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Eskonen V, Tong-Ochoa N, Valtonen S, Kopra K, Härmä H. Thermal Dissociation Assay for Time-Resolved Fluorescence Detection of Protein Post-Translational Modifications. ACS OMEGA 2019; 4:16501-16507. [PMID: 31616828 PMCID: PMC6787904 DOI: 10.1021/acsomega.9b02134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Post-translational modifications (PTMs) of proteins provide an important mechanism for cell signal transduction control. Impaired PTM control is a key feature in multiple different disease states, and thus the enzyme-controlling PTMs have drawn attention as highly promising drug targets. Due to the importance of PTMs, various methods to monitor PTM enzyme activity have been developed, but universal high-throughput screening (HTS), a compatible method for different PTMs, remains elusive. Here, we present a homogeneous single-label thermal dissociation assay for the detection of enzymatic PTM removal. The developed method allows the use of micromolar concentration of substrate peptide, which is expected to be beneficial when monitoring enzymes with low activity and peptide binding affinity. We prove the thermal dissociation concept functionality using peptides for dephosphorylation, deacetylation, and demethylation and demonstrate the HTS-compatible flash isothermal method for PTM enzyme activity monitoring. Using specific inhibitors, we detected literature-comparable IC50 values and Z' factors from 0.61 to 0.72, proving the HTS compatibility of the thermal peptide-break technology.
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Affiliation(s)
- Ville Eskonen
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Salla Valtonen
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Kari Kopra
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
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Kopra K, Tong-Ochoa N, Laine M, Eskonen V, Koskinen PJ, Härmä H. Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides. Anal Chim Acta 2019; 1055:126-132. [PMID: 30782363 DOI: 10.1016/j.aca.2018.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022]
Abstract
We have developed a rapid and sensitive universal peptide-based time-resolved luminescence assay for detection of enzymatic post-translational modifications (PTMs). PTMs play essential roles in intracellular signaling and cell regulation, thus providing functional protein diversity in cell. Due this, impaired PTM patterns have been linked to multiple disease states. Clear link between PTMs and pathological conditions have also driven assay development further, but still today most of the methodologies are based on single-specificity or group-specific PTM-recognition. We have previously introduced leuzine-zipper based peptide-break technology as a viable option for universal PTM detection. Here, we introduce peptide-break technology utilizing single-label homogeneous quenching resonance energy transfer (QRET) and charge-based peptide-peptide interaction. We demonstrate the functionality of the new assay concept in phosphorylation, deacetylation, and citrullination. In a comparable study between previously introduced leucine-zipper and the novel charge-based approach, we found equal PTM detection performance and sensitivity, but the peptide design for new targets is simplified with the charged peptides. The new concept allows the use of short <20 amino acid peptides without limitations rising from the leucine-zipper coiled-coil structure. Introduced methodology enables wash-free PTM detection in a 384-well plate format, using low nanomolar enzyme concentrations. Potentially, the peptide-break technique using charged peptides may be applicable for natural peptide sequences directly obtained from the target protein.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Mari Laine
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Päivi J Koskinen
- Section of Physiology and Genetics, Department of Biology, University of Turku, Vesilinnantie 5, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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Manoharan GB, Kopra K, Eskonen V, Härmä H, Abankwa D. High-throughput amenable fluorescence-assays to screen for calmodulin-inhibitors. Anal Biochem 2019; 572:25-32. [PMID: 30825429 DOI: 10.1016/j.ab.2019.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 02/17/2019] [Indexed: 12/12/2022]
Abstract
The KRAS gene is highly mutated in human cancers and the focus of current Ras drug development efforts. Recently the interface between the C-terminus of K-Ras and calmodulin (CaM) was proposed as a target site to block K-Ras driven cancer cell stemness. We therefore aimed at developing a high-throughput amenable screening assay to identify novel CaM-inhibitors as potential K-Ras stemness-signaling disruptors. A modulated time-resolved Förster resonance energy transfer (mTR-FRET)-assay was developed and benchmarked against an identically designed fluorescence anisotropy (FA)-assay. In both assays, two CaM-binding peptides were labeled with Eu(III)-chelate or fluorescein and used as single-label reporter probes that were displaced from CaM upon competitor binding. Thus, peptidic and small molecule competitors with nanomolar to micromolar affinities to CaM could be detected, including a peptide that was derived from the C-terminus of K-Ras. In order to detect CaM-residue specific covalent inhibitors, a cell lysate-based Förster resonance energy transfer (FRET)-assay was furthermore established. This assay enabled us to measure the slow, residue-specific, covalent inhibition by ophiobolin A in the presence of other endogenous proteins. In conclusion, we have developed a panel of fluorescence-assays that allows identification of conventional and covalent CaM-inhibitors as potential disruptors of K-Ras driven cancer cell stemness.
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Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
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Härmä H, Tong-Ochoa N, van Adrichem AJ, Jelesarov I, Wennerberg K, Kopra K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb) 2018; 54:2910-2913. [PMID: 29498735 DOI: 10.1039/c7cc09575a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Post-translational modification (PTM) of proteins plays essential regulatory roles in a variety of pathological conditions. Reliable and practical assays are required to accelerate the discovery of inhibitors and activators for PTM related diseases. Today, methodologies are based on specific or group-specific PTM recognition of e.g. phosphate for kinase activity without extending to other type of PTMs. Here we have established a universal time-resolved luminescence assay on a peptide-break platform for the direct detection of wide variety of PTMs. The developed assay is based on the leucine zipper concept wherein a europium-chelate labeled detection peptide and a non-labeled peptide substrate form a highly luminescent dimer. As an active PTM enzyme at sub or low nanomolar concentration modifies the substrate peptide, the luminescent signal of the detached detection peptide is quenched in the presence of soluble quenchers. The functionality of this universal assay technique has been demonstrated for the monitoring of phosphorylation, dephosphorylation, deacetylation, and citrullination with high applicability also to other PTMs in a high throughput format.
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Affiliation(s)
- Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Turku, Finland.
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Jeong EM, Lee MY, Lee JH, Lee BH, Oh KS. A Dual Readout Assay Based on Fluorescence Polarization and Time-Resolved Fluorescence Resonance Energy Transfer to Screen for RSK1 Inhibitors. Biol Pharm Bull 2017; 39:547-55. [PMID: 27040627 DOI: 10.1248/bpb.b15-00808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A dual readout assay based on fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET) exhibits many advantages over single assay technology in terms of screening quality and efficiency. In this study, we developed a dual readout assay combining FP and TR-FRET to identify ribosomal S6 kinase 1 (RSK1) inhibitors. This dual readout assay can monitor both FP and TR-FRET signals from a single RSK1 kinase reaction by using the immobilized metal affinity for phosphochemical (IMAP)-based assay. The Z' value and signal to background (S/B) ratio were 0.85 and 4.0 using FP, and 0.79 and 10.6 using TR-FRET, which led to performance of a pilot library screening against the drug repositioning set consisting of 2320 compounds with a reasonable reproducibility. From this screening, we identified 16 compounds showing greater than 50% inhibition against RSK1 for both FP and TR-FRET; 6 compounds with greater than 50% inhibition only for FP; and 4 compounds with greater than 50% inhibition only for TR-FRET. In a cell-based functional assay to validate the hit compounds, 10 compounds identified only in a single assay had little effect on the RSK-mediated phosphorylation of liver kinase B1, whereas 5 compounds showing greater than 80% inhibition for both FP and TR-FRET reduced the phosphorylation of liver kinase B1. These results demonstrate that the dual readout assay can be used to identify hit compounds by subsequently monitoring both FP and TR-FRET signals from one RSK1 reaction.
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Affiliation(s)
- Eun-mi Jeong
- Bio-Organic Science Division, Korea Research Institute of Chemical Technology
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Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ, Zweifach A. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening. ACTA ACUST UNITED AC 2016; 21:535-47. [DOI: 10.1177/1087057116634007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/31/2016] [Indexed: 11/16/2022]
Abstract
Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)–activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections.
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Affiliation(s)
- Jaimee Doucette
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Ziyan Zhao
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Rory J. Geyer
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Melanie M. Barra
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Marcy J. Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut at Storrs, Storrs, CT
| | - Adam Zweifach
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
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Tong-Ochoa N, Kopra K, Syrjänpää M, Legrand N, Härmä H. Homogeneous single-label tyrosine kinase activity assay for high throughput screening. Anal Chim Acta 2015; 897:96-101. [PMID: 26515010 DOI: 10.1016/j.aca.2015.09.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022]
Abstract
Protein post-translational modifications (PTMs) are regulatory mechanisms carried out by different enzymes in a cell. Kinase catalyzed phosphorylation is one of the most important PTM affecting the protein activity and function. We have developed a single-label quenching resonance energy transfer (QRET) assay to monitor tyrosine phosphorylation in a homogeneous high throughput compatible format. Epidermal growth factor receptor (EGFR) induced phosphorylation was monitored using Eu(3+)-chelate labeled peptide and label-free phosphotyrosine specific antibody in presence of a soluble quencher molecule. In the QRET kinase assay, antibody binding to phosphorylated Eu(3+)-peptide protects the Eu(3+)-chelate from luminescence quenching, monitoring high time-resolved luminescence (TRL) signals. In the presence of specific kinase inhibitor, antibody recognition and Eu(3+)-chelate protection is prevented, allowing an efficient luminescence quenching. The assay functionality was demonstrated with a panel of EGFR inhibitors (AG-1478, compound 56, erlotinib, PD174265, and staurosporine). The monitored IC50 values ranged from 0.08 to 155.3 nM and were comparable to those found in the literature. EGFR activity and inhibition assays were performed using low nanomolar enzyme and antibody concentration in a 384-well plate format, demonstrating its compatibility for high throughput screening (HTS).
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Affiliation(s)
- Natalia Tong-Ochoa
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland.
| | - Kari Kopra
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland
| | - Markku Syrjänpää
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland; Department of Biotechnology, University of Turku, Finland
| | - Nicolas Legrand
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland
| | - Harri Härmä
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland
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Lipchik AM, Perez M, Cui W, Parker LL. Multicolored, Tb³⁺-Based Antibody-Free Detection of Multiple Tyrosine Kinase Activities. Anal Chem 2015. [PMID: 26207839 DOI: 10.1021/acs.analchem.5b02233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Kinase signaling is a major mechanism driving many cancers. While many inhibitors have been developed and are employed in the clinic, resistance due to crosstalk and pathway reprogramming is an emerging problem. High-throughput assays to detect multiple pathway kinases simultaneously could better model these complex relationships and enable drug development to combat this type of resistance. We developed a strategy to take advantage of time-resolved luminescence of Tb(3+)-chelated phosphotyrosine-containing peptides, which facilitated efficient energy transfer to small molecule fluorophores conjugated to the peptides to produce orthogonally colored biosensors for two different kinases. This enabled multiplexed detection with high signal-to-noise in a high-throughput-compatible format. This proof-of-concept study provides a platform that could be applied to other lanthanide metal and fluorophore combinations to achieve even greater multiplexing without the need for phosphospecific antibodies.
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Affiliation(s)
- Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
| | - Minervo Perez
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
| | - Wei Cui
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
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Hildebrandt N, Wegner KD, Algar WR. Luminescent terbium complexes: Superior Förster resonance energy transfer donors for flexible and sensitive multiplexed biosensing. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.01.020] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Time-Resolved Förster Resonance Energy Transfer-Based Technologies to Investigate G Protein-Coupled Receptor Machinery. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:275-312. [DOI: 10.1016/b978-0-12-386932-6.00007-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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