biol 2016; 11:2390-7. [PMID: 27380526 DOI: 10.1021/acschembio.6b00470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Surface plasmon resonance (SPR) spectroscopy is widely used to probe interactions involving biological macromolecules by detecting changes in the refractive index in a metal/dielectric interface following the dynamic formation of a molecular complex. In past years, SPR-based experimental approaches were developed to monitor conformational changes induced by the binding of small analytes to proteins coupled to the surface of commercially available sensor chips. A significant contribution to our understanding of the phenomenon came from the study of several Ca(2+)-sensor proteins operating in diverse cellular scenarios, in which the conformational switch is triggered by specific Ca(2+) signals. Structural and physicochemical analyses demonstrated that the SPR signal not only depends on the change in protein size upon Ca(2+)-binding but likely originates from variations in the hydration shell structure. The resulting changes in the dielectric properties of water or of the protein-water interface eventually reflect different crowding conditions on the SPR sensor chip, which mimic the cellular environment. SPR could hence be used to monitor conformational transitions in proteins, especially when a significant variation in the hydrophobicity of the solvent-exposed protein surface occurs, thus leading to changes in the dielectric milieu of the whole sensor chip surface. We review recent work in which SPR has been successfully employed to provide a fingerprint of the conformational change dynamics in proteins under native and altered conditions, which include post-translational modifications, copresence of competing analytes, and point mutations of single amino acids associated with genetic diseases.
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Affiliation(s)
- Daniele Dell’Orco
- Department
of Neurosciences, Biomedicine and Movement Sciences, Section of Biological
Chemistry, University of Verona, I-37134 Verona, Italy
| | - Karl-Wilhelm Koch
- Department
of Neurosciences, Biochemistry Group, University of Oldenburg, D-26111 Oldenburg, Germany
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39
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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40
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Article does not explain the origin of free-solution protein interaction signals. Proc Natl Acad Sci U S A 2016; 113:E4930. [PMID: 27462112 DOI: 10.1073/pnas.1608094113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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41
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Origin and prediction of free-solution interaction studies performed label-free. Proc Natl Acad Sci U S A 2016; 113:E1595-604. [PMID: 26960999 DOI: 10.1073/pnas.1515706113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interaction/reaction assays have led to significant scientific discoveries in the biochemical, medical, and chemical disciplines. Several fundamental driving forces form the basis of intermolecular and intramolecular interactions in chemical and biochemical systems (London dispersion, hydrogen bonding, hydrophobic, and electrostatic), and in the past three decades the sophistication and power of techniques to interrogate these processes has developed at an unprecedented rate. In particular, label-free methods have flourished, such as NMR, mass spectrometry (MS), surface plasmon resonance (SPR), biolayer interferometry (BLI), and backscattering interferometry (BSI), which can facilitate assays without altering the participating components. The shortcoming of most refractive index (RI)-based label-free methods such as BLI and SPR is the requirement to tether one of the interaction entities to a sensor surface. This is not the case for BSI. Here, our hypothesis is that the signal origin for free-solution, label-free determinations can be attributed to conformation and hydration-induced changes in the solution RI. We propose a model for the free-solution response function (FreeSRF) and show that, when quality bound and unbound structural data are available, FreeSRF correlates well with the experiment (R(2)> 0.99, Spearman rank correlation coefficients >0.9) and the model is predictive within ∼15% of the experimental binding signal. It is also demonstrated that a simple mass-weighted dη/dC response function is the incorrect equation to determine that the change in RI is produced by binding or folding event in free solution.
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42
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Integrating biophysics with HTS-driven drug discovery projects. Drug Discov Today 2016; 21:491-8. [PMID: 26826422 DOI: 10.1016/j.drudis.2016.01.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/04/2016] [Accepted: 01/20/2016] [Indexed: 12/13/2022]
Abstract
Over the past decade biophysics has become an established discipline in HTS hit triaging, owing to its high fidelity in detecting protein-ligand interactions. Many pharma companies are using biophysical techniques to filter HTS output for false positives, as will be discussed in this review. Moreover, I will demonstrate how the earlier application of biophysics, already at the HTS assay development stage, is potentially even more impactful. Two key areas here are early mode-of-action studies and ensuring that the HTS assay and subsequent cascade are fit for purpose. Top-level results from 20 in-house projects are shown to underpin the impact of these studies.
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43
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Fjellström O, Larsson N, Yasuda SI, Tsuchida T, Oguma T, Marley A, Wennberg-Huldt C, Hovdal D, Fukuda H, Yoneyama Y, Sasaki K, Johansson A, Lundqvist S, Brengdahl J, Isaacs RJ, Brown D, Geschwindner S, Benthem L, Priest C, Turnbull A. Novel Zn2+ Modulated GPR39 Receptor Agonists Do Not Drive Acute Insulin Secretion in Rodents. PLoS One 2015; 10:e0145849. [PMID: 26720709 PMCID: PMC4697807 DOI: 10.1371/journal.pone.0145849] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
Type 2 diabetes (T2D) occurs when there is insufficient insulin release to control blood glucose, due to insulin resistance and impaired β-cell function. The GPR39 receptor is expressed in metabolic tissues including pancreatic β-cells and has been proposed as a T2D target. Specifically, GPR39 agonists might improve β-cell function leading to more adequate and sustained insulin release and glucose control. The present study aimed to test the hypothesis that GPR39 agonism would improve glucose stimulated insulin secretion in vivo. A high throughput screen, followed by a medicinal chemistry program, identified three novel potent Zn2+ modulated GPR39 agonists. These agonists were evaluated in acute rodent glucose tolerance tests. The results showed a lack of glucose lowering and insulinotropic effects not only in lean mice, but also in diet-induced obese (DIO) mice and Zucker fatty rats. It is concluded that Zn2+ modulated GPR39 agonists do not acutely stimulate insulin release in rodents.
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Affiliation(s)
- Ola Fjellström
- Medicinal Chemistry CVMD iMed, AstraZeneca R&D Gothenburg, Mölndal, Sweden
- * E-mail:
| | - Niklas Larsson
- Discovery Sciences, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Shin-ichiro Yasuda
- Pharmacology Research Laboratories II, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama, Japan
| | - Takuma Tsuchida
- Pharmacology Research Laboratories II, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama, Japan
| | - Takahiro Oguma
- Pharmacology Research Laboratories II, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama, Japan
| | - Anna Marley
- Discovery Sciences, AstraZeneca R&D, Mereside, United Kingdom
| | | | - Daniel Hovdal
- DMPK CVMD iMed, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Hajime Fukuda
- DMPK Research Laboratories, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama, Japan
| | - Yukimi Yoneyama
- DMPK Research Laboratories, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama, Japan
| | - Kazuyo Sasaki
- Pharmacology Research Laboratories II, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama, Japan
| | - Anders Johansson
- Medicinal Chemistry CVMD iMed, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Sara Lundqvist
- Discovery Sciences, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Johan Brengdahl
- Discovery Sciences, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Richard J. Isaacs
- Molecular Sensing, Inc., Nashville, Tennessee, United States of America
| | - Daniel Brown
- Molecular Sensing, Inc., Nashville, Tennessee, United States of America
| | | | | | - Claire Priest
- Discovery Sciences, AstraZeneca R&D, Mereside, United Kingdom
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44
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Characterization of the direct interaction between KcsA-Kv1.3 and its inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1974-80. [DOI: 10.1016/j.bbamem.2015.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/28/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022]
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45
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Valera E, Bailey RC. Eavesdropping on interactions. Nat Chem 2015; 7:767-9. [DOI: 10.1038/nchem.2355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Jepsen ST, Jørgensen TM, Zong W, Trydal T, Kristensen SR, Sørensen HS. Evaluation of back scatter interferometry, a method for detecting protein binding in solution. Analyst 2015; 140:895-901. [PMID: 25503796 DOI: 10.1039/c4an01129e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Back Scatter Interferometry (BSI) has been proposed to be a highly sensitive and versatile refractive index sensor usable for analytical detection of biomarker and protein interactions in solution. However the existing literature on BSI lacks a physical explanation of why protein interactions in general should contribute to the BSI signal. We have established a BSI system to investigate this subject in further detail. We contribute with a thorough analysis of the robustness of the sensor including unwanted contributions to the interferometric signal caused by temperature variation and dissolved gasses. We report a limit of the effective minimum detectability of refractive index at the 10(-7) level. Long term stability was examined by simultaneously monitoring the temperature inside the capillary revealing an average drift of 2.0 × 10(-7) per hour. Finally we show that measurements on protein A incubated with immunoglobulin G do not result in a signal that can be attributed to binding affinities as otherwise claimed in literature.
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Affiliation(s)
- S T Jepsen
- Dept. of Clinical Biochemistry, Aalborg University Hospital, Hobrovej 18-22, 9000 Aalborg, Denmark
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47
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Latent analysis of unmodified biomolecules and their complexes in solution with attomole detection sensitivity. Nat Chem 2015; 7:802-9. [DOI: 10.1038/nchem.2344] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
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48
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Kammer MN, Olmsted IR, Kussrow AK, Morris MJ, Jackson GW, Bornhop DJ. Characterizing aptamer small molecule interactions with backscattering interferometry. Analyst 2015; 139:5879-84. [PMID: 25229067 DOI: 10.1039/c4an01227e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Aptamers are segments of single-strand DNA or RNA used in a wide array of applications, including sensors, therapeutics, and cellular process regulators. Aptamers can bind many target species, including proteins, peptides, and small molecules (SM) with high affinity and specificity. They are advantageous because they can be identified in vitro by SELEX, produced rapidly and relatively economically using oligonucleotide synthesis. The use of aptamers as SM probes has experienced a recent rebirth, and because of their unique properties they represent an attractive alternative to antibodies. Current assay methodology for characterizing small molecule-aptamer binding is limited by either mass sensitivity, as in biolayer interferometry (BLI) and surface plasmon resonance (SPR), or the need for using a fluorophore, as in thermophoresis. Here we report that backscattering interferometry (BSI), a label-free and free-solution sensing technique, can be used to effectively characterize SM-aptamer interactions, providing Kd values on microliter sample quantities and at low nanomolar sensitivity. To demonstrate this capability we measured the aptamer affinity for three previously reported small molecules; bisphenol A, tenofovir, and epirubicin showing BSI provided values consistent with those published previously. We then quantified the Kd values for aptamers to ampicillin, tetracycline and norepinephrine. All measurements produced R(2) values >0.95 and an excellent signal to noise ratio at target concentrations that enable true Kd values to be obtained. No immobilization or labeling chemistry was needed, expediting the assay which is also insensitive to the large relative mass difference between the interacting molecules.
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Affiliation(s)
- Michael N Kammer
- Department of Chemistry, Vanderbilt University, 2201 West End Avenue, Nashville, Tennessee, USA.
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49
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Kim U, Song J, Lee D, Ryu S, Kim S, Hwang J, Joo C. Capillary-scale direct measurement of hemoglobin concentration of erythrocytes using photothermal angular light scattering. Biosens Bioelectron 2015; 74:469-75. [PMID: 26176206 DOI: 10.1016/j.bios.2015.06.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 06/26/2015] [Accepted: 06/26/2015] [Indexed: 11/19/2022]
Abstract
We present a direct, rapid and chemical-free detection method for hemoglobin concentration ([Hb]), based on photothermal angular light scattering. The iron oxides contained in hemoglobin molecules exhibit high absorption of 532-nm light and generate heat under the illumination of 532-nm light, which subsequently alters the refractive index of blood. We measured this photothermal change in refractive index by employing angular light scattering spectroscopy with the goal of quantifying [Hb] in blood samples. Highly sensitive [Hb] measurement of blood samples was performed by monitoring the shifts in angularly dispersed scattering patterns from the blood-loaded microcapillary tubes. Our system measured [Hb] over the range of 0.35-17.9 g/dL with a detection limit of ~0.12 g/dL. Our sensor was characterized by excellent correlation with a reference hematology analyzer (r>0.96), and yielded a precision of 0.63 g/dL for a blood sample of 9.0 g/dL.
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Affiliation(s)
- Uihan Kim
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Jaewoo Song
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Donghak Lee
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Suho Ryu
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Soocheol Kim
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Jaehyun Hwang
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Chulmin Joo
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea.
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50
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Vogus DR, Mansard V, Rapp MV, Squires TM. Measuring concentration fields in microfluidic channels in situ with a Fabry-Perot interferometer. LAB ON A CHIP 2015; 15:1689-1696. [PMID: 25661262 DOI: 10.1039/c5lc00095e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent advancements in microfluidic technology have allowed for the generation and control of complex chemical gradients; however, few general techniques can measure these spatio-temporal concentration profiles without fluorescent labeling. Here we describe a Fabry-Perot interferometric technique, capable of measuring concentration profiles in situ, without any chemical label, by tracking Fringes of Equal Chromatic Order (FECO). The technique has a sensitivity of 10(-5) RIU, which can be used to track local solute changes of ~0.05% (w/w). The technique is spatially resolved (1 μm) and easily measures evolving concentration fields with ~20 Hz rate. Here, we demonstrate by measuring the binary diffusion coefficients of various solutes and solvents (and their concentration-dependence) in both free solution and in polyethylene glycol diacrylate (PEG-DA) hydrogels.
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Affiliation(s)
- Douglas R Vogus
- Department of Chemical Engineering University of California, Santa Barbara, USA.
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