1
|
Takeuchi K, Nagase L, Kageyama S, Kanoh H, Oshima M, Ogawa-Iio A, Ikeda Y, Fujii Y, Kondo S, Osaka N, Masuda T, Ishihara T, Nakamura Y, Hirota Y, Sasaki T, Senda T, Sasaki AT. PI5P4K inhibitors: promising opportunities and challenges. FEBS J 2025. [PMID: 39828902 DOI: 10.1111/febs.17393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 09/30/2024] [Accepted: 12/30/2024] [Indexed: 01/22/2025]
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PI5P4K), also known as type II PIPKs or PIPKIIs, convert the lipid second messenger PI5P to PI(4,5)P2. The PI5P4K family consists of three isozymes in mammals-PI5P4Kα, β, and γ-which notably utilize both GTP and ATP as phosphodonors. Unlike the other two isozymes, which can utilize both ATP and GTP, PI5P4Kβ exhibits a marked preference for GTP over ATP, acting as an intracellular GTP sensor that alters its kinase activity in response to physiological changes in GTP concentration. Knockout studies have demonstrated a critical role for PI5P4Kα and β in tumorigenesis, while PI5P4Kγ has been implicated in regulating immune and neural systems. Pharmacological targeting of PI5P4K holds promise for the development of new therapeutic approaches against cancer, immune dysfunction, and neurodegenerative diseases. Although several PI5P4K inhibitors have already been developed, challenges remain in PI5P4K inhibitor development, including a discrepancy between in vitro and cellular efficacy. This discrepancy is attributable to mainly three factors. (a) Most PI5P4K inhibitors were developed at low ATP levels, where these enzymes exhibit minimal activity. (b) Non-catalytic functions of PI5P4K require careful interpretation of PI5P4K depletion studies, as their scaffolding roles suppress class I PI3K signaling. (c) The lack of pharmacodynamic markers for in vivo assessment complicates efficacy assessment. To address these issues and promote the development of effective and targeted therapeutic strategies, this review provides an analytical overview of the distinct roles of individual isozymes and recent developments in PI5P4K inhibitors, emphasizing structural insights and the importance of pharmacodynamic marker identification.
Collapse
Affiliation(s)
- Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
- Cellular and Molecular Biology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Lisa Nagase
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Shun Kageyama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Hirotaka Kanoh
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masashi Oshima
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Aki Ogawa-Iio
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Minuma-ku, Japan
| | - Yoshiki Ikeda
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Japan
| | - Yuki Fujii
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Sei Kondo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Natsuki Osaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Tsukasa Ishihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshikazu Nakamura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Yoshihisa Hirota
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Minuma-ku, Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, Japan
- Department of Lipid Biology, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, Japan
| | - Atsuo T Sasaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, OH, USA
- Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH, USA
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Japan
| |
Collapse
|
2
|
Qing T, Liu J, Liu F, Mitchell DC, Beresis RT, Gordan JD. Methods to assess small molecule allosteric modulators of the STRAD pseudokinase. Methods Enzymol 2022; 667:427-453. [PMID: 35525550 DOI: 10.1016/bs.mie.2022.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the increased appreciation of the biological relevance of pseudokinase (PSK) allostery, the broadening of small molecule strategies to target PSK function is of particular importance. We and others have pursued the development of small molecule allosteric modulators of the STRAD pseudokinase by targeting its ATP binding pocket. The purpose of this effort is to modulate the function of the LKB1 tumor suppressor kinase, which exists in a trimer with the STRAD PSK and the adaptor protein MO25. Here we provide detailed guidance regarding the different methods we have used for medium throughput screening to identify STRAD ligands and measure their impact on LKB1 kinase activity. Our experience supports preferential use of direct measurements of LKB1 kinase activity, and demonstrates the limitations of indirect assessment methods in the development trans-acting allosteric modulators.
Collapse
Affiliation(s)
- Tingting Qing
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Jin Liu
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Fen Liu
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Dom C Mitchell
- Division of Hematology Oncology and Quantitative Biosciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Richard T Beresis
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - John D Gordan
- Division of Hematology Oncology and Quantitative Biosciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States.
| |
Collapse
|
3
|
Liang D, Yu C, Qin X, Yang X, Dong X, Hu M, Du L, Li M. Discovery of small-molecule fluorescent probes for C-Met. Eur J Med Chem 2022; 230:114114. [PMID: 35051746 DOI: 10.1016/j.ejmech.2022.114114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/23/2021] [Accepted: 01/09/2022] [Indexed: 11/17/2022]
Abstract
C-mesenchymal-epithelia transition factor (c-Met) is highly expressed in various solid tumors such as gastric cancer, liver cancer, and lung cancer, playing a pivotal role in the growth, maintenance, and development of different tumor cells. In this study, three small-molecule fluorescent probes (5, 11, 16) targeting c-Met were developed, and their design strategies were also initially explored. In general, the fluorescence properties of the probes themselves could meet the imaging requirements, and they have shown sufficient inhibitory activities against c-Met, especially probe 16, reflecting the targeting and acceptance. Also, fluorescence polarization assays and flow cytometry analysis verified the binding between the probes and c-Met. Cell imaging confirmed that these probes could be used to label c-Met on living cells. It is of positive significance for the development of c-Met kinase inhibitors and tumor pathology research.
Collapse
Affiliation(s)
- Dong Liang
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Chen Yu
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiaojun Qin
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xingye Yang
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xuhui Dong
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Mingzhao Hu
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lupei Du
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Minyong Li
- Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| |
Collapse
|
4
|
Miles DH, Yan X, Thomas-Tran R, Fournier J, Sharif EU, Drew SL, Mata G, Lawson KV, Ginn E, Wong K, Soni D, Dhanota P, Shaqfeh SG, Meleza C, Chen A, Pham AT, Park T, Swinarski D, Banuelos J, Schindler U, Walters MJ, Walker NP, Zhao X, Young SW, Chen J, Jin L, Leleti MR, Powers JP, Jeffrey JL. Discovery of Potent and Selective 7-Azaindole Isoindolinone-Based PI3Kγ Inhibitors. ACS Med Chem Lett 2020; 11:2244-2252. [PMID: 33214836 DOI: 10.1021/acsmedchemlett.0c00387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
The successful application of immunotherapy in the treatment of cancer relies on effective engagement of immune cells in the tumor microenvironment. Phosphoinositide 3-kinase γ (PI3Kγ) is highly expressed in tumor-associated macrophages, and its expression levels are associated with tumor immunosuppression and growth. Selective inhibition of PI3Kγ offers a promising strategy in immuno-oncology, which has led to the development of numerous potent PI3Kγ inhibitors with variable selectivity profiles. To facilitate further investigation of the therapeutic potential of PI3Kγ inhibition, we required a potent and PI3Kγ-selective tool compound with sufficient metabolic stability for use in future in vivo studies. Herein, we describe some of our efforts to realize this goal through the systematic study of SARs within a series of 7-azaindole-based PI3Kγ inhibitors. The large volume of data generated from this study helped guide our subsequent lead optimization efforts and will inform further development of PI3Kγ-selective inhibitors for use in immunomodulation.
Collapse
Affiliation(s)
- Dillon H. Miles
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Xuelei Yan
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | | | - Jeremy Fournier
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Ehesan U. Sharif
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Samuel L. Drew
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Guillaume Mata
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | | | - Elaine Ginn
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Kent Wong
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Divyank Soni
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Puja Dhanota
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | | | - Cesar Meleza
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Ada Chen
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Amber T. Pham
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Timothy Park
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Debbie Swinarski
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Jesus Banuelos
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Ulrike Schindler
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | | | - Nigel P. Walker
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Xiaoning Zhao
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Stephen W. Young
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Jie Chen
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Lixia Jin
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | | | - Jay P. Powers
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| | - Jenna L. Jeffrey
- Arcus Biosciences, Inc., Hayward, California 94545, United States
| |
Collapse
|
5
|
Tai AW, Vidugiriene J. Measuring Activity of Phosphoinositide Lipid Kinases Using a Bioluminescent ADP-Detecting Assay. Methods Mol Biol 2016; 1360:75-85. [PMID: 26501903 DOI: 10.1007/978-1-4939-3073-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Phosphatidylinositol (PI) and its phosphorylated derivatives, collectively called phosphoinositides, are important second messengers involved in a variety of cellular processes, including cell proliferation, apoptosis, metabolism, and migration. These derivatives are generated by a family of kinases called phosphoinositide lipid kinases (PIKs). Due to the central role of these kinases in signaling pathways, assays for measuring their activity are often used for drug development. Lipid kinase substrates are present in unique membrane environments in vivo and are insoluble in aqueous solutions. Therefore the most important consideration in developing successful lipid kinase assays is the physical state of lipid kinase substrates. Here we describe the preparation of lipid substrates for two major classes of lipid kinases, phosphatidylinositol 3-kinases (PI3Ks) and phosphatidylinositol 4-kinases (PI4Ks). Using PI4Ks as an example, we also provide a detailed protocol for small-scale kinase expression and affinity purification from transiently transfected mammalian cells. For measuring lipid kinase activity we apply a universal bioluminescent ADP detection approach. The approach is compatible with diverse lipid substrates and can be used as a single integrated platform for measuring all classes of lipid and protein kinases.
Collapse
Affiliation(s)
- Andrew W Tai
- University of Michigan, 6520 MSRB I SPC 5682, 1150 W Medical Center Dr, Ann Arbor, MI, 48109-5682, USA.
| | - Jolanta Vidugiriene
- Promega Corporation, Research and Development Department, 2800 Woods Hollow Road, Madison, WI, 53711, USA.
| |
Collapse
|
6
|
A bioluminescent assay for monitoring conjugation of ubiquitin and ubiquitin-like proteins. Anal Biochem 2016; 510:41-51. [PMID: 27325501 DOI: 10.1016/j.ab.2016.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/30/2022]
Abstract
Post-translational modification of target proteins by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins is a critical mechanism for regulating protein functions affecting diverse cellular processes. Ub/Ubl proteins are conjugated to lysine residues in substrate proteins through an adenosine triphosphate (ATP)-dependent enzymatic cascade involving enzyme 1 (E1)-activating enzyme, E2-conjugating enzyme, and E3 ligase. The amount of adenosine monophosphate (AMP) produced in the first step, involving E1-mediated Ub/Ubl activation, represents an accurate measure of Ub/Ubl transfer during the process. Here we describe a novel bioluminescent assay platform, AMP-Glo, to quantify Ub/Ubl conjugation by measuring the AMP generated. The AMP-Glo assay is performed in a two-step reaction. The first step terminates the ubiquitination reaction, depletes the remaining ATP, and converts the AMP generated in the ubiquitination reaction to adenosine diphosphate (ADP), and in the second step the ADP generated is converted to ATP, which is detected as a bioluminescent signal using luciferase/luciferin, proportional to the AMP concentration and correlated with the Ub/Ubl transfer activity. We demonstrate the use of the assay to study Ub/Ubl conjugation and screen for chemical modulators of enzymes involved in the process. Because there is a sequential enhancement in light output in the presence of E1, E2, and E3, the AMP-Glo system can be used to deconvolute inhibitor specificity.
Collapse
|
7
|
Davis MI, Sasaki AT, Simeonov A. Method for Assaying the Lipid Kinase Phosphatidylinositol-5-phosphate 4-kinase α in Quantitative High-Throughput Screening (qHTS) Bioluminescent Format. Methods Mol Biol 2016; 1376:1-9. [PMID: 26552670 PMCID: PMC4696767 DOI: 10.1007/978-1-4939-3170-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lipid kinases are important regulators of a variety of cellular processes and their dysregulation causes diseases such as cancer and metabolic diseases. Distinct lipid kinases regulate the seven different phosphorylated forms of phosphatidylinositol (PtdIns). Some lipid kinases utilize long-chain lipid substrates that have limited solubility in aqueous solutions, which can lead to difficulties in developing a robust and miniaturizable biochemical assay. The ability to prepare the lipid substrate and develop assays to identify modulators of lipid kinases is important and is the focus of this methods chapter. Herein, we describe a method to prepare a DMSO-based lipid mixture that enables the 1536-well screening of the lipid kinase phosphatidylinositol-5-phosphate 4-kinase α (PI5P4Kα) utilizing the D-myo-di16-PtIns(5)P substrate in quantitative high-throughput screening (qHTS) format using the ADP-Glo™ technology to couple the production of ADP to a bioluminescent readout.
Collapse
Affiliation(s)
- Mindy I Davis
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Atsuo T Sasaki
- Department of Internal Medicine, Division of Hematology Oncology, UC Cancer Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
- Department of Neurosurgery, Brain Tumor Center, UC Neuroscience Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
| |
Collapse
|
8
|
Yanamandra M, Mitra S, Giri A. Development and application of PI3K assays for novel drug discovery. Expert Opin Drug Discov 2014; 10:171-86. [DOI: 10.1517/17460441.2015.997205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mahesh Yanamandra
- 1Scientist, GVK Biosciences Private Ltd, Biology, Campus MLR 1, Survey Nos. 125 (part) and 126, IDA Mallapur, Hyderabad, Telangana, 500076, India
- 2Jawaharlal Nehru Technological University, Institute of Science and Technology, Centre for Biotechnology, Kukatpally, Hyderabad, Telangana, 500085, India
| | - Sayan Mitra
- 3GVK Biosciences Private Ltd, Biology, Campus MLR 1, Survey Nos. 125 (part) and 126, IDA Mallapur, Hyderabad, Telangana, 500076, India
| | - Archana Giri
- 4Jawaharlal Nehru Technological University, Institute of Science and Technology, Centre for Biotechnology, Kukatpally, Hyderabad, Telangana, 500085, India
| |
Collapse
|
9
|
Lima S, Milstien S, Spiegel S. A real-time high-throughput fluorescence assay for sphingosine kinases. J Lipid Res 2014; 55:1525-30. [PMID: 24792926 DOI: 10.1194/jlr.d048132] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Indexed: 11/20/2022] Open
Abstract
Sphingosine kinases (SphKs), of which there are two isoforms, SphK1 and SphK2, have been implicated in regulation of many important cellular processes. We have developed an assay for monitoring SphK1 and SphK2 activity in real time without the need for organic partitioning of products, radioactive materials, or specialized equipment. The assay conveniently follows SphK-dependent changes in 7-nitro-2-1,3-benzoxadiazol-4-yl (NBD)-labeled sphingosine (Sph) fluorescence and can be easily performed in 384-well plate format with small reaction volumes. We present data showing dose-proportional responses to enzyme, substrate, and inhibitor concentrations. The SphK1 and SphK2 binding affinities for NBD-Sph and the IC50 values of inhibitors determined were consistent with those reported with other methods. Because of the versatility and simplicity of the assay, it should facilitate the routine characterization of inhibitors and SphK mutants and can be readily used for compound library screening in high-throughput format.
Collapse
Affiliation(s)
- Santiago Lima
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| |
Collapse
|
10
|
Considerations for the design and reporting of enzyme assays in high-throughput screening applications. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2013.12.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
11
|
Yanamandra M, Kole L, Giri A, Mitra S. Development of phosphocellulose paper-based screening of inhibitors of lipid kinases: case study with PI3Kβ. Anal Biochem 2013; 449:132-8. [PMID: 24380788 DOI: 10.1016/j.ab.2013.12.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 10/25/2022]
Abstract
The phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases that regulate the cellular signal transduction pathways involved in cell growth, proliferation, survival, apoptosis, and adhesion. Deregulation of these pathways are common in oncogenesis, and they are known to be altered in other metabolic disorders as well. Despite its huge potential as an attractive target in these diseases, there is an unmet need for the development of a successful inhibitor. Unlike protein kinase inhibitors, screening for lipid kinase inhibitors has been challenging. Here we report, for the first time, the development of a radioactive lipid kinase screening platform using a phosphocellulose plate that involves transfer of radiolabeled [γ-(32)P]ATP to phosphatidylinositol 4,5-phosphate forming phosphatidylinositol 3,4,5-phosphate, captured on the phosphocellulose plate. Enzyme kinetics and inhibitory properties were established in the plate format using standard inhibitors, such as LY294002, TGX-221, and wortmannin, having different potencies toward PI3K isoforms. ATP and lipid apparent Km for both were determined and IC50 values generated that matched the historical data. Here we report the use of a phosphocellulose plate for a lipid kinase assay (PI3Kβ as the target) as an excellent platform for the identification of novel chemical entities in PI3K drug discovery.
Collapse
Affiliation(s)
- Mahesh Yanamandra
- Biology Division, GVK Biosciences Pvt. Ltd., Hyderabad 500076, Andhra Pradesh, India; Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, 500085 Hyderabad, Andhra Pradesh, India
| | - Labanyamoy Kole
- VINS BIO, Kothur Mandal, Mahaboobnagar District 509325, Andhra Pradesh, India
| | - Archana Giri
- Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, 500085 Hyderabad, Andhra Pradesh, India
| | - Sayan Mitra
- Biology Division, GVK Biosciences Pvt. Ltd., Hyderabad 500076, Andhra Pradesh, India.
| |
Collapse
|
12
|
Davis MI, Sasaki AT, Shen M, Emerling BM, Thorne N, Michael S, Pragani R, Boxer M, Sumita K, Takeuchi K, Auld DS, Li Z, Cantley LC, Simeonov A. A homogeneous, high-throughput assay for phosphatidylinositol 5-phosphate 4-kinase with a novel, rapid substrate preparation. PLoS One 2013; 8:e54127. [PMID: 23326584 PMCID: PMC3542272 DOI: 10.1371/journal.pone.0054127] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/05/2012] [Indexed: 12/20/2022] Open
Abstract
Phosphoinositide kinases regulate diverse cellular functions and are important targets for therapeutic development for diseases, such as diabetes and cancer. Preparation of the lipid substrate is crucial for the development of a robust and miniaturizable lipid kinase assay. Enzymatic assays for phosphoinositide kinases often use lipid substrates prepared from lyophilized lipid preparations by sonication, which result in variability in the liposome size from preparation to preparation. Herein, we report a homogeneous 1536-well luciferase-coupled bioluminescence assay for PI5P4Kα. The substrate preparation is novel and allows the rapid production of a DMSO-containing substrate solution without the need for lengthy liposome preparation protocols, thus enabling the scale-up of this traditionally difficult type of assay. The Z’-factor value was greater than 0.7 for the PI5P4Kα assay, indicating its suitability for high-throughput screening applications. Tyrphostin AG-82 had been identified as an inhibitor of PI5P4Kα by assessing the degree of phospho transfer of γ-32P-ATP to PI5P; its inhibitory activity against PI5P4Kα was confirmed in the present miniaturized assay. From a pilot screen of a library of bioactive compounds, another tyrphostin, I-OMe tyrphostin AG-538 (I-OMe-AG-538), was identified as an ATP-competitive inhibitor of PI5P4Kα with an IC50 of 1 µM, affirming the suitability of the assay for inhibitor discovery campaigns. This homogeneous assay may apply to other lipid kinases and should help in the identification of leads for this class of enzymes by enabling high-throughput screening efforts.
Collapse
Affiliation(s)
- Mindy I. Davis
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Atsuo T. Sasaki
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Hematology and Oncology, Department of Internal Medicine, Neuroscience Institute: Brain Tumor Center, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Min Shen
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Brooke M. Emerling
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Natasha Thorne
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Sam Michael
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Rajan Pragani
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Matthew Boxer
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kazutaka Sumita
- Division of Hematology and Oncology, Department of Internal Medicine, Neuroscience Institute: Brain Tumor Center, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Koh Takeuchi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo, Japan
| | - Douglas S. Auld
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Zhuyin Li
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lewis C. Cantley
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anton Simeonov
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
| |
Collapse
|
13
|
Tai AW, Bojjireddy N, Balla T. A homogeneous and nonisotopic assay for phosphatidylinositol 4-kinases. Anal Biochem 2011; 417:97-102. [PMID: 21704602 PMCID: PMC3143478 DOI: 10.1016/j.ab.2011.05.046] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/25/2011] [Accepted: 05/31/2011] [Indexed: 11/25/2022]
Abstract
Phosphatidylinositol 4-kinases (PI 4-kinases) catalyze the conversion of phosphatidylinositol to phosphatidylinositol 4-phosphate (PtdIns4P). The four known mammalian PI 4-kinases, PI4KA, PI4KB, PI4K2A, and PI4K2B have roles in intracellular lipid and protein trafficking. PI4KA and PI4KB also assist in the replication of several positive-sense RNA viruses. The identification of selective inhibitors of these kinases would be facilitated by assays suitable for high-throughput screening. We describe a homogeneous and nonisotopic assay for PI 4-kinase activity based on the bioluminescent detection of the ADP produced by kinase reactions. We have evaluated this assay with known nonselective inhibitors of PI 4-kinases and show that it performs similar to radiometric assay formats previously described in the literature. In addition, this assay generates Z-factor values of >0.7 for PI4KA in a 384-well format, demonstrating its suitability for high-throughput screening applications.
Collapse
Affiliation(s)
- Andrew W Tai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48105, USA.
| | | | | |
Collapse
|
14
|
Kharel Y, Mathews TP, Kennedy AJ, Houck JD, Macdonald TL, Lynch KR. A rapid assay for assessment of sphingosine kinase inhibitors and substrates. Anal Biochem 2011; 411:230-5. [PMID: 21216217 PMCID: PMC3049835 DOI: 10.1016/j.ab.2011.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 12/31/2010] [Accepted: 01/04/2011] [Indexed: 01/26/2023]
Abstract
Sphingosine kinases (SphKs) catalyze the transfer of phosphate from adenosine triphosphate (ATP) to sphingosine to generate sphingosine 1-phosphate (S1P), an important bioactive lipid molecule that mediates a diverse range of cell signaling processes. The conventional assay of SphK enzymatic activity uses [γ-(32)P]ATP and sphingosine as substrates, with the radiolabeled S1P product recovered by organic extraction, displayed by thin layer chromatography, and quantified by liquid scintillation counting. Although this assay is sensitive and accurate, it is slow and labor-intensive; thus, it precludes the simultaneous screening of more than a few inhibitor compounds. Here we describe a 96-well assay for SphKs that is rapid and reproducible. Our method, which takes advantage of the limited solubility of S1P, detects radioactive S1P adhering to the plate by scintillation proximity counting. Our procedure obviates extraction into organic solvents, postreaction transfers, and chromatography. Furthermore, our assay enables assessment of both inhibitors and substrates, and it can detect endogenous SphK activity in cell and tissue extracts. The SphK kinetic parameter, K(m), and the K(i) values of inhibitors determined with our assay and the conventional assay were indistinguishable. These results document that our assay is well-suited for the screening of chemical libraries of SphK inhibitors.
Collapse
Affiliation(s)
- Yugesh Kharel
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22904, USA.
| | | | | | | | | | | |
Collapse
|
15
|
HaloTag-based purification of functional human kinases from mammalian cells. Protein Expr Purif 2010; 76:154-64. [PMID: 21129486 DOI: 10.1016/j.pep.2010.11.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 11/19/2010] [Accepted: 11/23/2010] [Indexed: 12/20/2022]
Abstract
Although cultured mammalian cells are preferred for producing functional mammalian proteins with appropriate post-translational modifications, purification of recombinant proteins is frequently hampered by low expression. We have addressed this by creating a new method configured specifically for mammalian cell culture that provides rapid detection and efficient purification. This approach is based on HaloTag, a protein fusion tag designed to bind rapidly, selectively and covalently to a series of synthetic ligands that can carry a variety of functional groups, including fluorescent dyes for detection or solid supports for purification. Since the binding of HaloTag to the HaloLink resin is essentially irreversible, it overcomes the equilibrium-based binding limitations associated with affinity tags and enables efficient capture and purification of target protein, even at low expression levels. The target protein is released from the HaloLink resin by specific cleavage using a TEV protease fused to HaloTag (HaloTEV), leaving both HaloTag and HaloTEV permanently attached to the resin and highly pure, tag-free protein in solution. HaloTag fluorescent ligands enable fluorescent labeling of HaloTag fusion proteins, providing a convenient way to monitor expression, and thus facilitate the identification of optimal transient transfection conditions as well as the selection of high expression stable cell lines. The capabilities of this method have been demonstrated by the efficient purification of five functional human kinases from HEK293T cells. In addition, when purifications using FLAG, 3xFLAG, His(6)Tag and HaloTag were performed in parallel, HaloTag was shown to provide significantly higher yields, purity and overall recovery of the expressed proteins.
Collapse
|
16
|
Inglese J, Napper A, Auld D. Improving Success by Balanced Critical Evaluations of Assay Methods. Assay Drug Dev Technol 2010; 8:1. [DOI: 10.1089/adt.2010.0804.com] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- James Inglese
- Editor-in-Chief, ASSAY and Drug Development Technologies
| | - Andrew Napper
- Deputy Editor, ASSAY and Drug Development Technologies
| | - Douglas Auld
- Member, Editorial Board; ASSAY and Drug Development Technologies
| |
Collapse
|