1
|
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: 1.6] [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
|
2
|
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: 0.5] [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
|
3
|
Superior performance of liposomes over enzymatic amplification in a high-throughput assay for myoglobin in human serum. Anal Bioanal Chem 2013; 405:4017-26. [DOI: 10.1007/s00216-013-6807-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/24/2013] [Accepted: 01/29/2013] [Indexed: 11/28/2022]
|
4
|
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: 3.4] [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
|
5
|
Liu HW, Shi RF, Wang XF, Pan YX, Zang GY, Ma ZY. Cloning of a phosphatidylinositol 4-kinase gene based on fiber strength transcriptome QTL mapping in the cotton species Gossypium barbadense. GENETICS AND MOLECULAR RESEARCH 2012; 11:3367-78. [PMID: 22869083 DOI: 10.4238/2012.july.13.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sea Island cotton (Gossypium barbadense) is highly valued for its superior fiber qualities, especially fiber strength. Based on a transcript-derived fragment originated from transcriptome QTL mapping, a fiber strength related candidate gene of phosphatidylinositol 4-kinase cDNA, designated as GbPI4K, was first cloned, and its expression was characterized in the secondary cell wall thickening stage of G. barbadense fibers. The ORF of GbPI4K was found to be 1926 bp in length and encoded a predicted protein of 641 amino acid residues. The putative protein contained a clear PI3/4K kinase catalytic domain and fell into the plant type II PI4K cluster in phylogenetic analysis. In this study, the expression of cotton PI4K protein was also induced in Escherichia coli BL21 (DE3) as a fused protein. Semi-quantitative RT-PCR analysis showed that the gene expressed in the root, hypocotyl and leaf of the cotton plants. Real-time RT-PCR indicated that this gene in Sea Island cotton fibers expressed 10 days longer than that in Upland cotton fibers, and the main expression difference of PI4K between Sea Island cotton and Upland cotton in fibers was located in the secondary cell wall thickening stage of the fiber. Further analysis indicated that PI4K is a crucial factor in the ability of Rac proteins to regulate phospholipid signaling pathways.
Collapse
Affiliation(s)
- H W Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | | | | | | | | | | |
Collapse
|
6
|
Vidugiriene J, Zegzouti H, Goueli SA. Evaluating the utility of a bioluminescent ADP-detecting assay for lipid kinases. Assay Drug Dev Technol 2010; 7:585-97. [PMID: 20035616 DOI: 10.1089/adt.2009.0223] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The lipid second messengers phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3) and sphingosine 1-phosphate (S1P) are well recognized to play important roles in a variety of cellular processes, including cell proliferation, apoptosis, metabolism, and migration. Disruption of lipid signaling pathways often leads to human cancers, making lipid kinases attractive drug targets. In order to develop novel drugs against these enzymes, an assay that monitors their activity and amenable to high-throughput scale for screening large number of compounds is essential. The newly developed ADP-Glo assay is such an assay that measures kinase activity of lipid kinases by detecting the formation of ADP using a highly robust and sensitive bioluminescence approach. We evaluated this technology for studying lipid kinases, class I PI3 kinases, and sphingosine kinases and we show that the assay exhibits good tolerance to different lipids substrates. It generates kinetic parameters for substrates and inhibitors similar to those reported in the literature using other published assay formats. The sensitivity and robustness of this assay allow the detection of 5% of substrate conversion with Z' values >0.7 making it attractive for high-throughput screening (HTS) applications. It is noteworthy that ADP-Glo assay addresses the need for a single integrated platform to comprehensively measure all classes of lipid and protein kinases. The selected inhibitors of lipid kinases can be screened against the panel of desired protein kinases, making ADP-Glo assay a simple, inexpensive platform for HTS and profiling of lipid kinases.
Collapse
Affiliation(s)
- Jolanta Vidugiriene
- Promega Corporation, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | | | | |
Collapse
|
7
|
Demian DJ, Clugston SL, Foster MM, Rameh L, Sarkes D, Townson SA, Yang L, Zhang M, Charlton ME. High-throughput, cell-free, liposome-based approach for assessing in vitro activity of lipid kinases. ACTA ACUST UNITED AC 2009; 14:838-44. [PMID: 19641220 DOI: 10.1177/1087057109339205] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lipid kinases are central players in lipid signaling pathways involved in inflammation, tumorigenesis, and metabolic syndrome. A number of these kinase targets have proven difficult to investigate in higher throughput cell-free assay systems. This challenge is partially due to specific substrate interaction requirements for several of the lipid kinase family members and the resulting incompatibility of these substrates with most established, homogeneous assay formats. Traditional, cell-free in vitro investigational methods for members of the lipid kinase family typically involve substrate incorporation of [gamma-32P] and resolution of signal by thin-layer chromatography (TLC) and autoradiograph densitometry. This approach, although highly sensitive, does not lend itself to high-throughput testing of large numbers of small molecules (100 s to 1 MM+). The authors present the development and implementation of a fully synthetic, liposome-based assay for assessing in vitro activity of phosphatidylinositol-5-phosphate-4-kinase isoforms (PIP4KIIbeta and alpha) in 2 commonly used homogeneous technologies. They have validated these assays through compound testing in both traditional TLC and radioactive filterplate approaches as well as binding validation using isothermic calorimetry. A directed library representing known kinase pharmacophores was screened against type IIbeta phosphatidylinositol-phosphate kinase (PIPK) to identify small-molecule inhibitors. This assay system can be applied to other types and isoforms of PIPKs as well as a variety of other lipid kinase targets.
Collapse
Affiliation(s)
- Douglas J Demian
- Research Technology Center, Pfizer, Inc., Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Abstract
As an important metabolic pathway, phosphatidylinositol metabolism generates both constitutive and signalling molecules that are crucial for plant growth and development. Recent studies using genetic and molecular approaches reveal the important roles of phospholipid molecules and signalling in multiple processes of higher plants, including root growth, pollen and vascular development, hormone effects and cell responses to environmental stimuli plants. The present review summarizes the current progress in our understanding of the functional mechanism of phospholipid signalling, with an emphasis on the regulation of Ins(1,4,5)P3-Ca2+ oscillation, the second messenger molecule phosphatidic acid and the cytoskeleton.
Collapse
|