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Rai P, Hoba SN, Buchmann C, Subirana-Slotos RJ, Kersten C, Schirmeister T, Endres K, Bufe B, Tarasov A. Protease detection in the biosensor era: A review. Biosens Bioelectron 2024; 244:115788. [PMID: 37952320 DOI: 10.1016/j.bios.2023.115788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023]
Abstract
Proteases have been proposed as potential biomarkers for several pathological conditions including cancers, multiple sclerosis and cardiovascular diseases, due to their ability to break down the components of extracellular matrix and basement membrane. The development of protease biosensors opened up the possibility to investigate the proteolytic activity of dysregulated proteases with higher efficiency over the traditional detection assays due to their quick detection capability, high sensitivity and selectivity, simple instrumentation and cost-effective fabrication processes. In contrast to the recently published review papers that primarily focused on one specific class of proteases or one specific detection method, this review article presents different optical and electrochemical detection methods that can be used to design biosensors for all major protease families. The benefits and drawbacks of various transducer techniques integrated into protease biosensing platforms are analyzed and compared. The main focus is on activity-based biosensors that use peptides as biorecognition elements. The effects of nanomaterials on biosensor performance are also discussed. This review should help readers to select the biosensor that best fits their needs, and contribute to the further development of this research field. Protease biosensors may allow better comprehension of protease overexperession and potentially enable novel devices for point-of-care testing.
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Affiliation(s)
- Pratika Rai
- Faculty of Computer Sciences and Microsystems Technology, Kaiserslautern University of Applied Sciences, Amerikastr.1, 66482, Zweibrücken, Germany
| | - Sabrina N Hoba
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Celine Buchmann
- Faculty of Computer Sciences and Microsystems Technology, Kaiserslautern University of Applied Sciences, Amerikastr.1, 66482, Zweibrücken, Germany
| | - Robert J Subirana-Slotos
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg University Mainz, Untere Zahlbacher Str. 8, 55131, Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg University Mainz, Untere Zahlbacher Str. 8, 55131, Mainz, Germany
| | - Bernd Bufe
- Faculty of Computer Sciences and Microsystems Technology, Kaiserslautern University of Applied Sciences, Amerikastr.1, 66482, Zweibrücken, Germany
| | - Alexey Tarasov
- Faculty of Computer Sciences and Microsystems Technology, Kaiserslautern University of Applied Sciences, Amerikastr.1, 66482, Zweibrücken, Germany.
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2
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Naneh O, Kozorog M, Merzel F, Gilbert R, Anderluh G. Surface plasmon resonance and microscale thermophoresis approaches for determining the affinity of perforin for calcium ions. Front Immunol 2023; 14:1181020. [PMID: 37545534 PMCID: PMC10400287 DOI: 10.3389/fimmu.2023.1181020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/16/2023] [Indexed: 08/08/2023] Open
Abstract
Perforin is a pore-forming protein that plays a crucial role in the immune system by clearing virus-infected or tumor cells. It is released from cytotoxic granules of immune cells and forms pores in targeted lipid membranes to deliver apoptosis-inducing granzymes. It is a very cytotoxic protein and is therefore adapted not to act in producing cells. Its activity is regulated by the requirement for calcium ions for optimal activity. However, the exact affinity of perforin for calcium ions has not yet been determined. We conducted a molecular dynamics simulation in the absence or presence of calcium ions that showed that binding of at least three calcium ions is required for stable perforin binding to the lipid membrane. Biophysical studies using surface plasmon resonance and microscale thermophoresis were then performed to estimate the binding affinities of native human and recombinant mouse perforin for calcium ions. Both approaches showed that mouse perforin has a several fold higher affinity for calcium ions than that of human perforin. This was attributed to a particular residue, tryptophan at position 488 in mouse perforin, which is replaced by arginine in human perforin. This represents an additional mechanism to control the activity of human perforin.
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Affiliation(s)
- Omar Naneh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Mirijam Kozorog
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Robert Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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Dobrovodský D, Di Primo C. Do conformational changes contribute to the surface plasmon resonance signal? Biosens Bioelectron 2023; 232:115296. [PMID: 37079993 DOI: 10.1016/j.bios.2023.115296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/23/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Surface plasmon resonance (SPR)-based biosensors are widely used instruments for characterizing molecular interactions. In theory the SPR signal depends only on mass changes for interacting molecules of same chemical nature. Whether conformational changes of interacting molecules also contribute to the SPR signal is still a subject of lively debates. Works have been published claiming that conformational changes were detected but all factors contributing to the SPR signal were not carefully considered, in addition to often using no or improper controls. In the present work we used a very well-characterized oligonucleotide, the thrombin-binding DNA aptamer (TBA), which upon binding of potassium ions folds into a two G-tetrad antiparallel G-quadruplex structure. All terms contributing to the maximal expected SPR response, Rmax, in particular the refractive index increment, RII, of both partners and the fraction of immobilized TBA target available, ca, were experimentally assessed. The resulting Rmax was then compared to the maximal experimental SPR response for potassium ions binding to TBA using appropriate controls. Regardless how the RIIs were measured, by SPR or refractometry, and how much TBA available for interacting with potassium ions was considered, the theoretical and the experimental SPR responses never matched, the former being always lower than the latter. Using a straightforward experimental model system and by thoroughly taking into account all contributing factors we therefore conclude that conformational changes can indeed contribute to the measured SPR signal.
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State of the Art in Smart Portable, Wearable, Ingestible and Implantable Devices for Health Status Monitoring and Disease Management. SENSORS 2022; 22:s22114228. [PMID: 35684847 PMCID: PMC9185336 DOI: 10.3390/s22114228] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023]
Abstract
Several illnesses that are chronic and acute are becoming more relevant as the world's aging population expands, and the medical sector is transforming rapidly, as a consequence of which the need for "point-of-care" (POC), identification/detection, and real time management of health issues that have been required for a long time are increasing. Biomarkers are biological markers that help to detect status of health or disease. Biosensors' applications are for screening for early detection, chronic disease treatment, health management, and well-being surveillance. Smart devices that allow continual monitoring of vital biomarkers for physiological health monitoring, medical diagnosis, and assessment are becoming increasingly widespread in a variety of applications, ranging from biomedical to healthcare systems of surveillance and monitoring. The term "smart" is used due to the ability of these devices to extract data with intelligence and in real time. Wearable, implantable, ingestible, and portable devices can all be considered smart devices; this is due to their ability of smart interpretation of data, through their smart sensors or biosensors and indicators. Wearable and portable devices have progressed more and more in the shape of various accessories, integrated clothes, and body attachments and inserts. Moreover, implantable and ingestible devices allow for the medical diagnosis and treatment of patients using tiny sensors and biomedical gadgets or devices have become available, thus increasing the quality and efficacy of medical treatments by a significant margin. This article summarizes the state of the art in portable, wearable, ingestible, and implantable devices for health status monitoring and disease management and their possible applications. It also identifies some new technologies that have the potential to contribute to the development of personalized care. Further, these devices are non-invasive in nature, providing information with accuracy and in given time, thus making these devices important for the future use of humanity.
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Jung V, Roger K, Chhuon C, Pannetier L, Lipecka J, Gomez JS, Chappert P, Charbit A, Guerrera IC. BLI-MS: Combining biolayer interferometry and mass spectrometry. Proteomics 2021; 22:e2100031. [PMID: 34958708 DOI: 10.1002/pmic.202100031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Biolayer Interferometry (BLI) is a technology which allows to study the affinity between two interacting macro-molecules and to visualize their kinetic of interaction in real time. In this work we combine BLI interaction measurement with mass spectrometry in order to identify the proteins interacting with the bait. We provide for the first time the proof of concept of the feasibility of BLI-MS in complex biological mixtures. Data are available via ProteomeXchange with the identifier PXD019440. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vincent Jung
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Kévin Roger
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Cerina Chhuon
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Louise Pannetier
- Université de Paris, Sorbonne Paris Cité, INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris, France
| | - Joanna Lipecka
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Josué Sulub Gomez
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Pascal Chappert
- Université de Paris, Sorbonne Paris Cité, INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris, France
- INSERM U955, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Alain Charbit
- Université de Paris, Sorbonne Paris Cité, INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris, France
| | - Ida Chiara Guerrera
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
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Hasan MR, Sharma P, Anzar N, Pundir C, Pilloton R, Narang J, Shetti NP. Analytical methods for detection of human cytomegalovirus clinched biosensor a cutting-edge diagnostic tool. BIOMEDICAL ENGINEERING ADVANCES 2021. [DOI: 10.1016/j.bea.2021.100006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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7
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Xue J, Bai Y, Liu H. Hybrid methods of surface plasmon resonance coupled to mass spectrometry for biomolecular interaction analysis. Anal Bioanal Chem 2019; 411:3721-3729. [DOI: 10.1007/s00216-019-01906-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/23/2019] [Accepted: 05/08/2019] [Indexed: 01/02/2023]
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8
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A class of highly selective inhibitors bind to an active state of PI3Kγ. Nat Chem Biol 2019; 15:348-357. [DOI: 10.1038/s41589-018-0215-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022]
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9
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Nguyen HH, Lee SH, Lee UJ, Fermin CD, Kim M. Immobilized Enzymes in Biosensor Applications. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E121. [PMID: 30609693 PMCID: PMC6337536 DOI: 10.3390/ma12010121] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/15/2018] [Accepted: 12/24/2018] [Indexed: 11/17/2022]
Abstract
Enzyme-based biosensing devices have been extensively developed over the last few decades, and have proven to be innovative techniques in the qualitative and quantitative analysis of a variety of target substrates over a wide range of applications. Distinct advantages that enzyme-based biosensors provide, such as high sensitivity and specificity, portability, cost-effectiveness, and the possibilities for miniaturization and point-of-care diagnostic testing make them more and more attractive for research focused on clinical analysis, food safety control, or disease monitoring purposes. Therefore, this review article investigates the operating principle of enzymatic biosensors utilizing electrochemical, optical, thermistor, and piezoelectric measurement techniques and their applications in the literature, as well as approaches in improving the use of enzymes for biosensors.
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Affiliation(s)
- Hoang Hiep Nguyen
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-Gu, Daejeon 34141, Korea.
- Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeongno, Yuseong-Gu, Daejeon 34113, Korea.
| | - Sun Hyeok Lee
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-Gu, Daejeon 34141, Korea.
- Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeongno, Yuseong-Gu, Daejeon 34113, Korea.
| | - Ui Jin Lee
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-Gu, Daejeon 34141, Korea.
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, 99 Daehangno, Yuseong-Gu, Daejeon 34134, Korea.
| | - Cesar D Fermin
- Department of Biology, College of Arts & Sciences, Tuskegee University, Tuskegee, AL 36830, USA.
| | - Moonil Kim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-Gu, Daejeon 34141, Korea.
- Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeongno, Yuseong-Gu, Daejeon 34113, Korea.
- Department of Biology, College of Arts & Sciences, Tuskegee University, Tuskegee, AL 36830, USA.
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10
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Quinn JG, Pitts KE, Steffek M, Mulvihill MM. Determination of Affinity and Residence Time of Potent Drug-Target Complexes by Label-free Biosensing. J Med Chem 2018; 61:5154-5161. [PMID: 29772180 DOI: 10.1021/acs.jmedchem.7b01829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prolonged drug-target occupancy has become increasingly important in lead optimization, and biophysical assays that measure residence time are in high demand. Here we report a practical label-free assay methodology that provides kinetic and affinity measurements suitable for most target classes without long preincubations and over comparatively short sample contact times. The method, referred to as a "chaser" assay, has been applied to three sets of unrelated kinase/inhibitor panels in order to measure the residence times, where correlation with observed efficacy was suspected. A lower throughput chaser assay measured a residence time of 3.6 days ±3.4% (95% CI) and provided single digit pM sensitivity. A higher throughput chaser methodology enabled a maximum capacity of 108 compounds in duplicate/day with an upper residence time limit of 9 h given an assay dissociation time of 34 min.
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Affiliation(s)
- John G Quinn
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Keith E Pitts
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Micah Steffek
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Melinda M Mulvihill
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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11
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Han Y, Gao Y, He T, Wang D, Guo N, Zhang X, Chen S, Wang H. PD-1/PD-L1 inhibitor screening of caffeoylquinic acid compounds using surface plasmon resonance spectroscopy. Anal Biochem 2018; 547:52-56. [DOI: 10.1016/j.ab.2018.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/13/2018] [Accepted: 02/07/2018] [Indexed: 12/11/2022]
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12
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Kumar PKR. Systematic screening of viral entry inhibitors using surface plasmon resonance. Rev Med Virol 2017; 27. [PMID: 29047180 DOI: 10.1002/rmv.1952] [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] [Received: 08/10/2016] [Revised: 08/02/2017] [Accepted: 09/07/2017] [Indexed: 12/12/2022]
Abstract
Viral binding and entry into host cells for various viruses have been studied extensively, yielding a detailed understanding of the overall viral entry process. As cell entry is an essential and requisite process by which a virus initiates infection, it is an attractive target for therapeutic intervention. The advantages of targeting viral entry are an extracellular target site, relatively easy access for biological interventions, and lower toxicity. Several cell-based strategies and biophysical techniques have been used to screen compounds that block viral entry. These studies led to the discovery of inhibitors against HIV, HCV, influenza, Ebola, and RSV. In recent years, several compounds screened by fragment-based drug discovery have been approved as drugs or are in the final stages of clinical trials. Among fragment screening technologies, surface plasmon resonance has been widely used because it provides accurate information on binding kinetics, allows real-time monitoring of ligand-drug interactions, requires very small sample amounts to perform analyses, and requires no modifications to or labeling of ligands. This review focuses on surface plasmon resonance-based schemes for screening viral entry inhibitors.
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Affiliation(s)
- Penmetcha K R Kumar
- National Institute of Advanced Industrial Science and Technology, Tsukuba City, Ibaraki, Japan
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13
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Monitoring drug–serum protein interactions for early ADME prediction through Surface Plasmon Resonance technology. J Pharm Biomed Anal 2017; 144:188-194. [DOI: 10.1016/j.jpba.2017.03.054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/03/2017] [Accepted: 03/26/2017] [Indexed: 12/16/2022]
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14
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Fabini E, Zambelli B, Mazzei L, Ciurli S, Bertucci C. Surface plasmon resonance and isothermal titration calorimetry to monitor the Ni(II)-dependent binding of Helicobacter pylori NikR to DNA. Anal Bioanal Chem 2016; 408:7971-7980. [DOI: 10.1007/s00216-016-9894-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/17/2016] [Indexed: 02/03/2023]
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15
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Wang W, Zhou W, Wei W, Li J, Hao D, Su Z, Ma G. Towards A Deeper Understanding of the Interfacial Adsorption of Enzyme Molecules in Gigaporous Polymeric Microspheres. Polymers (Basel) 2016; 8:polym8040116. [PMID: 30979221 PMCID: PMC6431888 DOI: 10.3390/polym8040116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/06/2016] [Accepted: 03/24/2016] [Indexed: 11/21/2022] Open
Abstract
Compared with the one immobilized in the conventional mesoporous microspheres, the enzyme immobilized in gigaporous microspheres showed much higher activity and better stability. To gain a deeper understanding, we herein selected lipase as a prototype to comparatively analyze the adsorption behavior of lipase at interfaces in gigaporous and mesoporous polystyrene microspheres at very low lipase concentration, and further compared with the adsorption on a completely flat surface (a chip). Owing to the limited space of narrow pores, lipase molecules were inclined to be adsorbed as a monolayer in mesoporous microspheres. During this process, the interaction between lipase molecules and the interface was stronger, which could result in the structural change of lipase molecular and compromised specific activity. In addition to monolayer adsorption, more multilayer adsorption of enzyme molecules also occurred in gigaporous microspheres. Besides the adsorption state, the pore curvature also affected the lipase adsorption. Due to the multilayer adsorption, the excellent mass transfer properties for the substrate and the product in the large pores, and the small pore curvature, lipase immobilized in gigaporous microspheres showed better behaviors.
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Affiliation(s)
- Weichen Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Weiqing Zhou
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Wei Wei
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Juan Li
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dongxia Hao
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhiguo Su
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Guanghui Ma
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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16
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Surface plasmon resonance: a versatile technique for biosensor applications. SENSORS 2015; 15:10481-510. [PMID: 25951336 PMCID: PMC4481982 DOI: 10.3390/s150510481] [Citation(s) in RCA: 552] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/28/2015] [Indexed: 02/07/2023]
Abstract
Surface plasmon resonance (SPR) is a label-free detection method which has emerged during the last two decades as a suitable and reliable platform in clinical analysis for biomolecular interactions. The technique makes it possible to measure interactions in real-time with high sensitivity and without the need of labels. This review article discusses a wide range of applications in optical-based sensors using either surface plasmon resonance (SPR) or surface plasmon resonance imaging (SPRI). Here we summarize the principles, provide examples, and illustrate the utility of SPR and SPRI through example applications from the biomedical, proteomics, genomics and bioengineering fields. In addition, SPR signal amplification strategies and surface functionalization are covered in the review.
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18
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Efficient screening of marine extracts for protease inhibitors by combining FRET based activity assays and surface plasmon resonance spectroscopy based binding assays. Mar Drugs 2013; 11:4279-93. [PMID: 24177674 PMCID: PMC3853728 DOI: 10.3390/md11114279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 01/27/2023] Open
Abstract
The screening of extracts from marine organisms is a widely used strategy to discover new drug leads. A common problem in the screening process is the generation of false positive hits through unspecific effects from the complex chemical composition of the crude extracts. In this study, we explored a combination of a fluorescence resonance energy transfer (FRET) based activity assay and a surface plasmon resonance (SPR) based binding assay to avoid this problem. An aqueous extract was prepared from rest raw material of the Norwegian spring spawning herring, and further fractionated by methanol solubility and solid phase extraction. FRET based activity assays were used to determine the influence of each extract on the activity of different proteases. Several extracts showed more than 50% inhibition. The inhibition mechanisms were elucidated by SPR based competition experiments with known inhibitors. For the secreted aspartic proteases 1, 2, 3 and HIV-1 protease, the results indicated that some extracts contain inhibitors interacting specifically with the active site of the enzymes. The study shows that a combination of an activity assay and an SPR based binding assay is a powerful tool to identify potent inhibitors in marine extracts. Furthermore, the study shows that marine vertebrates offer an interesting source for new bioactive compounds, although they have rarely been explored for this purpose.
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Seeger C, Gorny X, Reddy PP, Seidenbecher C, Danielson UH. Kinetic and mechanistic differences in the interactions between caldendrin and calmodulin with AKAP79 suggest different roles in synaptic function. J Mol Recognit 2013; 25:495-503. [PMID: 22996592 DOI: 10.1002/jmr.2215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The kinetic and mechanistic details of the interaction between caldendrin, calmodulin and the B-domain of AKAP79 were determined using a biosensor-based approach. Caldendrin was found to compete with calmodulin for binding at AKAP79, indicating overlapping binding sites. Although the AKAP79 affinities were similar for caldendrin (K(D) = 20 nM) and calmodulin (K(D) = 30 nM), their interaction characteristics were different. The calmodulin interaction was well described by a reversible one-step model, but was only detected in the presence of Ca(2+). Caldendrin interacted with a higher level of complexity, deduced to be an induced fit mechanism with a slow relaxation back to the initial encounter complex. It interacted with AKAP79 also in the absence of Ca(2+), but with different kinetic rate constants. The data are consistent with a similar initial Ca(2+)-dependent binding step for the two proteins. For caldendrin, a second Ca(2+)-independent rearrangement step follows, resulting in a stable complex. The study shows the importance of establishing the mechanism and kinetics of protein-protein interactions and that minor differences in the interaction of two homologous proteins can have major implications in their functional characteristics. These results are important for the further elucidation of the roles of caldendrin and calmodulin in synaptic function.
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Geitmann M, Retra K, de Kloe GE, Homan E, Smit AB, de Esch IJP, Danielson UH. Interaction Kinetic and Structural Dynamic Analysis of Ligand Binding to Acetylcholine-Binding Protein. Biochemistry 2010; 49:8143-54. [DOI: 10.1021/bi1006354] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kim Retra
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
| | - Gerdien E. de Kloe
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
| | - Evert Homan
- Beactica AB, Box 567, SE-751 22 Uppsala, Sweden
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
| | - U. Helena Danielson
- Beactica AB, Box 567, SE-751 22 Uppsala, Sweden
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
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Geitmann M, Dahl G, Danielson UH. Mechanistic and kinetic characterization of hepatitis C virus NS3 protein interactions with NS4A and protease inhibitors. J Mol Recognit 2010; 24:60-70. [DOI: 10.1002/jmr.1023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Integrating surface plasmon resonance biosensor-based interaction kinetic analyses into the lead discovery and optimization process. Future Med Chem 2009; 1:1399-414. [DOI: 10.4155/fmc.09.100] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Surface plasmon resonance biosensor technology has come of age and become an important tool for drug discovery. It is a label-free biophysical technique for the kinetic analysis of molecular interactions that provides exceptionally information-rich data. Recent improvements in sensitivity, experimental design, data analysis and sample throughput makes it suitable for use throughout the drug-discovery process. This article outlines the use of SPR biosensor technology for small-molecule drug discovery and exemplifies how it complements other techniques. The technology is especially valuable for fragment-based lead discovery since it has the required sensitivity and throughput for screening of fragment libraries. Hits can be identified with respect to multiple criteria, defined by the experimental design used for screening. Expansion of hits and subsequent characterization and optimization of leads can be performed with a variety of experiments exploiting the kinetic resolution of the technology. Leads identified by this strategy can therefore be extensively characterized with respect to their interactions, with their target as well as with nontarget proteins. Although it may take some time for the methods to become well established, and for the research community to reach proficiency and fully embrace the information-rich data that can be obtained, it can be predicted that this technology will be widely used for drug discovery within the near future. It is expected that the technology will be particularly important for fragment-based strategies and integrated with other experimental technologies as well as with computational methods.
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Christopeit T, Gossas T, Danielson UH. Characterization of Ca2+ and phosphocholine interactions with C-reactive protein using a surface plasmon resonance biosensor. Anal Biochem 2009; 391:39-44. [PMID: 19435596 DOI: 10.1016/j.ab.2009.04.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/27/2009] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
Abstract
The interactions between Ca2+ and C-reactive protein (CRP) have been characterized using a surface plasmon resonance (SPR) biosensor. The protein was immobilized on a sensor chip, and increasing concentrations of Ca2+ or phosphocholine were injected. Binding of Ca2+ induced a 10-fold higher signal than expected from the molecular weight of Ca2+. It was interpreted to result from the conformational change that occurs on binding of Ca2+. Two sites with different characteristics were distinguished: a high-affinity site with K(D)=0.03 mM and a low-affinity site with K(D)=5.45 mM. The pH dependencies of the two Ca2+ interactions were different and enabled the assignment of the different sites in the three-dimensional structure of CRP. There was no evidence for cooperativity in the phosphocholine interaction, which had K(D)=5 microM at 10 mM Ca2+. SPR biosensors can clearly detect and quantify the binding of very small molecules or ions to immobilized proteins despite the theoretically very low signals expected on binding, provided that significant conformational changes are involved. Both the interactions and the conformational changes can be characterized. The data have important implications for the understanding of the function of CRP and suggest that Ca2+ is an efficient regulator under physiological conditions.
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Affiliation(s)
- Tony Christopeit
- Department of Biochemistry and Organic Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
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Enzyme solid-state support assays: a surface plasmon resonance and mass spectrometry coupled study of immobilized insulin degrading enzyme. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:407-14. [DOI: 10.1007/s00249-008-0384-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 11/06/2008] [Accepted: 11/11/2008] [Indexed: 02/02/2023]
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25
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Aukrust I, Hollås H, Strand E, Evensen L, Travé G, Flatmark T, Vedeler A. The mRNA-binding site of annexin A2 resides in helices C-D of its domain IV. J Mol Biol 2007; 368:1367-78. [PMID: 17395201 DOI: 10.1016/j.jmb.2007.02.094] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 11/27/2022]
Abstract
Annexin A2 (AnxA2) is a Ca(2+)-binding and phospholipid-binding protein involved in different intracellular processes including exocytosis, endocytosis and membrane-cytoskeleton movements. We have previously identified AnxA2 as an mRNA-binding protein present in cytoskeleton-bound polysomes, that binds to a specific approximately 100 nucleotide region in the 3'-untranslated region of c-myc and its cognate mRNA. In the present study, we show by UV cross-linking assays and surface plasmon resonance analyses that the mRNA-binding site of AnxA2 resides in its domain IV. Furthermore, the interaction of full-length AnxA2 with the 3'-untranslated region of anxA2 mRNA is Ca(2+)-dependent. By contrast, the interaction is Ca(2+)-independent for the isolated domain IV of AnxA2, suggesting that the mRNA-binding site is masked in Apo-AnxA2 and gains exposure through a Ca(2+)-induced conformational change of AnxA2 generating a favourable mRNA-binding site. The AnxA2-mRNA interaction is specific and involves helices C and D in domain IV of AnxA2, since point mutagenesis of several charged and polar exposed residues of these helices in the full-length protein strongly reduce RNA binding. The interaction appears to be sequential involving an initial phase of recognition dominated by electrostatic interactions, most likely between lysine residues and the phosphate backbone of RNA, followed by a second phase contributing to the specificity of the interaction.
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Affiliation(s)
- Ingvild Aukrust
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, N-5009 Bergen, Norway
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Gronewold TMA, Schlecht U, Quandt E. Analysis of proteolytic degradation of a crude protein mixture using a surface acoustic wave sensor. Biosens Bioelectron 2006; 22:2360-5. [PMID: 17079128 DOI: 10.1016/j.bios.2006.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 08/30/2006] [Accepted: 09/13/2006] [Indexed: 11/18/2022]
Abstract
Degradation of a crude protein mixture by proteases with pH optima from acidic to basic was followed in real time using a surface acoustic wave biosensor in Love-wave geometry. Proteases EC 3.4.23.18 from Aspergillus saitoi, EC 3.4.21.62 from Bacillus licheniformis, and Novozyme from Bacillus sp. have been used. Kinetic constants extracted from the curves resulted for comparable protease concentrations in maximal degradation rates between 1.1 x 10(-2) and 1.5 x 10(-2)s(-1). For the three proteases investigated, similar amounts of up to about two-thirds of the estimated 28 ng/cm2 bound molecules were proteolyzed. The residual material not degraded by the proteases was removed from the surface with 0.5% SDS. The analysis of the sensor signal allows: (1) estimation of the total mass of protein bound to the sensor surface and of the degradable fraction; (2) extraction of the pure mass signal; and (3) kinetic evaluation.
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Affiliation(s)
- T M A Gronewold
- Center of Advanced European Studies and Research, S-sens, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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Geitmann M, Unge T, Danielson UH. Biosensor-based kinetic characterization of the interaction between HIV-1 reverse transcriptase and non-nucleoside inhibitors. J Med Chem 2006; 49:2367-74. [PMID: 16610780 DOI: 10.1021/jm0504048] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Details of the interaction between HIV-1 reverse transcriptase and non-nucleoside inhibitors (NNRTIs) have been elucidated using a biosensor-based approach. This initial study was performed with HIV-1 reverse transcriptase mutant K103N, the phenethylthioazolylthiourea compound (PETT) MIV-150, and the three NNRTIs licensed for clinical use: nevirapine, delavirdine, and efavirenz. Mathematical evaluation of the experimental data with several interaction models revealed that the four inhibitors interacted with HIV-1 RT with varying degrees of complexity. The simplest adequate model accounted for two different conformations of the free enzyme, of which only one can bind the inhibitor, consistent with a previously hypothesized population-shift model including a preformation of the NNRTI binding site. In addition, a heterogeneous binding was observed for delavirdine, efavirenz, and MIV-150, indicating that two noncompetitive and kinetically distinct enzyme-inhibitor complexes could be formed. Furthermore, for these compounds, there were indications for ligand-induced conformational changes.
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Affiliation(s)
- Matthis Geitmann
- Department of Biochemistry and Organic Chemistry, Box 576, Uppsala University, SE-751 23 Uppsala, Sweden
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Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Huber W. A new strategy for improved secondary screening and lead optimization using high-resolution SPR characterization of compound-target interactions. J Mol Recognit 2005; 18:273-81. [PMID: 15997470 DOI: 10.1002/jmr.744] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Biophysical label-free assays such as those based on SPR are essential tools in generating high-quality data on affinity, kinetic, mechanistic and thermodynamic aspects of interactions between target proteins and potential drug candidates. Here we show examples of the integration of SPR with bioinformatic approaches and mutation studies in the early drug discovery process. We call this combination 'structure-based biophysical analysis'. Binding sites are identified on target proteins using information that is either extracted from three-dimensional structural analysis (X-ray crystallography or NMR), or derived from a pharmacore model based on known binders. The binding site information is used for in silico screening of a large substance library (e.g. available chemical directory), providing virtual hits. The three-dimensional structure is also used for the design of mutants where the binding site has been impaired. The wild-type target and the impaired mutant are then immobilized on different spots of the sensor chip and the interactions of compounds with the wild-type and mutant are compared in order to identify selective binders for the binding site of the target protein. This method can be used as a cost-effective alternative to high-throughput screening methods in cases when detailed binding site information is available. Here, we present three examples of how this technique can be applied to provide invaluable data during different phases of the drug discovery process.
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Affiliation(s)
- Walter Huber
- F. Hoffman-La Roche Ltd, Pharmaceutical Research, Discovery Chemistry, Basel, Switzerland.
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