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Kumar V, Chunchagatta Lakshman PK, Prasad TK, Manjunath K, Bairy S, Vasu AS, Ganavi B, Jasti S, Kamariah N. Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening. Heliyon 2024; 10:e23864. [PMID: 38226204 PMCID: PMC10788520 DOI: 10.1016/j.heliyon.2023.e23864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of in-vitro activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), Förster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target's role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.
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Affiliation(s)
| | | | - Thazhe Kootteri Prasad
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Sneha Bairy
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Akshaya S. Vasu
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - B. Ganavi
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Subbarao Jasti
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Neelagandan Kamariah
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
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2
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Greenhough LA, Clarke G, Phillipou AN, Mazani F, Karamshi B, Rowe S, Rowland P, Messenger C, Haslam CP, Bingham RP, Craggs PD. Reducing False Positives through the Application of Fluorescence Lifetime Technology: A Comparative Study Using TYK2 Kinase as a Model System. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:663-675. [PMID: 33783261 DOI: 10.1177/24725552211002472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The predominant assay detection methodologies used for enzyme inhibitor identification during early-stage drug discovery are fluorescence-based. Each fluorophore has a characteristic fluorescence decay, known as the fluorescence lifetime, that occurs throughout a nanosecond-to-millisecond timescale. The measurement of fluorescence lifetime as a reporter for biological activity is less common than fluorescence intensity, even though the latter has numerous issues that can lead to false-positive readouts. The confirmation of hit compounds as true inhibitors requires additional assays, cost, and time to progress from hit identification to lead drug-candidate optimization. To explore whether the use of fluorescence lifetime technology (FLT) can offer comparable benefits to label-free-based approaches such as RapidFire mass spectroscopy (RF-MS) and a superior readout compared to time-resolved fluorescence resonance energy transfer (TR-FRET), three equivalent assays were developed against the clinically validated tyrosine kinase 2 (TYK2) and screened against annotated compound sets. FLT provided a marked decrease in the number of false-positive hits when compared to TR-FRET. Further cellular screening confirmed that a number of potential inhibitors directly interacted with TYK2 and inhibited the downstream phosphorylation of the signal transducer and activator of transcription 4 protein (STAT4).
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Affiliation(s)
- Luke A Greenhough
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Gabriella Clarke
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Alexander N Phillipou
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Faith Mazani
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Bhumika Karamshi
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Sam Rowe
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Paul Rowland
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Cassie Messenger
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Carl P Haslam
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Ryan P Bingham
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
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3
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Martin K, Junker U, Tritto E, Sutter E, Rubic-Schneider T, Morgan H, Niwa S, Li J, Schlapbach A, Walker D, Bigaud M, Beerli C, Littlewood-Evans A, Rudolph B, Laisney M, Ledieu D, Beltz K, Quancard J, Bornancin F, Zamurovic Ribrioux N, Calzascia T. Pharmacological Inhibition of MALT1 Protease Leads to a Progressive IPEX-Like Pathology. Front Immunol 2020; 11:745. [PMID: 32425939 PMCID: PMC7203682 DOI: 10.3389/fimmu.2020.00745] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/01/2020] [Indexed: 01/14/2023] Open
Abstract
Genetic disruption or short-term pharmacological inhibition of MALT1 protease is effective in several preclinical models of autoimmunity and B cell malignancies. Despite these protective effects, the severe reduction in regulatory T cells (Tregs) and the associated IPEX-like pathology occurring upon congenital disruption of the MALT1 protease in mice has raised concerns about the long-term safety of MALT1 inhibition. Here we describe the results of a series of toxicology studies in rat and dog species using MLT-943, a novel potent and selective MALT1 protease inhibitor. While MLT-943 effectively prevented T cell-dependent B cell immune responses and reduced joint inflammation in the collagen-induced arthritis rat pharmacology model, in both preclinical species, pharmacological inhibition of MALT1 was associated with a rapid and dose-dependent reduction in Tregs and resulted in the progressive appearance of immune abnormalities and clinical signs of an IPEX-like pathology. At the 13-week time point, rats displayed severe intestinal inflammation associated with mast cell activation, high serum IgE levels, systemic T cell activation and mononuclear cell infiltration in multiple tissues. Importantly, using thymectomized rats we demonstrated that MALT1 protease inhibition affects peripheral Treg frequency independently of effects on thymic Treg output and development. Our data confirm the therapeutic potential of MALT1 protease inhibitors but highlight the safety risks and challenges to consider before potential application of such inhibitors into the clinic.
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Affiliation(s)
- Kea Martin
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ursula Junker
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Elaine Tritto
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Esther Sutter
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tina Rubic-Schneider
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Hannah Morgan
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Satoru Niwa
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jianping Li
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Achim Schlapbach
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dana Walker
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA, United States
| | - Marc Bigaud
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Christian Beerli
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Amanda Littlewood-Evans
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Bettina Rudolph
- PK Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marc Laisney
- PK Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - David Ledieu
- Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Karen Beltz
- PK Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jean Quancard
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Frédéric Bornancin
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Thomas Calzascia
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
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4
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Hammler D, Stuber K, Offensperger F, Scheffner M, Zumbusch A, Marx A. Fluorescently Labelled ATP Analogues for Direct Monitoring of Ubiquitin Activation. Chemistry 2020; 26:6279-6284. [PMID: 32154932 PMCID: PMC7317923 DOI: 10.1002/chem.202001091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/06/2020] [Indexed: 12/18/2022]
Abstract
Simple and robust assays to monitor enzymatic ATP cleavage with high efficiency in real‐time are scarce. To address this shortcoming, we developed fluorescently labelled adenosine tri‐, tetra‐ and pentaphosphate analogues of ATP. The novel ATP analogues bear — in contrast to earlier reports — only a single acridone‐based dye at the terminal phosphate group. The dye's fluorescence is quenched by the adenine component of the ATP analogue and is restored upon cleavage of the phosphate chain and dissociation of the dye from the adenosine moiety. Thereby the activity of ATP‐cleaving enzymes can be followed in real‐time. We demonstrate this proficiency for ubiquitin activation by the ubiquitin‐activating enzymes UBA1 and UBA6 which represents the first step in an enzymatic cascade leading to the covalent attachment of ubiquitin to substrate proteins, a process that is highly conserved from yeast to humans. We found that the efficiency to serve as cofactor for UBA1/UBA6 very much depends on the length of the phosphate chain of the ATP analogue: triphosphates are used poorly while pentaphosphates are most efficiently processed. Notably, the novel pentaphosphate‐harbouring ATP analogue supersedes the efficiency of recently reported dual‐dye labelled analogues and thus, is a promising candidate for broad applications.
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Affiliation(s)
- Daniel Hammler
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Katrin Stuber
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Fabian Offensperger
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Martin Scheffner
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied PhotonicsUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Andreas Marx
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
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5
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Eamegdool SS, Sitiwin EI, Cioanca AV, Madigan MC. Extracellular matrix and oxidative stress regulate human retinal pigment epithelium growth. Free Radic Biol Med 2020; 146:357-371. [PMID: 31751761 DOI: 10.1016/j.freeradbiomed.2019.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/01/2019] [Accepted: 11/13/2019] [Indexed: 11/23/2022]
Abstract
Age-related macular degeneration (AMD), the most common cause of vision loss with ageing, is characterised by degeneration of the photoreceptors and retinal pigment epithelium (RPE) and changes in the extracellular matrix (ECM) underlying the RPE. The pathogenesis of AMD is still not fully understood. In this study we investigated the in vitro growth and function of primary human RPE cells in response to different ECM substrates, including nitrite-modified ECM. We initially confirmed the presence of disorganised retinal glial and photoreceptor cells, marked retinal cytoplasmic and Bruch's membrane expression of nitro-tyrosine (an oxidative stress marker) and increased numbers of Iba1+ macrophages/microglia in human donor eye sections (aged and AMD) using multi-marker immunohistochemistry (n = 3). Concurrently, we utilised two-photon microscopy to reveal topographical changes in flatmounts of RPE-associated ECM and in the underlying choroid of aged and AMD donor eyes (n = 3). To recapitulate these observations in vitro, we then used primary human RPE cells to investigate how different ECM proteins, including nitrite cross-linked RPE-secreted ECM, modified RPE cell growth and function. Collagen I or IV increased RPE attachment and spreading two-to three-fold, associated with significantly increased cell migration and proliferation, consistent with a preferential interaction with these matrix substrates. Primary human RPE cells grown on collagen I and IV also showed increased secretion of pro-inflammatory cytokines, MCP-1 and IL-8. Nitrite-modification of RPE-secreted ECM (simulating ageing of Bruch's membrane) significantly reduced in vitro RPE attachment to the ECM and this was mitigated with collagen IV coating of the modified ECM. Taken together, our observations confirm the importance of RPE-ECM interactions for normal RPE growth and function, and for inducing RPE secretion of pro-inflammatory cytokines. Furthermore, the findings are consistent with ageing and/or oxidative stress-induced disruption of RPE-ECM interactions contributing to the pathogenesis of AMD.
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Affiliation(s)
- Steven S Eamegdool
- Save Sight Institute, University of Sydney, 2000, Australia; Eye Genetics Research Unit, Children's Medical Research Institute, 2145, Australia.
| | - Ephrem I Sitiwin
- Save Sight Institute, University of Sydney, 2000, Australia; School of Optometry and Vision Science, UNSW, 2052, Australia; Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Adrian V Cioanca
- Save Sight Institute, University of Sydney, 2000, Australia; The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Michele C Madigan
- Save Sight Institute, University of Sydney, 2000, Australia; School of Optometry and Vision Science, UNSW, 2052, Australia.
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6
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Hammler D, Marx A, Zumbusch A. Fluorescence-Lifetime-Sensitive Probes for Monitoring ATP Cleavage. Chemistry 2018; 24:15329-15335. [PMID: 30070405 DOI: 10.1002/chem.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/14/2022]
Abstract
Adenosine triphosphate (ATP) probes modified with fluorescence dyes that change their fluorescence properties upon cleavage are an interesting tool for monitoring enzymatic ATP turnover. As a readout parameter, fluorescence lifetime is attractive because it is nearly independent of concentration. In our study, we synthesised and investigated fifteen different ATP analogues, in which the fluorophores were attached to the γ-phosphate of ATP. All analogues showed distinctly different fluorescence lifetimes compared to the corresponding values of the free fluorophores. Both increases and decreases in fluorescence lifetime were observed upon attachment to ATP. To shed light on the photophysical processes governing the lifetime changes, we performed photoelectron spectroscopy in air (PESA) to determine HOMO energy levels and time-resolved fluorescence spectroscopy to obtain rate constants. We present evidence that fluorescence quenching in the compounds tested is dynamic and attributed to photoinduced electron transfer (PET), whereas fluorescence lifetime increases are caused by stacking interactions between chromophore and the nucleobase reducing non-radiative relaxation. Finally, we demonstrate that enzymatic cleavage of the ATP analogues presented can be followed by continuous monitoring of fluorescence lifetime changes.
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Affiliation(s)
- Daniel Hammler
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied Photonics, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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7
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Anders G, Hassiepen U, Theisgen S, Heymann S, Muller L, Panigada T, Huster D, Samsonov SA. The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from a Combined Bioinformatical and Experimental Approach. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:300-308. [PMID: 28113517 DOI: 10.1109/tcbb.2016.2614821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interleukin-8 (IL-8, CXCL8) is a neutrophil chemotactic factor belonging to the family of chemokines. IL-8 was shown to resist pepsin cleavage displaying its high resistance to this protease. However, the molecular mechanisms underlying this resistance are not fully understood. Using our in-house database containing the data on three-dimensional arrangements of secondary structure elements from the whole Protein Data Bank, we found a striking structural similarity between IL-8 and pepsin inhibitor-3. Such similarity could play a key role in understanding IL-8 resistance to the protease pepsin. To support this hypothesis, we applied pepsin assays confirming that intact IL-8 is not degraded by pepsin in comparison to IL-8 in a denaturated state. Applying 1H-15N Heteronuclear Single Quantum Coherence NMR measurements, we determined the putative regions at IL-8 that are potentially responsible for interactions with the pepsin. The results obtained in this work contribute to the understanding of the resistance of IL-8 to pepsin proteolysis in terms of its structural properties.
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8
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Abstract
Fluorescence lifetime (FLT) is a robust intrinsic property and material constant of fluorescent matter. Measuring this important physical indicator has evolved from a laboratory curiosity to a powerful and established technique for a variety of applications in drug discovery, medical diagnostics and basic biological research. This distinct trend was mainly driven by improved and meanwhile affordable laser and detection instrumentation on the one hand, and the development of suitable FLT probes and biological assays on the other. In this process two essential working approaches emerged. The first one is primarily focused on high throughput applications employing biochemical in vitro assays with no requirement for high spatial resolution. The second even more dynamic trend is the significant expansion of assay methods combining highly time and spatially resolved fluorescence data by fluorescence lifetime imaging. The latter approach is currently pursued to enable not only the investigation of immortal tumor cell lines, but also specific tissues or even organs in living animals. This review tries to give an actual overview about the current status of FLT based bioassays and the wide range of application opportunities in biomedical and life science areas. In addition, future trends of FLT technologies will be discussed.
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Affiliation(s)
- Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, D-64295 Darmstadt, Germany
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9
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Skilitsi AI, Turko T, Cianfarani D, Barre S, Uhring W, Hassiepen U, Léonard J. Towards sensitive, high-throughput, biomolecular assays based on fluorescence lifetime. Methods Appl Fluoresc 2017; 5:034002. [PMID: 28699919 DOI: 10.1088/2050-6120/aa7f66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing time-correlated single photon counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by time-correlated single photon counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second.
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Affiliation(s)
- Anastasia Ioanna Skilitsi
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67000 Strasbourg, France
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10
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The effect of angiotensin receptor neprilysin inhibitor, sacubitril/valsartan, on central nervous system amyloid-β concentrations and clearance in the cynomolgus monkey. Toxicol Appl Pharmacol 2017; 323:53-65. [DOI: 10.1016/j.taap.2017.03.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 01/11/2023]
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11
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Boettcher A, Gradoux N, Lorthiois E, Brandl T, Orain D, Schiering N, Cumin F, Woelcke J, Hassiepen U. Fluorescence Lifetime–Based Competitive Binding Assays for Measuring the Binding Potency of Protease Inhibitors In Vitro. ACTA ACUST UNITED AC 2014; 19:870-7. [DOI: 10.1177/1087057114521295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 12/20/2013] [Indexed: 11/17/2022]
Abstract
Fluorescence lifetime (FLT)–based assays have developed to become highly attractive tools in drug discovery. All recently published examples of FLT-based assays essentially describe their use for monitoring enzyme-mediated peptide modifications, such as proteolytic cleavage or phosphorylation/dephosphorylation. Here we report the development of competitive binding assays as novel, inhibitor-centric assays, principally employing the FLT of the acridone dye Puretime 14 (PT14) as the readout parameter. Exemplified with two case studies on human serine proteases, the details of the rationale for both the design and synthesis of probes (i.e., active site–directed low-molecular-weight inhibitors conjugated to PT14) are provided. Data obtained from testing inhibitors with the novel assay format match those obtained with alternative formats such as FLT-based protease activity and time-resolved fluorescence resonance energy transfer–based competitive binding assays.
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Affiliation(s)
- Andreas Boettcher
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Nathalie Gradoux
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Edwige Lorthiois
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Trixi Brandl
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - David Orain
- Novartis Institutes for BioMedical Research (NIBR), Global Discovery Chemistry, Novartis Pharma AG, Basel, Switzerland
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Frederic Cumin
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Julian Woelcke
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
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12
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Speight LC, Samanta M, Petersson EJ. Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck. Aust J Chem 2014. [DOI: 10.1071/ch13554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.
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13
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Pritz S, Doering K, Woelcke J, Hassiepen U. Fluorescence lifetime assays: current advances and applications in drug discovery. Expert Opin Drug Discov 2011; 6:663-70. [DOI: 10.1517/17460441.2011.571250] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Use of fluorescence lifetime technology to provide efficient protection from false hits in screening applications. Anal Biochem 2011; 409:89-97. [DOI: 10.1016/j.ab.2010.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 10/12/2010] [Accepted: 10/13/2010] [Indexed: 11/23/2022]
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15
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Pritz S, Meder G, Doering K, Drueckes P, Woelcke J, Mayr LM, Hassiepen U. A Fluorescence Lifetime-Based Assay for Abelson Kinase. ACTA ACUST UNITED AC 2010; 16:65-72. [DOI: 10.1177/1087057110385817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We present a novel homogeneous in vitro assay format and apply it to the quantitative determination of the enzymatic activity of a tyrosine kinase. The assay employs a short peptidic substrate containing a single tyrosine and a single probe attached via a cysteine side chain. The structural flexibility of the peptide allows for the dynamic quenching of the probe by the nonphosphorylated tyrosine side chain. The probe responds with changes in its fluorescence lifetime depending on the phosphorylation state of the tyrosine. We use this effect to directly follow the enzymatic phosphorylation of the substrate, without having to resort to additional assay components such as an antibody against the phosphotyrosine. As an example for the application of this assay principle, we present results from the development of an assay for Abelson kinase (c-Abl) used for compound profiling. Adjustments in the peptide sequence would make this assay format suitable to a wide variety of other tyrosine kinases.
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Affiliation(s)
| | - Gabriele Meder
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | | | - Peter Drueckes
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Kinases, Novartis Pharma AG, Basel, Switzerland
| | - Julian Woelcke
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Lorenz M. Mayr
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases, Novartis Pharma AG, Basel, Switzerland
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Boettcher A, Ruedisser S, Erbel P, Vinzenz D, Schiering N, Hassiepen U, Rigollier P, Mayr LM, Woelcke J. Fragment-Based Screening by Biochemical Assays. ACTA ACUST UNITED AC 2010; 15:1029-41. [DOI: 10.1177/1087057110380455] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based screening (FBS) has gained acceptance in the pharmaceutical industry as an attractive approach for the identification of new chemical starting points for drug discovery programs in addition to classical strategies such as high-throughput screening. There is the concern that screening of fragments at high µM concentrations in biochemical assays results in increased false-positive and false-negative rates. Here the authors systematically compare the data quality of FBS obtained by enzyme activity-based fluorescence intensity, fluorescence lifetime, and mobility shift assays with the data quality from surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR) methods. The serine protease trypsin and the matrix metalloprotease MMP12 were selected as model systems. For both studies, 352 fragments were selected each. From the data generated, all 3 biochemical protease assay methods can be used for screening of fragments with low false-negative and low false-positive rates, comparable to those achieved with the SPR-based assays. It can also be concluded that only fragments with a solubility higher than the screening concentration determined by means of NMR should be used for FBS purposes. Extrapolated to 10,000 fragments, the biochemical assays speed up the primary FBS process by approximately a factor of 10 and reduce the protease consumption by approximately 10,000-fold compared to NMR protein observation experiments.
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Affiliation(s)
- Andreas Boettcher
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Simon Ruedisser
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Paulus Erbel
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Daniela Vinzenz
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Pascal Rigollier
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Lorenz M. Mayr
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Julian Woelcke
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
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Maltman BA, Dunsmore CJ, Couturier SCM, Tirnaveanu AE, Delbederi Z, McMordie RAS, Naredo G, Ramage R, Cotton G. 9-Aminoacridine peptide derivatives as versatile reporter systems for use in fluorescence lifetime assays. Chem Commun (Camb) 2010; 46:6929-31. [DOI: 10.1039/c0cc01901a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Resch-Genger U, Grabolle M, Nitschke R, Nann T. Nanocrystals and Nanoparticles Versus Molecular Fluorescent Labels as Reporters for Bioanalysis and the Life Sciences: A Critical Comparison. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY II 2010. [DOI: 10.1007/978-3-642-04701-5_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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