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Rabara D, Stephen AG. Measurement of KRAS-GTPase Activity. Methods Mol Biol 2024; 2797:91-102. [PMID: 38570454 DOI: 10.1007/978-1-0716-3822-4_7] [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] [Indexed: 04/05/2024]
Abstract
Oncogenic mutations in KRAS typically impact the GAP-mediated and intrinsic GTP hydrolysis activity resulting in elevated levels of cellular KRAS-GTP. The development of biochemical assays for GTPase activity provides an opportunity to quantitatively measure the impact of these mutations on GTP hydrolysis. Here we describe a biochemical assay that measures the release of free phosphate upon hydrolysis of the GTP nucleotide and allows the measurement of intrinsic or GAP-stimulated GTP hydrolysis by KRAS. This assay can be used to measure GTPase activity under single turnover conditions.
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Affiliation(s)
- Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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2
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Kopra K, Mahran R, Yli-Hollo T, Tabata S, Vuorinen E, Fujii Y, Vuorinen I, Ogawa-Iio A, Hirayama A, Soga T, Sasaki AT, Härmä H. Homogeneous luminescent quantitation of cellular guanosine and adenosine triphosphates (GTP and ATP) using QT-Luc GTP&ATP assay. Anal Bioanal Chem 2023; 415:6689-6700. [PMID: 37714971 PMCID: PMC10598090 DOI: 10.1007/s00216-023-04944-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023]
Abstract
Guanosine triphosphate (GTP) and adenosine triphosphate (ATP) are essential nucleic acid building blocks and serve as energy molecules for a wide range of cellular reactions. Cellular GTP concentration fluctuates independently of ATP and is significantly elevated in numerous cancers, contributing to malignancy. Quantitative measurement of ATP and GTP has become increasingly important to elucidate how concentration changes regulate cell function. Liquid chromatography-coupled mass spectrometry (LC-MS) and capillary electrophoresis-coupled MS (CE-MS) are powerful methods widely used for the identification and quantification of biological metabolites. However, these methods have limitations related to specialized instrumentation and expertise, low throughput, and high costs. Here, we introduce a novel quantitative method for GTP concentration monitoring (GTP-quenching resonance energy transfer (QRET)) in homogenous cellular extracts. CE-MS analysis along with pharmacological control of cellular GTP levels shows that GTP-QRET possesses high dynamic range and accuracy. Furthermore, we combined GTP-QRET with luciferase-based ATP detection, leading to a new technology, termed QT-LucGTP&ATP, enabling high-throughput compatible dual monitoring of cellular GTP and ATP in a homogenous fashion. Collectively, GTP-QRET and QT-LucGTP&ATP offer a unique, high-throughput opportunity to explore cellular energy metabolism, serving as a powerful platform for the development of novel therapeutics and extending its usability across a range of disciplines.
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Affiliation(s)
- Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Titta Yli-Hollo
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Sho Tabata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Emmiliisa Vuorinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Yuki Fujii
- Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave, Cincinnati, OH, 45267-0508, USA
| | - Iida Vuorinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Aki Ogawa-Iio
- Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave, Cincinnati, OH, 45267-0508, USA
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Atsuo T Sasaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave, Cincinnati, OH, 45267-0508, USA
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. Int J Mol Sci 2022; 23:ijms23137095. [PMID: 35806100 PMCID: PMC9266822 DOI: 10.3390/ijms23137095] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Thermal unfolding methods are commonly used as a predictive technique by tracking the protein's physical properties. Inherent protein thermal stability and unfolding profiles of biotherapeutics can help to screen or study potential drugs and to find stabilizing or destabilizing conditions. Differential scanning calorimetry (DSC) is a 'Gold Standard' for thermal stability assays (TSA), but there are also a multitude of other methodologies, such as differential scanning fluorimetry (DSF). The use of an external probe increases the assay throughput, making it more suitable for screening studies, but the current methodologies suffer from relatively low sensitivity. While DSF is an effective tool for screening, interpretation and comparison of the results is often complicated. To overcome these challenges, we compared three thermal stability probes in small GTPase stability studies: SYPRO Orange, 8-anilino-1-naphthalenesulfonic acid (ANS), and the Protein-Probe. We studied mainly KRAS, as a proof of principle to obtain biochemical knowledge through TSA profiles. We showed that the Protein-Probe can work at lower concentration than the other dyes, and its sensitivity enables effective studies with non-covalent and covalent drugs at the nanomolar level. Using examples, we describe the parameters, which must be taken into account when characterizing the effect of drug candidates, of both small molecules and Designed Ankyrin Repeat Proteins.
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Methods to Monitor Ras Activation State. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:137-167. [PMID: 33977475 DOI: 10.1007/978-1-0716-1190-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Various biochemical methods have been introduced to detect and characterize small GTPases and Ras. Luminescence-based techniques cover most of the currently used methods, utilizing single- or multi-luminophore-conjugated molecules and external probes. Here we describe methods enabling Ras activity and activation state monitoring in vitro. This chapter focuses mainly on luminescence-based techniques.
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Kopra K, Sharina I, Martin E, Härmä H. Homogeneous single-label cGMP detection platform for the functional study of nitric oxide-sensitive (soluble) guanylyl cyclases and cGMP-specific phosphodiesterases. Sci Rep 2020; 10:17469. [PMID: 33060787 PMCID: PMC7562898 DOI: 10.1038/s41598-020-74611-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Cardiovascular diseases are the number one death worldwide. Nitric oxide (NO)-NO-sensitive (soluble) guanylyl cyclase (sGC)-cyclic guanosine monophosphate (cGMP) pathway regulates diverse set of important physiological functions, including maintenance of cardiovascular homeostasis. Resting and activated sGC enzyme converts guanosine triphosphate to an important second messenger cGMP. In addition to traditional NO generators, a number of sGC activators and stimulators are currently in clinical trials aiming to support or increase sGC activity in various pathological conditions. cGMP-specific phosphodiesterases (PDEs), which degrade cGMP to guanosine monophosphate, play key role in controlling the cGMP level and the strength or length of the cGMP-dependent cellular signaling. Thus, PDE inhibitors also have clear clinical applications. Here, we introduce a homogeneous quenching resonance energy transfer (QRET) for cGMP to monitor both sGC and PDE activities using high throughput screening adoptable method. We demonstrate that using cGMP-specific antibody, sGC or PDE activity and the effect of small molecules modulating their function can be studied with sub-picomole cGMP sensitivity. The results further indicate that the method is suitable for monitoring enzyme reactions also in complex biological cellular homogenates and mixture.
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Affiliation(s)
- Kari Kopra
- Department of Chemistry, Chemistry of Drug Development, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Iraida Sharina
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical School At Houston, 1941 East Road, Houston, TX, 77054, USA
| | - Emil Martin
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical School At Houston, 1941 East Road, Houston, TX, 77054, USA
| | - Harri Härmä
- Department of Chemistry, Chemistry of Drug Development, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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Kopra K, Seppälä T, Rabara D, Abreu-Blanco M, Kulmala S, Holderfield M, Härmä H. Label-Free Time-Gated Luminescent Detection Method for the Nucleotides with Varying Phosphate Content. SENSORS 2018; 18:s18113989. [PMID: 30453509 PMCID: PMC6264117 DOI: 10.3390/s18113989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 01/26/2023]
Abstract
A new label-free molecular probe for luminescent nucleotide detection in neutral aqueous solution is presented. Phosphate-containing molecules, such as nucleotides possess vital role in cell metabolism, energy economy, and various signaling processes. Thus, the monitoring of nucleotide concentration and nucleotide related enzymatic reactions is of high importance. Two component lanthanide complex formed from Tb(III) ion carrier and light harvesting antenna, readily distinguishes nucleotides containing different number of phosphates and enable direct detection of enzymatic reactions converting nucleotide triphosphate (NTP) to nucleotide di/monophosphate or the opposite. Developed sensor enables the detection of enzymatic activity with a low nanomolar sensitivity, as highlighted with K-Ras and apyrase enzymes in their hydrolysis assays performed in a high throughput screening compatible 384-well plate format.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
| | - Tanja Seppälä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
| | - Dana Rabara
- NCI-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA.
| | - Maria Abreu-Blanco
- NCI-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA.
| | - Sakari Kulmala
- Laboratory of Analytical Chemistry, Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Matthew Holderfield
- NCI-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA.
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
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Hewitt SH, Butler SJ. Application of lanthanide luminescence in probing enzyme activity. Chem Commun (Camb) 2018; 54:6635-6647. [PMID: 29790500 DOI: 10.1039/c8cc02824a] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
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Kopra K, van Adrichem AJ, Salo-Ahen OMH, Peltonen J, Wennerberg K, Härmä H. High-Throughput Dual Screening Method for Ras Activities and Inhibitors. Anal Chem 2017; 89:4508-4516. [PMID: 28318223 DOI: 10.1021/acs.analchem.6b04904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ras GTPases act as "molecular switches", alternating between inactive GDP-bound and active GTP-bound conformation. Ras-oncogenes were discovered over three decades ago, but there are still no effective therapies for Ras-driven cancers. So far, drug discovery strategies have been unsuccessful, because of a lack of suitable screening methodologies and well-defined binding pockets on the Ras proteins. Here, we addressed the former by introducing a homogeneous quenching resonance energy transfer (QRET) technique-based screening strategy for Ras interfacial and competitive inhibitors. We demonstrate that using a unique GTP-specific antibody fragment to monitor GTPase cycling in the presence of a guanine nucleotide exchange factor (GEF) and a GTPase activating protein (GAP) is an efficient method for Ras inhibitor high-throughput screening. When compared to a conventional GEF-stimulated nucleotide exchange assay in a proof-of-concept screen, we identified an overlapping set of potential inhibitor compounds but also compounds found exclusively with the new GTP hydrolysis monitoring-based GTPase cycling assay.
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Affiliation(s)
- Kari Kopra
- Institute of Biomedicine, University of Turku , Kiinamyllynkatu 10 C, FI-20520 Turku, Finland
| | - Arjan J van Adrichem
- Institute for Molecular Medicine Finland, University of Helsinki , Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Outi M H Salo-Ahen
- Structural Bioinformatics Laboratory and Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Biochemistry and Pharmacy, Åbo Akademi University , Tykistökatu 6A, FI-20520 Turku, Finland
| | - Juha Peltonen
- Institute of Biomedicine, University of Turku , Kiinamyllynkatu 10 C, FI-20520 Turku, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland, University of Helsinki , Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Harri Härmä
- Institute of Biomedicine, University of Turku , Kiinamyllynkatu 10 C, FI-20520 Turku, Finland
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Kopra K, Härmä H. Quenching resonance energy transfer (QRET): a single-label technique for inhibitor screening and interaction studies. N Biotechnol 2015; 32:575-80. [PMID: 25721971 DOI: 10.1016/j.nbt.2015.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/10/2015] [Accepted: 02/13/2015] [Indexed: 12/01/2022]
Abstract
The increased number of therapeutic targets has led to a growing need for screening methods enabling possible inhibitor compound selection. Information for new therapeutic targets has been found mostly from sequencing of the human genome but this knowledge cannot be directly converted into clinically relevant drug molecules. After target identification, the multistep drug development process takes many years and hundreds of millions of dollars are spent without certainty of the outcome. The first and the most critical step in the drug development process is hit selection. The optimal high throughput screening method should provide the highest possible number of true positive hits for further studies and lead discovery. The result should be achieved with low material consumption in a rapid and automated process. Radioactive label based methods are sensitive, but due to the problems arising from the radioactivity, luminescence-based methods have become increasingly popular in screening. In this review, the time-resolved luminescence based quenching resonance energy transfer (QRET) technique is discussed for primary screening.
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Affiliation(s)
- Kari Kopra
- 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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