1
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Mansat M, Kpotor AO, Chicanne G, Picot M, Mazars A, Flores-Flores R, Payrastre B, Hnia K, Viaud J. MTM1-mediated production of phosphatidylinositol 5-phosphate fuels the formation of podosome-like protrusions regulating myoblast fusion. Proc Natl Acad Sci U S A 2024; 121:e2217971121. [PMID: 38805272 PMCID: PMC11161799 DOI: 10.1073/pnas.2217971121] [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: 10/21/2022] [Accepted: 04/10/2024] [Indexed: 05/30/2024] Open
Abstract
Myogenesis is a multistep process that requires a spatiotemporal regulation of cell events resulting finally in myoblast fusion into multinucleated myotubes. Most major insights into the mechanisms underlying fusion seem to be conserved from insects to mammals and include the formation of podosome-like protrusions (PLPs) that exert a driving force toward the founder cell. However, the machinery that governs this process remains poorly understood. In this study, we demonstrate that MTM1 is the main enzyme responsible for the production of phosphatidylinositol 5-phosphate, which in turn fuels PI5P 4-kinase α to produce a minor and functional pool of phosphatidylinositol 4,5-bisphosphate that concentrates in PLPs containing the scaffolding protein Tks5, Dynamin-2, and the fusogenic protein Myomaker. Collectively, our data reveal a functional crosstalk between a PI-phosphatase and a PI-kinase in the regulation of PLP formation.
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Affiliation(s)
- Mélanie Mansat
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Afi Oportune Kpotor
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Gaëtan Chicanne
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Mélanie Picot
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Anne Mazars
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Rémy Flores-Flores
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Bernard Payrastre
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
- Hematology Laboratory, University Hospital of Toulouse31059, Toulouse Cedex 03, France
| | - Karim Hnia
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
| | - Julien Viaud
- INSERM UMR1297, University of Toulouse 3, Institute of Metabolic and Cardiovascular Diseases (I2MC)31432, Toulouse Cedex 04, France
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2
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Palamiuc L, Johnson JL, Haratipour Z, Loughran RM, Choi WJ, Arora GK, Tieu V, Ly K, Llorente A, Crabtree S, Wong JCY, Ravi A, Wiederhold T, Murad R, Blind RD, Emerling BM. Hippo and PI5P4K signaling intersect to control the transcriptional activation of YAP. Sci Signal 2024; 17:eado6266. [PMID: 38805583 DOI: 10.1126/scisignal.ado6266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
Phosphoinositides are essential signaling molecules. The PI5P4K family of phosphoinositide kinases and their substrates and products, PI5P and PI4,5P2, respectively, are emerging as intracellular metabolic and stress sensors. We performed an unbiased screen to investigate the signals that these kinases relay and the specific upstream regulators controlling this signaling node. We found that the core Hippo pathway kinases MST1/2 phosphorylated PI5P4Ks and inhibited their signaling in vitro and in cells. We further showed that PI5P4K activity regulated several Hippo- and YAP-related phenotypes, specifically decreasing the interaction between the key Hippo proteins MOB1 and LATS and stimulating the YAP-mediated genetic program governing epithelial-to-mesenchymal transition. Mechanistically, we showed that PI5P interacted with MOB1 and enhanced its interaction with LATS, thereby providing a signaling connection between the Hippo pathway and PI5P4Ks. These findings reveal how these two important evolutionarily conserved signaling pathways are integrated to regulate metazoan development and human disease.
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Affiliation(s)
| | - Jared L Johnson
- Weill Cornell Medicine, Meyer Cancer Center, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zeinab Haratipour
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Austin Peay State University, Clarksville, TN 37044, USA
| | | | - Woong Jae Choi
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Vivian Tieu
- Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Kyanh Ly
- Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | | | | | - Jenny C Y Wong
- Weill Cornell Medicine, Meyer Cancer Center, New York, NY 10021, USA
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Archna Ravi
- Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | | | - Rabi Murad
- Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Raymond D Blind
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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3
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Jin Y, Xue J. Lipid kinases PIP5Ks and PIP4Ks: potential drug targets for breast cancer. Front Oncol 2023; 13:1323897. [PMID: 38156113 PMCID: PMC10753794 DOI: 10.3389/fonc.2023.1323897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023] Open
Abstract
Phosphoinositides, a small group of lipids found in all cellular membranes, have recently garnered heightened attention due to their crucial roles in diverse biological processes and different diseases. Among these, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), the most abundant bis-phosphorylated phosphoinositide within the signaling system, stands notably connected to breast cancer. Not only does it serve as a key activator of the frequently altered phosphatidylinositol 3-kinase (PI3K) pathway in breast cancer, but also its conversion to phosphatidylinositol-3,4,5-triphosphate (PI(3,4,5)P3) is an important direction for breast cancer research. The generation and degradation of phosphoinositides intricately involve phosphoinositide kinases. PI(4,5)P2 generation emanates from the phosphorylation of PI4P or PI5P by two lipid kinase families: Type I phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and Type II phosphatidylinositol-5-phosphate 4-kinases (PIP4Ks). In this comprehensive review, we focus on these two lipid kinases and delineate their compositions and respective cellular localization. Moreover, we shed light on the expression patterns and functions of distinct isoforms of these kinases in breast cancer. For a deeper understanding of their functional dynamics, we expound upon various mechanisms governing the regulation of PIP5Ks and PIP4Ks activities. A summary of effective and specific small molecule inhibitors designed for PIP5Ks or PIP4Ks are also provided. These growing evidences support PIP5Ks and PIP4Ks as promising drug targets for breast cancer.
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Affiliation(s)
- Yue Jin
- Department of Molecular Diagnosis, Northern Jiangsu People’s Hospital, Yangzhou University Clinical Medical College, Yangzhou, China
| | - Jian Xue
- Department of Emergency Medicine, Yizheng People’s Hospital, Yangzhou University Clinical Medical College, Yangzhou, China
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4
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Aldred GG, Rooney TPC, Willems HMG, Boffey HK, Green C, Winpenny D, Skidmore J, Clarke JH, Andrews SP. The rational design of ARUK2007145, a dual inhibitor of the α and γ isoforms of the lipid kinase phosphatidylinositol 5-phosphate 4-kinase (PI5P4K). RSC Med Chem 2023; 14:2035-2047. [PMID: 37859710 PMCID: PMC10583824 DOI: 10.1039/d3md00355h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 10/21/2023] Open
Abstract
The phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are therapeutic targets for diseases such as cancer, neurodegeneration and immunological disorders as they are key components in regulating cell signalling pathways. In an effort to make probe molecules available for further exploring these targets, we have previously reported PI5P4Kα-selective and PI5P4Kγ-selective ligands. Herein we report the rational design of PI5P4Kα/γ dual inhibitors, using knowledge gained during the development of selective inhibitors for these proteins. ARUK2007145 (39) is disclosed as a potent, cell-active probe molecule with ADMET properties amenable to conducting experiments in cells.
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Affiliation(s)
- Gregory G Aldred
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Timothy P C Rooney
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Henriette M G Willems
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Helen K Boffey
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Christopher Green
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - David Winpenny
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - John Skidmore
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Jonathan H Clarke
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Stephen P Andrews
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
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5
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Ghosh A, Venugopal A, Shinde D, Sharma S, Krishnan M, Mathre S, Krishnan H, Saha S, Raghu P. PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase. Life Sci Alliance 2023; 6:e202301920. [PMID: 37316298 PMCID: PMC10267561 DOI: 10.26508/lsa.202301920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023] Open
Abstract
Phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) are low-abundance phosphoinositides crucial for key cellular events such as endosomal trafficking and autophagy. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is an enzyme that regulates PI5P in vivo but can act on both PI5P and PI3P in vitro. In this study, we report a role for PIP4K in regulating PI3P levels in Drosophila Loss-of-function mutants of the only Drosophila PIP4K gene show reduced cell size in salivary glands. PI3P levels are elevated in dPIP4K 29 and reverting PI3P levels back towards WT, without changes in PI5P levels, can rescue the reduced cell size. dPIP4K 29 mutants also show up-regulation in autophagy and the reduced cell size can be reverted by depleting Atg8a that is required for autophagy. Lastly, increasing PI3P levels in WT can phenocopy the reduction in cell size and associated autophagy up-regulation seen in dPIP4K 29 Thus, our study reports a role for a PIP4K-regulated PI3P pool in the control of autophagy and cell size.
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Affiliation(s)
- Avishek Ghosh
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | | | - Dhananjay Shinde
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Sanjeev Sharma
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Meera Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Swarna Mathre
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Harini Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Sankhanil Saha
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
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6
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Wei L, Xu M, Liu Z, Jiang C, Lin X, Hu Y, Wen X, Zou R, Peng C, Lin H, Wang G, Yang L, Fang L, Yang M, Zhang P. Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study. J Chem Inf Model 2023; 63:5341-5355. [PMID: 37549337 DOI: 10.1021/acs.jcim.3c00543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Computer-aided drug design (CADD), especially artificial intelligence-driven drug design (AIDD), is increasingly used in drug discovery. In this paper, a novel and efficient workflow for hit identification was developed within the ID4Inno drug discovery platform, featuring innovative artificial intelligence, high-accuracy computational chemistry, and high-performance cloud computing. The workflow was validated by discovering a few potent hit compounds (best IC50 is ∼0.80 μM) against PI5P4K-β, a novel anti-cancer target. Furthermore, by applying the tools implemented in ID4Inno, we managed to optimize these hit compounds and finally obtained five hit series with different scaffolds, all of which showed high activity against PI5P4K-β. These results demonstrate the effectiveness of ID4inno in driving hit identification based on artificial intelligence, computational chemistry, and cloud computing.
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Affiliation(s)
- Lin Wei
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Min Xu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Zhiqiang Liu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Chongguo Jiang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Xiaohua Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Yaogang Hu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Xiaoming Wen
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Rongfeng Zou
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Hongrui Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Guo Wang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Lijun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Lei Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Peiyu Zhang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
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7
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Wills RC, Doyle CP, Zewe JP, Pacheco J, Hansen SD, Hammond GRV. A novel homeostatic mechanism tunes PI(4,5)P2-dependent signaling at the plasma membrane. J Cell Sci 2023; 136:jcs261494. [PMID: 37534432 PMCID: PMC10482388 DOI: 10.1242/jcs.261494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
The lipid molecule phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] controls all aspects of plasma membrane (PM) function in animal cells, from its selective permeability to the attachment of the cytoskeleton. Although disruption of PI(4,5)P2 is associated with a wide range of diseases, it remains unclear how cells sense and maintain PI(4,5)P2 levels to support various cell functions. Here, we show that the PIP4K family of enzymes, which synthesize PI(4,5)P2 via a minor pathway, also function as sensors of tonic PI(4,5)P2 levels. PIP4Ks are recruited to the PM by elevated PI(4,5)P2 levels, where they inhibit the major PI(4,5)P2-synthesizing PIP5Ks. Perturbation of this simple homeostatic mechanism reveals differential sensitivity of PI(4,5)P2-dependent signaling to elevated PI(4,5)P2 levels. These findings reveal that a subset of PI(4,5)P2-driven functions might drive disease associated with disrupted PI(4,5)P2 homeostasis.
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Affiliation(s)
- Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Colleen P. Doyle
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - James P. Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Scott D. Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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8
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Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
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Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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9
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Willems HMG, Edwards S, Boffey HK, Chawner SJ, Green C, Romero T, Winpenny D, Skidmore J, Clarke JH, Andrews SP. Identification of ARUK2002821 as an isoform-selective PI5P4Kα inhibitor. RSC Med Chem 2023; 14:934-946. [PMID: 37252102 PMCID: PMC10211317 DOI: 10.1039/d3md00039g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
The phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) play a central role in regulating cell signalling pathways and, as such, have become therapeutic targets for diseases such as cancer, neurodegeneration and immunological disorders. Many of the PI5P4Kα inhibitors that have been reported to date have suffered from poor selectivity and/or potency and the availability of better tool molecules would facilitate biological exploration. Herein we report a novel PI5P4Kα inhibitor chemotype that was identified through virtual screening. The series was optimised to deliver ARUK2002821 (36), a potent PI5P4Kα inhibitor (pIC50 = 8.0) which is selective vs. other PI5P4K isoforms and has broad selectivity against lipid and protein kinases. ADMET and target engagement data are provided for this tool molecule and others in the series, as well as an X-ray structure of 36 solved in complex with its PI5P4Kα target.
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Affiliation(s)
- Henriëtte M G Willems
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Simon Edwards
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Helen K Boffey
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Stephen J Chawner
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Christopher Green
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Tamara Romero
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - David Winpenny
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - John Skidmore
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Jonathan H Clarke
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
| | - Stephen P Andrews
- The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK
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10
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Teng M, Jiang J, Wang ES, Geng Q, Toenjes ST, Donovan KA, Mageed N, Yue H, Nowak RP, Wang J, Manz TD, Fischer ES, Cantley LC, Gray NS. Targeting the Dark Lipid Kinase PIP4K2C with a Potent and Selective Binder and Degrader. Angew Chem Int Ed Engl 2023; 62:e202302364. [PMID: 36898968 PMCID: PMC10150580 DOI: 10.1002/anie.202302364] [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: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/12/2023]
Abstract
Phosphatidylinositol 5-phosphate 4-kinase, type II, gamma (PIP4K2C) remains a poorly understood lipid kinase with minimal enzymatic activity but potential scaffolding roles in immune modulation and autophagy-dependent catabolism. Achieving potent and selective agents for PIP4K2C while sparing other lipid and non-lipid kinases has been challenging. Here, we report the discovery of the highly potent PIP4K2C binder TMX-4102, which shows exclusive binding selectivity for PIP4K2C. Furthermore, we elaborated the PIP4K2C binder into TMX-4153, a bivalent degrader capable of rapidly and selectively degrading endogenous PIP4K2C. Collectively, our work demonstrates that PIP4K2C is a tractable and degradable target, and that TMX-4102 and TMX-4153 are useful leads to further interrogate the biological roles and therapeutic potential of PIP4K2C.
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Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Eric S. Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 (USA)
| | - Qixiang Geng
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305 (USA)
| | - Sean T. Toenjes
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305 (USA)
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Theresa D. Manz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Lewis C. Cantley
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305 (USA)
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11
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Triscott J, Reist M, Küng L, Moselle FC, Lehner M, Gallon J, Ravi A, Arora GK, de Brot S, Lundquist M, Gallart-Ayala H, Ivanisevic J, Piscuoglio S, Cantley LC, Emerling BM, Rubin MA. PI5P4Kα supports prostate cancer metabolism and exposes a survival vulnerability during androgen receptor inhibition. SCIENCE ADVANCES 2023; 9:eade8641. [PMID: 36724278 PMCID: PMC9891700 DOI: 10.1126/sciadv.ade8641] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/03/2023] [Indexed: 05/07/2023]
Abstract
Phosphatidylinositol (PI)regulating enzymes are frequently altered in cancer and have become a focus for drug development. Here, we explore the phosphatidylinositol-5-phosphate 4-kinases (PI5P4K), a family of lipid kinases that regulate pools of intracellular PI, and demonstrate that the PI5P4Kα isoform influences androgen receptor (AR) signaling, which supports prostate cancer (PCa) cell survival. The regulation of PI becomes increasingly important in the setting of metabolic stress adaptation of PCa during androgen deprivation (AD), as we show that AD influences PI abundance and enhances intracellular pools of PI-4,5-P2. We suggest that this PI5P4Kα-AR relationship is mitigated through mTORC1 dysregulation and show that PI5P4Kα colocalizes to the lysosome, the intracellular site of mTORC1 complex activation. Notably, this relationship becomes prominent in mouse prostate tissue following surgical castration. Finally, multiple PCa cell models demonstrate marked survival vulnerability following stable PI5P4Kα inhibition. These results nominate PI5P4Kα as a target to disrupt PCa metabolic adaptation to castrate resistance.
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Affiliation(s)
- Joanna Triscott
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Matthias Reist
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Lukas Küng
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Francielle C. Moselle
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Institute of Biosciences, São Paulo State University, São Paulo, Brazil
| | - Marika Lehner
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Archna Ravi
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Gurpreet K. Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Mark Lundquist
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Brooke M. Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Mark A. Rubin
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Bern Center for Precision Medicine, University of Bern and Inselspital, Bern 3008, Switzerland
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12
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Wells C, Liang Y, Pulliam TL, Lin C, Awad D, Eduful B, O’Byrne S, Hossain MA, Catta-Preta CMC, Ramos PZ, Gileadi O, Gileadi C, Couñago RM, Stork B, Langendorf CG, Nay K, Oakhill JS, Mukherjee D, Racioppi L, Means AR, York B, McDonnell DP, Scott JW, Frigo DE, Drewry DH. SGC-CAMKK2-1: A Chemical Probe for CAMKK2. Cells 2023; 12:287. [PMID: 36672221 PMCID: PMC9856672 DOI: 10.3390/cells12020287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The serine/threonine protein kinase calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) plays critical roles in a range of biological processes. Despite its importance, only a handful of inhibitors of CAMKK2 have been disclosed. Having a selective small molecule tool to interrogate this kinase will help demonstrate that CAMKK2 inhibition can be therapeutically beneficial. Herein, we disclose SGC-CAMKK2-1, a selective chemical probe that targets CAMKK2.
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Affiliation(s)
- Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi Liang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas L. Pulliam
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chenchu Lin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dominik Awad
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Benjamin Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sean O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina Moura Costa Catta-Preta
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Opher Gileadi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Carina Gileadi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Brittany Stork
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Kevin Nay
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
| | | | - Debarati Mukherjee
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Luigi Racioppi
- Department of Medicine, Division of Hematological Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Anthony R. Means
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - John W. Scott
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
| | - Daniel E. Frigo
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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13
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Llorente A, Arora GK, Grenier SF, Emerling BM. PIP kinases: A versatile family that demands further therapeutic attention. Adv Biol Regul 2023; 87:100939. [PMID: 36517396 PMCID: PMC9992244 DOI: 10.1016/j.jbior.2022.100939] [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: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are membrane-localized phospholipids that regulate a plethora of essential cellular processes. These lipid signaling molecules are critical for cell homeostasis and therefore their levels are strictly regulated by the coordinated action of several families of lipid kinases and phosphatases. In this review, we provide a focused perspective on the phosphatidylinositol phosphate kinase (PIPK) family and the three subfamilies that compose it: Type I PIPKs or phosphatidylinositol-4-phosphate 5-kinases (PI4P5Ks), Type II PIPKs or phosphatidylinositol-5-phosphate 4-kinases (PI5P4Ks), and Type III PIPKs or phosphatidylinositol-3-phosphate 5-kinases (PIKfyve). Each subfamily is responsible for catalyzing a hydroxyl phosphorylation on specific phosphoinositide species to generate a double phosphorylated lipid, therefore regulating the levels of both substrate and product. Here, we summarize our current knowledge about the functions and regulation of each PIPK subfamily. Further, we highlight the roles of these kinases in various in vivo genetic models and give an overview of their involvement in multiple pathological conditions. The phosphoinositide field has been long focused on targeting PI3K signaling, but growing evidence suggests that it is time to draw attention to the other phosphoinositide kinases. The discovery of the involvement of PIPKs in the pathogenesis of multiple diseases has prompted substantial efforts to turn these enzymes into pharmacological targets. An increasingly refined knowledge of the biology of PIPKs in a variety of in vitro and in vivo models will facilitate the development of effective approaches for therapeutic intervention with the potential to translate into meaningful clinical benefits for patients suffering from cancer, immunological and infectious diseases, and neurodegenerative disorders.
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Affiliation(s)
- Alicia Llorente
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Shea F Grenier
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA.
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14
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Rooney TC, Aldred GG, Boffey HK, Willems HG, Edwards S, Chawner SJ, Scott DE, Green C, Winpenny D, Skidmore J, Clarke JH, Andrews SP. The Identification of Potent, Selective, and Brain Penetrant PI5P4Kγ Inhibitors as In Vivo-Ready Tool Molecules. J Med Chem 2022; 66:804-821. [PMID: 36516442 PMCID: PMC9841522 DOI: 10.1021/acs.jmedchem.2c01693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Owing to their central role in regulating cell signaling pathways, the phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are attractive therapeutic targets in diseases such as cancer, neurodegeneration, and immunological disorders. Until now, tool molecules for these kinases have been either limited in potency or isoform selectivity, which has hampered further investigation of biology and drug development. Herein we describe the virtual screening workflow which identified a series of thienylpyrimidines as PI5P4Kγ-selective inhibitors, as well as the medicinal chemistry optimization of this chemotype, to provide potent and selective tool molecules for further use. In vivo pharmacokinetics data are presented for exemplar tool molecules, along with an X-ray structure for ARUK2001607 (15) in complex with PI5P4Kγ, along with its selectivity data against >150 kinases and a Cerep safety panel.
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15
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Burke JE, Triscott J, Emerling BM, Hammond GRV. Beyond PI3Ks: targeting phosphoinositide kinases in disease. Nat Rev Drug Discov 2022; 22:357-386. [PMID: 36376561 PMCID: PMC9663198 DOI: 10.1038/s41573-022-00582-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
Lipid phosphoinositides are master regulators of almost all aspects of a cell's life and death and are generated by the tightly regulated activity of phosphoinositide kinases. Although extensive efforts have focused on drugging class I phosphoinositide 3-kinases (PI3Ks), recent years have revealed opportunities for targeting almost all phosphoinositide kinases in human diseases, including cancer, immunodeficiencies, viral infection and neurodegenerative disease. This has led to widespread efforts in the clinical development of potent and selective inhibitors of phosphoinositide kinases. This Review summarizes our current understanding of the molecular basis for the involvement of phosphoinositide kinases in disease and assesses the preclinical and clinical development of phosphoinositide kinase inhibitors.
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Affiliation(s)
- John E. Burke
- grid.143640.40000 0004 1936 9465Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia Canada
| | - Joanna Triscott
- grid.5734.50000 0001 0726 5157Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Brooke M. Emerling
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys, La Jolla, CA USA
| | - Gerald R. V. Hammond
- grid.21925.3d0000 0004 1936 9000Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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16
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WDR73 Depletion Destabilizes PIP4K2C Activity and Impairs Focal Adhesion Formation in Galloway–Mowat Syndrome. BIOLOGY 2022; 11:biology11101397. [PMID: 36290302 PMCID: PMC9598763 DOI: 10.3390/biology11101397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Galloway–Mowat syndrome is a rare genetic disease, classically characterized by a combination of various neurological symptoms and nephrotic syndrome. WDR73 is the pathogenic gene responsible for Galloway–Mowat syndrome. However, the pathological and molecular mechanisms of Galloway–Mowat syndrome, especially nephrotic syndrome caused by WDR73 deficiency, remains unknown. In this study, we knocked out the WDR73 in human embryonic kidney 293 cells to observe the morphological characteristics of the cells and elucidate the functions of WDR73. Additionally, we used a combination of proteomics, transcriptomics, and biochemical assays to identify the regulated targets of WDR73. We aimed to discover directly interacting molecules and the regulatory pathway of WDR73 and to illustrate the molecular mechanism between the WDR73 pathway and nephrotic disease in Galloway–Mowat syndrome. From the molecular mechanism we found in vitro, we draw a hypothesis that the damage to focal adhesion of podocytes caused by WDR73 defect is the key issue of kidney dysfunction. Finally, we verified the hypothesis in a podocyte-specific conditional knockout Wdr73 mouse model. Abstract (1) Background: Galloway–Mowat syndrome (GAMOS) is a rare genetic disease, classically characterized by a combination of various neurological symptoms and nephrotic syndrome. WDR73 is the pathogenic gene responsible for GAMOS1. However, the pathological and molecular mechanisms of GAMOS1, especially nephrotic syndrome caused by WDR73 deficiency, remain unknown. (2) Methods and Results: In this study, we first observed remarkable cellular morphological changes including impaired cell adhesion, decreased pseudopodia, and G2/M phase arrest in WDR73 knockout (KO) HEK 293 cells. The differentially expressed genes in WDR73 KO cells were enriched in the focal adhesion (FA) pathway. Additionally, PIP4K2C, a phospholipid kinase also involved in the FA pathway, was subsequently validated to interact with WDR73 via protein microarray and GST pulldown. WDR73 regulates PIP4K2C protein stability through the autophagy–lysosomal pathway. The stability of PIP4K2C was significantly disrupted by WDR73 KO, leading to a remarkable reduction in PIP2 and thus weakening the FA formation. In addition, we found that podocyte-specific conditional knockout (Wdr73 CKO) mice showed high levels of albuminuria and podocyte foot process injury in the ADR-induced model. FA formation was impaired in primary podocytes derived from Wdr73 CKO mice. (3) Conclusions: Since FA has been well known for its critical roles in maintaining podocyte structures and function, our study indicated that nephrotic syndrome in GAMOS1 is associated with disruption of FA caused by WDR73 deficiency.
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17
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Boffey H, Rooney TPC, Willems HMG, Edwards S, Green C, Howard T, Ogg D, Romero T, Scott DE, Winpenny D, Duce J, Skidmore J, Clarke JH, Andrews SP. Development of Selective Phosphatidylinositol 5-Phosphate 4-Kinase γ Inhibitors with a Non-ATP-competitive, Allosteric Binding Mode. J Med Chem 2022; 65:3359-3370. [PMID: 35148092 PMCID: PMC9097471 DOI: 10.1021/acs.jmedchem.1c01819] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 12/31/2022]
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are emerging as attractive therapeutic targets in diseases, such as cancer, immunological disorders, and neurodegeneration, owing to their central role in regulating cell signaling pathways that are either dysfunctional or can be modulated to promote cell survival. Different modes of binding may enhance inhibitor selectivity and reduce off-target effects in cells. Here, we describe efforts to improve the physicochemical properties of the selective PI5P4Kγ inhibitor, NIH-12848 (1). These improvements enabled the demonstration that this chemotype engages PI5P4Kγ in intact cells and that compounds from this series do not inhibit PI5P4Kα or PI5P4Kβ. Furthermore, the first X-ray structure of PI5P4Kγ bound to an inhibitor has been determined with this chemotype, confirming an allosteric binding mode. An exemplar from this chemical series adopted two distinct modes of inhibition, including through binding to a putative lipid interaction site which is 18 Å from the ATP pocket.
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Affiliation(s)
- Helen
K. Boffey
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Timothy P. C. Rooney
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Henriette M. G. Willems
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Simon Edwards
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Christopher Green
- UK
Dementia Research Institute, University
of Cambridge, Island
Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Tina Howard
- Peak
Proteins, Alderley Park, Macclesfield SK10 4TG, Cheshire, U.K.
| | - Derek Ogg
- Peak
Proteins, Alderley Park, Macclesfield SK10 4TG, Cheshire, U.K.
| | - Tamara Romero
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Duncan E. Scott
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - David Winpenny
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - James Duce
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - John Skidmore
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Jonathan H. Clarke
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Stephen P. Andrews
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
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18
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Tariq K, Luikart BW. Striking a balance: PIP 2 and PIP 3 signaling in neuronal health and disease. EXPLORATION OF NEUROPROTECTIVE THERAPY 2022; 1:86-100. [PMID: 35098253 PMCID: PMC8797975 DOI: 10.37349/ent.2021.00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Phosphoinositides are membrane phospholipids involved in a variety of cellular processes like growth, development, metabolism, and transport. This review focuses on the maintenance of cellular homeostasis of phosphatidylinositol 4,5-bisphosphate (PIP2), and phosphatidylinositol 3,4,5-trisphosphate (PIP3). The critical balance of these PIPs is crucial for regulation of neuronal form and function. The activity of PIP2 and PIP3 can be regulated through kinases, phosphatases, phospholipases and cholesterol microdomains. PIP2 and PIP3 carry out their functions either indirectly through their effectors activating integral signaling pathways, or through direct regulation of membrane channels, transporters, and cytoskeletal proteins. Any perturbations to the balance between PIP2 and PIP3 signaling result in neurodevelopmental and neurodegenerative disorders. This review will discuss the upstream modulators and downstream effectors of the PIP2 and PIP3 signaling, in the context of neuronal health and disease.
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Affiliation(s)
- Kamran Tariq
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Bryan W Luikart
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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19
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Ravi A, Palamiuc L, Emerling BM. Crucial Players for Inter-Organelle Communication: PI5P4Ks and Their Lipid Product PI-4,5-P 2 Come to the Surface. Front Cell Dev Biol 2022; 9:791758. [PMID: 35071233 PMCID: PMC8776650 DOI: 10.3389/fcell.2021.791758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
While organelles are individual compartments with specialized functions, it is becoming clear that organellar communication is essential for maintaining cellular homeostasis. This cooperation is carried out by various interactions taking place on the membranes of organelles. The membranes themselves contain a multitude of proteins and lipids that mediate these connections and one such class of molecules facilitating these relations are the phospholipids. There are several phospholipids, but the focus of this perspective is on a minor group called the phosphoinositides and specifically, phosphatidylinositol 4,5-bisphosphate (PI-4,5-P2). This phosphoinositide, on intracellular membranes, is largely generated by the non-canonical Type II PIPKs, namely, Phosphotidylinositol-5-phosphate-4-kinases (PI5P4Ks). These evolutionarily conserved enzymes are emerging as key stress response players in cells. Further, PI5P4Ks have been shown to modulate pathways by regulating organelle crosstalk, revealing roles in preserving metabolic homeostasis. Here we will attempt to summarize the functions of the PI5P4Ks and their product PI-4,5-P2 in facilitating inter-organelle communication and how they impact cellular health as well as their relevance to human diseases.
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Affiliation(s)
- Archna Ravi
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, United States
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, United States
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, United States
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20
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Arora GK, Palamiuc L, Emerling BM. Expanding role of PI5P4Ks in cancer: A promising druggable target. FEBS Lett 2021; 596:3-16. [PMID: 34822164 DOI: 10.1002/1873-3468.14237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Cancer cells are challenged by a myriad of microenvironmental stresses, and it is their ability to efficiently adapt to the constantly changing nutrient, energy, oxidative, and/or immune landscape that allows them to survive and proliferate. Such adaptations, however, result in distinct vulnerabilities that are attractive therapeutic targets. Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are a family of druggable stress-regulated phosphoinositide kinases that become conditionally essential as a metabolic adaptation, paving the way to targeting cancer cell dependencies. Further, PI5P4Ks have a synthetic lethal interaction with the tumor suppressor p53, the loss of which is one of the most prevalent genetic drivers of malignant transformation. PI5P4K's emergence as a crucial axis in the expanding landscape of phosphoinositide signaling in cancer has already stimulated the development of specific inhibitors. Thus, a better understanding of the biology of the PI5P4Ks will allow for targeted and effective therapeutic interventions. Here, we attempt to summarize the mounting roles of the PI5P4Ks in cancer, including evidence that targeting them is a therapeutic vulnerability and promising next-in-line treatment for multiple cancer subtypes.
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Affiliation(s)
- Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
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21
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Yousuf M, Rafi S, Ishrat U, Shafiga A, Dashdamirova G, Leyla V, Iqbal H. Potential Biological Targets Prediction, ADME Profiling, & Molecular Docking studies of Novel Steroidal Products from Cunninghamella Blakesleana. Med Chem 2021; 18:288-305. [PMID: 34102986 DOI: 10.2174/1573406417666210608143128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND New potential biological targets prediction through inverse molecular docking technique is an another smart strategy to forecast the possibility of compounds being biologically active against various target receptors. OBJECTIVES In this case of designed study, we screened our recently obtained novel acetylinic steroidal biotransformed products [(1) 8-β-methyl-14-α-hydroxy∆4tibolone (2) 9-α-Hydroxy∆4 tibolone (3) 8-β-methyl-11-β-hydroxy∆4tibolone (4) 6-β-hydroxy∆4tibolone, (5) 6-β-9-α-dihydroxy∆4tibolone (6) 7-β-hydroxy∆4tibolone) ] from fungi Cunninghemella Blakesleana to predict their possible biological targets and profiling of ADME properties. METHOD The prediction of pharmacokinetics properties membrane permeability as well as bioavailability radar properties were carried out by using Swiss target prediction, and Swiss ADME tools, respectively these metabolites were also subjected to predict the possible mechanism of action along with associated biological network pathways by using Reactome data-base. RESULTS All the six screened compounds possess excellent drug ability criteria, and exhibited exceptionally excellent non inhibitory potential against all five isozymes of CYP450 enzyme complex, including (CYP1A2, CYP2C19, CYP2C9, CYP2D6, and CYP3A4) respectively. All the screened compounds are lying within the acceptable pink zone of bioavailability radar and showing excellent descriptive properties. Compounds [1-4 & 6] are showing high BBB (Blood Brain Barrier) permeation, while compound 5 is exhibiting high HIA (Human Intestinal Absorption) property of (Egan Egg). CONCLUSION In conclusion, the results of this study smartly reveals that in-silico based studies are considered to provide robustness towards a rational drug designing and development approach, therefore in this way it helps to avoid the possibility of failure of drug candidates in the later experimental stages of drug development phases.
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Affiliation(s)
- Maria Yousuf
- Dow College of Biotechnology, Department of Bioinformatics, Dow University of Health Sciences Karachi, Pakistan
| | - Sidra Rafi
- International Centre for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Urooj Ishrat
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | | | | | | | - Heydarov Iqbal
- Botany Institute of, Azerbaijan National Academy of Sciences, Azerbaijan
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22
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Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells. Proc Natl Acad Sci U S A 2021; 118:2002486118. [PMID: 34001596 DOI: 10.1073/pnas.2002486118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Most human cancer cells harbor loss-of-function mutations in the p53 tumor suppressor gene. Genetic experiments have shown that phosphatidylinositol 5-phosphate 4-kinase α and β (PI5P4Kα and PI5P4Kβ) are essential for the development of late-onset tumors in mice with germline p53 deletion, but the mechanism underlying this acquired dependence remains unclear. PI5P4K has been previously implicated in metabolic regulation. Here, we show that inhibition of PI5P4Kα/β kinase activity by a potent and selective small-molecule probe disrupts cell energy homeostasis, causing AMPK activation and mTORC1 inhibition in a variety of cell types. Feedback through the S6K/insulin receptor substrate (IRS) loop contributes to insulin hypersensitivity and enhanced PI3K signaling in terminally differentiated myotubes. Most significantly, the energy stress induced by PI5P4Kαβ inhibition is selectively toxic toward p53-null tumor cells. The chemical probe, and the structural basis for its exquisite specificity, provide a promising platform for further development, which may lead to a novel class of diabetes and cancer drugs.
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23
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Raghu P. Emerging cell biological functions of phosphatidylinositol 5 phosphate 4 kinase. Curr Opin Cell Biol 2021; 71:15-20. [PMID: 33677148 DOI: 10.1016/j.ceb.2021.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/19/2021] [Accepted: 01/30/2021] [Indexed: 12/22/2022]
Abstract
The generation of phosphoinositides (PIs) with spatial and temporal control is a key mechanism in cellular organization and signaling. The synthesis of PIs is mediated by PI kinases, proteins that are able to phosphorylate unique substrates at specific positions on the inositol headgroup to generate signaling molecules. Phosphatidylinositol 5 phosphate 4 kinase (PIP4K) is one such lipid kinase that is able to specifically phosphorylate phosphatidylinositol 5 phosphate, the most recently discovered PI to generate the well-known and abundant PI, phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2]. PIP4K appears to be encoded only in metazoan genomes, and several genetic studies indicate important physiological functions for these enzymes in metabolism, immune function, and growth control. PIP4K has recently been reported to localize to multiple cellular compartments, including the nucleus, plasma membrane, endosomal systems, and autophagosome. However, the biochemical activity of these enzymes that is relevant to these physiological functions remains elusive. We review recent developments in this area and highlight emerging roles for these enzymes in cellular organization.
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Affiliation(s)
- Padinjat Raghu
- Cellular Organization and Signaling, National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore, 560065, India.
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24
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Wang DG, Paddock MN, Lundquist MR, Sun JY, Mashadova O, Amadiume S, Bumpus TW, Hodakoski C, Hopkins BD, Fine M, Hill A, Yang TJ, Baskin JM, Dow LE, Cantley LC. PIP4Ks Suppress Insulin Signaling through a Catalytic-Independent Mechanism. Cell Rep 2020; 27:1991-2001.e5. [PMID: 31091439 PMCID: PMC6619495 DOI: 10.1016/j.celrep.2019.04.070] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/06/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
Insulin stimulates the conversion of phosphatidylino-sitol-4,5-bisphosphate (PI(4,5)P2) to phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3), which mediates downstream cellular responses. PI(4,5)P2 is produced by phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and by phosphatidylinositol-5-phos-phate 4-kinases (PIP4Ks). Here, we show that the loss of PIP4Ks (PIP4K2A, PIP4K2B, and PIP4K2C) in vitro results in a paradoxical increase in PI(4,5)P2 and a concomitant increase in insulin-stimulated production of PI(3,4,5)P3. The reintroduction of either wild-type or kinase-dead mutants of the PIP4Ks restored cellular PI(4,5)P2 levels and insulin stimulation of the PI3K pathway, suggesting a catalytic-independent role of PIP4Ks in regulating PI(4,5)P2 levels. These effects are explained by an increase in PIP5K activity upon the deletion of PIP4Ks, which normally suppresses PIP5K activity through a direct binding interaction mediated by the N-terminal motif VMLϕFPDD of PIP4K. Our work uncovers an allosteric function of PIP4Ks in suppressing PIP5K-mediated PI(4,5)P2 synthesis and insulin-dependent conversion to PI(3,4,5)P3 and suggests that the pharmacological depletion of PIP4K enzymes could represent a strategy for enhancing insulin signaling. PI(4,5)P2 is produced by both phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and by phosphatidylinositol-5-phosphate 4-kinases (PIP4Ks). Wang et al. report an allosteric function of a conserved N-terminal motif of PIP4Ks in suppressing PIP5K-mediated PI(4,5)P2 synthesis and insulin-dependent conversion to PI(3,4,5) P3. This non-catalytic role has implications for the development of PIP4K targeted therapies.
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Affiliation(s)
- Diana G Wang
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell Medicine/Rockefeller University/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Marcia N Paddock
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Hematology and Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Mark R Lundquist
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Janet Y Sun
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Oksana Mashadova
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Solomon Amadiume
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Timothy W Bumpus
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Cindy Hodakoski
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Matthew Fine
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Amanda Hill
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - T Jonathan Yang
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Hematology and Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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25
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Pemberton JG, Kim YJ, Balla T. Integrated regulation of the phosphatidylinositol cycle and phosphoinositide-driven lipid transport at ER-PM contact sites. Traffic 2019; 21:200-219. [PMID: 31650663 DOI: 10.1111/tra.12709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Abstract
Among the structural phospholipids that form the bulk of eukaryotic cell membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the common precursor for low-abundance regulatory lipids, collectively referred to as polyphosphoinositides (PPIn). The metabolic turnover of PPIn species has received immense attention because of the essential functions of these lipids as universal regulators of membrane biology and their dysregulation in numerous human pathologies. The diverse functions of PPIn lipids occur, in part, by orchestrating the spatial organization and conformational dynamics of peripheral or integral membrane proteins within defined subcellular compartments. The emerging role of stable contact sites between adjacent membranes as specialized platforms for the coordinate control of ion exchange, cytoskeletal dynamics, and lipid transport has also revealed important new roles for PPIn species. In this review, we highlight the importance of membrane contact sites formed between the endoplasmic reticulum (ER) and plasma membrane (PM) for the integrated regulation of PPIn metabolism within the PM. Special emphasis will be placed on non-vesicular lipid transport during control of the PtdIns biosynthetic cycle as well as toward balancing the turnover of the signaling PPIn species that define PM identity.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
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26
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An Y, Jessen HJ, Wang H, Shears SB, Kireev D. Dynamics of Substrate Processing by PPIP5K2, a Versatile Catalytic Machine. Structure 2019; 27:1022-1028.e2. [PMID: 30956131 DOI: 10.1016/j.str.2019.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/18/2018] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
Processing of substrates by enzymes can only be fully understood through their conformational dynamics; this is particularly true for the diphosphoinositol pentakisphosphate kinase PPIP5K2, an enzyme with critical roles in cell signaling and bioenergetic homeostasis. PPIP5K2 is remarkable for the reversible nature of its kinase activity, its unique ligand-stimulated ATPase activity, and the substrate traveling between two ligand-binding sites. Here we use molecular dynamics and data analysis techniques to rationalize these PPIP5K2 activities, thereby increasing our understanding of complex enzymatic mechanisms. In particular, we demonstrate how the enzyme's distinctive, ratchet-like mechanism harnesses the energy of random fluctuations to significantly reduce the entropy toll for intramolecular substrate transfer. We show that pre-reaction pulling forces along the reaction coordinate are predictive of the various PPIP5K2 catalytic activities. An unexpected possibility, raised by these computational studies, that 3,5-IP8 might be a substrate for dephosphorylation was experimentally interrogated and confirmed in a luciferase assay.
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Affiliation(s)
- Yi An
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513, USA
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513, USA.
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27
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Phosphatidylinositol 5 Phosphate (PI5P): From Behind the Scenes to the Front (Nuclear) Stage. Int J Mol Sci 2019; 20:ijms20092080. [PMID: 31035587 PMCID: PMC6539119 DOI: 10.3390/ijms20092080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphatidylinositol (PI)-related signaling plays a pivotal role in many cellular aspects, including survival, cell proliferation, differentiation, DNA damage, and trafficking. PI is the core of a network of proteins represented by kinases, phosphatases, and lipases which are able to add, remove or hydrolyze PI, leading to different phosphoinositide products. Among the seven known phosphoinositides, phosphatidylinositol 5 phosphate (PI5P) was the last to be discovered. PI5P presence in cells is very low compared to other PIs. However, much evidence collected throughout the years has described the role of this mono-phosphoinositide in cell cycles, stress response, T-cell activation, and chromatin remodeling. Interestingly, PI5P has been found in different cellular compartments, including the nucleus. Here, we will review the nuclear role of PI5P, describing how it is synthesized and regulated, and how changes in the levels of this rare phosphoinositide can lead to different nuclear outputs.
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28
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Khadka B, Gupta RS. Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family. Genes (Basel) 2019; 10:genes10040312. [PMID: 31010098 PMCID: PMC6523245 DOI: 10.3390/genes10040312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023] Open
Abstract
Members of the PIP4K/PIP5K family of proteins, which generate the highly important secondary messenger phosphatidylinositol-4,5-bisphosphate, play central roles in regulating diverse signaling pathways. In eukaryotic organisms, multiple isozymes and subfamilies of PIP4K/PIP5K proteins are found and it is of much interest to understand their evolution and species distribution and what unique molecular and biochemical characteristics distinguish specific isozymes and subfamilies of proteins. We report here the species distribution of different PIP4K/PIP5K family of proteins in eukaryotic organisms and phylogenetic analysis based on their protein sequences. Our results indicate that the distinct homologs of both PIP4K and PIP5K are found in different organisms belonging to the Holozoa clade of eukaryotes, which comprises of various metazoan phyla as well as their close unicellular relatives Choanoflagellates and Filasterea. In contrast, the deeper-branching eukaryotic lineages, as well as plants and fungi, contain only a single homolog of the PIP4K/PIP5K proteins. In parallel, our comparative analyses of PIP4K/PIP5K protein sequences have identified six highly-specific molecular markers consisting of conserved signature indels (CSIs) that are uniquely shared by either the PIP4K or PIP5K proteins, or both, or specific subfamilies of these proteins. Of these molecular markers, 2 CSIs are distinctive characteristics of all PIP4K homologs, 1 CSI distinguishes the PIP4K and PIP5K homologs from the Holozoa clade of species from the ancestral form of PIP4K/PIP5K found in deeper-branching eukaryotic lineages. The remaining three CSIs are specific for the PIP5Kα, PIP5Kβ, and PIP4Kγ subfamilies of proteins from vertebrate species. These molecular markers provide important means for distinguishing different PIP4K/PIP5K isozymes as well as some of their subfamilies. In addition, the distribution patterns of these markers in different isozymes provide important insights into the evolutionary divergence of PIP4K/PIP5K proteins. Our results support the view that the Holozoa clade of eukaryotic organisms shared a common ancestor exclusive of the other eukaryotic lineages and that the initial gene duplication event leading to the divergence of distinct types of PIP4K and PIP5K homologs occurred in a common ancestor of this clade. Based on the results gleaned from different studies presented here, a model for the evolutionary divergence of the PIP4K/PIP5K family of proteins is presented.
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Affiliation(s)
- Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
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29
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Functional analysis of the biochemical activity of mammalian phosphatidylinositol 5 phosphate 4-kinase enzymes. Biosci Rep 2019; 39:BSR20182210. [PMID: 30718367 PMCID: PMC6379509 DOI: 10.1042/bsr20182210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/20/2019] [Accepted: 01/29/2019] [Indexed: 01/12/2023] Open
Abstract
Phosphatidylinositol 5 phosphate 4-kinase (PIP4K) are enzymes that catalyse the phosphorylation of phosphatidylinositol 5-phosphate (PI5P) to generate PI(4,5)P2. Mammalian genomes contain three genes, PIP4K2Α, 2B and 2C and murine knockouts for these suggested important physiological roles in vivo. The proteins encoded by PIP4K2A, 2B and 2C show widely varying specific activities in vitro; PIP4K2A is highly active and PIP4K2C 2000-times less active, and the relationship between this biochemical activity and in vivo function is unknown. By contrast, the Drosophila genome encodes a single PIP4K (dPIP4K) that shows high specific activity in vitro and loss of this enzyme results in reduced salivary gland cell size in vivo. We find that the kinase activity of dPIP4K is essential for normal salivary gland cell size in vivo. Despite their highly divergent specific activity, we find that all three mammalian PIP4K isoforms are able to enhance salivary gland cell size in the Drosophila PIP4K null mutant implying a lack of correlation between in vitro activity measurements and in vivo function. Further, the kinase activity of PIP4K2C, reported to be almost inactive in vitro, is required for in vivo function. Our findings suggest the existence of unidentified factors that regulate PIP4K enzyme activity in vivo.
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30
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Grabon A, Bankaitis VA, McDermott MI. The interface between phosphatidylinositol transfer protein function and phosphoinositide signaling in higher eukaryotes. J Lipid Res 2018; 60:242-268. [PMID: 30504233 DOI: 10.1194/jlr.r089730] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Phosphoinositides are key regulators of a large number of diverse cellular processes that include membrane trafficking, plasma membrane receptor signaling, cell proliferation, and transcription. How a small number of chemically distinct phosphoinositide signals are functionally amplified to exert specific control over such a diverse set of biological outcomes remains incompletely understood. To this end, a novel mechanism is now taking shape, and it involves phosphatidylinositol (PtdIns) transfer proteins (PITPs). The concept that PITPs exert instructive regulation of PtdIns 4-OH kinase activities and thereby channel phosphoinositide production to specific biological outcomes, identifies PITPs as central factors in the diversification of phosphoinositide signaling. There are two evolutionarily distinct families of PITPs: the Sec14-like and the StAR-related lipid transfer domain (START)-like families. Of these two families, the START-like PITPs are the least understood. Herein, we review recent insights into the biochemical, cellular, and physiological function of both PITP families with greater emphasis on the START-like PITPs, and we discuss the underlying mechanisms through which these proteins regulate phosphoinositide signaling and how these actions translate to human health and disease.
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Affiliation(s)
- Aby Grabon
- E. L. Wehner-Welch Laboratory, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114
| | - Vytas A Bankaitis
- E. L. Wehner-Welch Laboratory, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114
| | - Mark I McDermott
- E. L. Wehner-Welch Laboratory, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114
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31
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Structural Basis for Regulation of Phosphoinositide Kinases and Their Involvement in Human Disease. Mol Cell 2018; 71:653-673. [DOI: 10.1016/j.molcel.2018.08.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/22/2018] [Accepted: 07/30/2018] [Indexed: 01/09/2023]
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32
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Al-Ramahi I, Giridharan SSP, Chen YC, Patnaik S, Safren N, Hasegawa J, de Haro M, Wagner Gee AK, Titus SA, Jeong H, Clarke J, Krainc D, Zheng W, Irvine RF, Barmada S, Ferrer M, Southall N, Weisman LS, Botas J, Marugan JJ. Inhibition of PIP4Kγ ameliorates the pathological effects of mutant huntingtin protein. eLife 2017; 6:29123. [PMID: 29256861 PMCID: PMC5743427 DOI: 10.7554/elife.29123] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022] Open
Abstract
The discovery of the causative gene for Huntington’s disease (HD) has promoted numerous efforts to uncover cellular pathways that lower levels of mutant huntingtin protein (mHtt) and potentially forestall the appearance of HD-related neurological defects. Using a cell-based model of pathogenic huntingtin expression, we identified a class of compounds that protect cells through selective inhibition of a lipid kinase, PIP4Kγ. Pharmacological inhibition or knock-down of PIP4Kγ modulates the equilibrium between phosphatidylinositide (PI) species within the cell and increases basal autophagy, reducing the total amount of mHtt protein in human patient fibroblasts and aggregates in neurons. In two Drosophila models of Huntington’s disease, genetic knockdown of PIP4K ameliorated neuronal dysfunction and degeneration as assessed using motor performance and retinal degeneration assays respectively. Together, these results suggest that PIP4Kγ is a druggable target whose inhibition enhances productive autophagy and mHtt proteolysis, revealing a useful pharmacological point of intervention for the treatment of Huntington’s disease, and potentially for other neurodegenerative disorders.
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Affiliation(s)
- Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Baylor College of Medicine, Texas Medical Center, Houston, United States
| | | | - Yu-Chi Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Samarjit Patnaik
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor, United States
| | - Junya Hasegawa
- Department of Cell and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Maria de Haro
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Baylor College of Medicine, Texas Medical Center, Houston, United States
| | - Amanda K Wagner Gee
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Steven A Titus
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Hyunkyung Jeong
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Jonathan Clarke
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Dimitri Krainc
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Robin F Irvine
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Sami Barmada
- Department of Neurology, University of Michigan, Ann Arbor, United States
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Lois S Weisman
- Department of Cell and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Baylor College of Medicine, Texas Medical Center, Houston, United States
| | - Juan Jose Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
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Gupta RS, Epand RM. Phylogenetic analysis of the diacylglycerol kinase family of proteins and identification of multiple highly-specific conserved inserts and deletions within the catalytic domain that are distinctive characteristics of different classes of DGK homologs. PLoS One 2017; 12:e0182758. [PMID: 28829789 PMCID: PMC5567653 DOI: 10.1371/journal.pone.0182758] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/24/2017] [Indexed: 01/01/2023] Open
Abstract
Diacylglycerol kinase (DGK) family of proteins, which phosphorylates diacylglycerol into phosphatidic acid, play important role in controlling diverse cellular processes in eukaryotic organisms. Most vertebrate species contain 10 different DGK isozymes, which are grouped into 5 different classes based on the presence or absence of specific functional domains. However, the relationships among different DGK isozymes or how they have evolved from a common ancestor is unclear. The catalytic domain constitutes the single largest sequence element within the DGK proteins that is commonly and uniquely shared by all family members, but there is limited understanding of the overall function of this domain. In this work, we have used the catalytic domain sequences to construct a phylogenetic tree for the DGK family members from representatives of the main vertebrate classes and have also examined the distributions of various DGK isozymes in eukaryotic phyla. In a tree based on catalytic domain sequences, the DGK homologs belonging to different classes formed strongly supported clusters which were separated by long branches, and the different isozymes within each class also generally formed monophyletic groupings. Further, our analysis of the sequence alignments of catalytic domains has identified >10 novel sequence signatures consisting of conserved signature indels (inserts or deletions, CSIs) that are distinctive characteristics of either particular classes of DGK isozymes, or are commonly shared by members of two or more classes of DGK isozymes. The conserved indels in protein sequences are known to play important functional roles in the proteins/organisms where they are found. Thus, our identification of multiple highly specific CSIs that are distinguishing characteristics of different classes of DGK homologs points to the existence of important differences in the catalytic domain function among the DGK isozymes. The identified CSIs in conjunction with the results of blast searches on species distribution of DGK isozymes also provide useful insights into the evolutionary relationships among the DGK family of proteins.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
| | - Richard M. Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Alnajar S, Khadka B, Gupta RS. Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog. Front Microbiol 2017; 8:1409. [PMID: 28824557 PMCID: PMC5535262 DOI: 10.3389/fmicb.2017.01409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/11/2017] [Indexed: 01/05/2023] Open
Abstract
Bifidobacteria comprises an important group/order of bacteria whose members have widespread usage in the food and health industry due to their health-promoting activity in the human gastrointestinal tract. However, little is known about the underlying molecular properties that are responsible for the probiotic effects of these bacteria. The enzyme ribonucleotide reductase (RNR) plays a key role in all organisms by reducing nucleoside di- or tri- phosphates into corresponding deoxyribose derivatives required for DNA synthesis, and RNR homologs belonging to classes I and III are present in either most or all Bifidobacteriales. Comparative analyses of these RNR homologs have identified several novel sequence features in the forms of conserved signature indels (CSIs) that are exclusively found in bifidobacterial RNRs. Specifically, in the large subunit of the aerobic class Ib RNR, three CSIs have been identified that are uniquely found in the Bifidobacteriales homologs. Similarly, the large subunit of the anaerobic class III RNR contains five CSIs that are also distinctive characteristics of bifidobacteria. Phylogenetic analyses indicate that these CSIs were introduced in a common ancestor of the Bifidobacteriales and retained by all descendants, likely due to their conferring advantageous functional roles. The identified CSIs in the bifidobacterial RNR homologs provide useful tools for further exploration of the novel functional aspects of these important enzymes that are exclusive to these bacteria. We also report here the results of homology modeling studies, which indicate that most of the bifidobacteria-specific CSIs are located within the surface loops of the RNRs, and of these, a large 43 amino acid insert in the class III RNR homolog forms an extension of the allosteric regulatory site known to be essential for protein function. Preliminary docking studies suggest that this large CSI may be playing a role in enhancing the stability of the RNR dimer complex. The possible significances of the identified CSIs, as well as the distribution of RNR homologs in the Bifidobacteriales, are discussed.
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Affiliation(s)
- Seema Alnajar
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada
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35
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Takeuchi K, Senda M, Lo YH, Kofuji S, Ikeda Y, Sasaki AT, Senda T. Structural reverse genetics study of the PI5P4Kβ-nucleotide complexes reveals the presence of the GTP bioenergetic system in mammalian cells. FEBS J 2017; 283:3556-3562. [PMID: 27090388 DOI: 10.1111/febs.13739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 12/13/2022]
Abstract
Reverse genetic analysis can connect a gene and its protein counterpart to a biological function(s) by knockout or knockdown of the specific gene. However, when a protein has multiple biochemical activities, the conventional genetics strategy is incapable of distinguishing which biochemical activity of the protein is critical for the particular biological function(s). Here, we propose a structural reverse genetics strategy to overcome this problem. In a structural reverse genetics study, multiple biochemical activities of a protein are segregated by mapping those activities to a structural element(s) in the atomic resolution tertiary structure. Based on the structural mapping, a mutant lacking one biochemical activity of interest can be produced with the other activities kept intact. Expression of the mutant by knockin or ectopic expression in the knockout strain along with the following analysis can connect the single biochemical activity of interest to a biological function. Using the structural reverse genetics strategy, we have dissected the newly identified GTP-dependent activity of a lipid kinase PI5P4Kβ from its ATP-dependent activity. The GTP-insensitive mutant has demonstrated the existence of the GTP bioenergetic sensor system in mammalian cells and its critical role in tumorigenesis. As structural reverse genetics can identify in vivo significance of individual biochemical activity, it is a powerful approach to reveal hidden biological functions, which could be a novel pharmacological target for therapeutic intervention. Given the recent expansion of choices in structural biological methods and advances in genome editing technologies, the time is ripe for structural reverse genetics strategies.
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Affiliation(s)
- Koh Takeuchi
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo, Japan.,JST, PRESTO, Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Yu-Hua Lo
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Satoshi Kofuji
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA. .,Department of Cancer Biology, Brain Tumor Center, Neuroscience Institute, University of Cincinnati College of Medicine, OH, USA. .,Department of Neurosurgery, Brain Tumor Center, Neuroscience Institute, University of Cincinnati College of Medicine, OH, USA.
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan. .,Department of Materials Structure Science, School of High Energy Accelerator Science, The graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki, Japan.
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36
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Hasegawa J, Strunk BS, Weisman LS. PI5P and PI(3,5)P 2: Minor, but Essential Phosphoinositides. Cell Struct Funct 2017; 42:49-60. [PMID: 28302928 DOI: 10.1247/csf.17003] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In most eukaryotes, phosphoinositides (PIs) have crucial roles in multiple cellular functions. Although the cellular levels of phosphatidylinositol 5-phosphate (PI5P) and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) are extremely low relative to some other PIs, emerging evidence demonstrates that both lipids are crucial for the endocytic pathway, intracellular signaling, and adaptation to stress. Mutations that causes defects in the biosynthesis of PI5P and PI(3,5)P2 are linked to human diseases including neurodegenerative disorders. Here, we review recent findings on cellular roles of PI5P and PI(3,5)P2, as well as the pathophysiological importance of these lipids.Key words: Phosphoinositides, Membrane trafficking, Endocytosis, Vacuoles/Lysosomes, Fab1/PIKfyve.
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37
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Nuclear localizations of phosphatidylinositol 5-phosphate 4-kinases α and β are dynamic and independently regulated during starvation-induced stress. Biochem J 2016; 473:2155-63. [PMID: 27208178 DOI: 10.1042/bcj20160380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/16/2016] [Indexed: 01/15/2023]
Abstract
The chicken B-cell line DT40 has two isoforms of phosphatidylinositol 5-phosphate 4-kinase (PI5P4K), α and β, which are likely to exist as a mixture of obligate homo- and hetero-dimers. Previous work has led us to speculate that an important role of the β isoform may be to target the more active PI5P4Kα isoform to the nucleus. In the present study we expand upon that work by genomically tagging the PI5P4Ks with fluorochromes in the presence or absence of stable or acute depletions of PI5P4Kβ. Consistent with our original hypothesis we find that PI5P4Kα is predominantly (possible entirely) cytoplasmic when PI5P4Kβ is stably deleted from cells. In contrast, when PI5P4Kβ is inducibly removed within 1 h PI5P4Kα retains its wild-type distribution of approximately 50:50 between cytoplasm and nucleus even through a number of cell divisions. This leads us to speculate that PI5P4Kα is chromatin-associated. We also find that when cells are in the exponential phase of growth PI5P4Kβ is primarily cytoplasmic but translocates to the nucleus upon growth into the stationary phase or upon serum starvation. Once again this is not accompanied by a change in PI5P4Kα localization and we show, using an in vitro model, that this is possible because the dimerization between the two isoforms is dynamic. Given this shift in PI5P4Kβ upon nutrient deprivation we explore the phenotype of PI5P4K B-null cells exposed to this stress and find that they can sustain a greater degree of nutrient deprivation than their wild-type counterparts possibly as a result of up-regulation of autophagy.
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38
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Sumita K, Lo YH, Takeuchi K, Senda M, Kofuji S, Ikeda Y, Terakawa J, Sasaki M, Yoshino H, Majd N, Zheng Y, Kahoud ER, Yokota T, Emerling BM, Asara JM, Ishida T, Locasale JW, Daikoku T, Anastasiou D, Senda T, Sasaki AT. The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis. Mol Cell 2016; 61:187-98. [PMID: 26774281 DOI: 10.1016/j.molcel.2015.12.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/21/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022]
Abstract
While cellular GTP concentration dramatically changes in response to an organism's cellular status, whether it serves as a metabolic cue for biological signaling remains elusive due to the lack of molecular identification of GTP sensors. Here we report that PI5P4Kβ, a phosphoinositide kinase that regulates PI(5)P levels, detects GTP concentration and converts them into lipid second messenger signaling. Biochemical analyses show that PI5P4Kβ preferentially utilizes GTP, rather than ATP, for PI(5)P phosphorylation, and its activity reflects changes in direct proportion to the physiological GTP concentration. Structural and biological analyses reveal that the GTP-sensing activity of PI5P4Kβ is critical for metabolic adaptation and tumorigenesis. These results demonstrate that PI5P4Kβ is the missing GTP sensor and that GTP concentration functions as a metabolic cue via PI5P4Kβ. The critical role of the GTP-sensing activity of PI5P4Kβ in cancer signifies this lipid kinase as a cancer therapeutic target.
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Affiliation(s)
- Kazutaka Sumita
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu-Hua Lo
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Koh Takeuchi
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Satoshi Kofuji
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jumpei Terakawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Hirofumi Yoshino
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Nazanin Majd
- Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Yuxiang Zheng
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Emily Rose Kahoud
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Takehiro Yokota
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Brooke M Emerling
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - John M Asara
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tetsuo Ishida
- Department of Chemistry, Biology & Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute and Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Takiko Daikoku
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki 305-0801, Japan.
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Cancer Biology and Department of Neurosurgery, University of Cincinnati College of Medicine, Brain Tumor Center at University of Cincinnati Neuroscience Institute, Cincinnati, OH 45267, USA.
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39
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Poli A, Billi AM, Mongiorgi S, Ratti S, McCubrey JA, Suh PG, Cocco L, Ramazzotti G. Nuclear Phosphatidylinositol Signaling: Focus on Phosphatidylinositol Phosphate Kinases and Phospholipases C. J Cell Physiol 2015; 231:1645-55. [DOI: 10.1002/jcp.25273] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Alessandro Poli
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Anna Maria Billi
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Sara Mongiorgi
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Stefano Ratti
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - James A. McCubrey
- Department of Microbiology and Immunology; Brody School of Medicine; East Carolina University; Greenville North Carolina
| | - Pann-Ghill Suh
- School of Life Sciences; Ulsan National Institute of Science and Technology; Ulsan Republic of Korea
| | - Lucio Cocco
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
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40
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Giudici ML, Clarke JH, Irvine RF. Phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ), a lipid signalling enigma. Adv Biol Regul 2015; 61:47-50. [PMID: 26710750 DOI: 10.1016/j.jbior.2015.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 11/26/2022]
Abstract
The phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are an important family of enzymes, whose physiological roles are being teased out by a variety of means. Phosphatidylinositol-5-phosphate 4-kinase γ (PI5P4Kγ) is especially intriguing as its in vitro activity is very low. Here we review what is known about this enzyme and discuss some recent advances towards an understanding of its physiology. Additionally, the effects of the ATP-competitive inhibitor I-OMe Tyrphostin AG-538 on all three mammalian PI5P4Ks was explored, including two PI5P4Kγ mutants with altered ATP- or PI5P-binding sites. The results suggest a strategy for targeting non-ATP binding sites on inositol lipid kinases.
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Affiliation(s)
| | - Jonathan H Clarke
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Robin F Irvine
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK.
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41
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The function of phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ) explored using a specific inhibitor that targets the PI5P-binding site. Biochem J 2015; 466:359-67. [PMID: 25495341 PMCID: PMC4687057 DOI: 10.1042/bj20141333] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NIH-12848 (NCGC00012848-02), a putative phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ) inhibitor, was explored as a tool for investigating this enigmatic, low activity, lipid kinase. PI5P4K assays in vitro showed that NIH-12848 inhibited PI5P4Kγ with an IC50 of approximately 1 μM but did not inhibit the α and β PI5P4K isoforms at concentrations up to 100 μM. A lack of inhibition of PI5P4Kγ ATPase activity suggested that NIH-12848 does not interact with the enzyme's ATP-binding site and direct exploration of binding using hydrogen–deuterium exchange (HDX)-MS (HDX-MS) revealed the putative PI5P-binding site of PI5P4Kγ to be the likely region of interaction. This was confirmed by a series of mutation experiments which led to the identification of a single PI5P4Kγ amino acid residue that can be mutated to its PI5P4Ks α and β homologue to render PI5P4Kγ resistant NIH-12848 inhibition. NIH-12848 (10 μM) was applied to cultured mouse principal kidney cortical collecting duct (mpkCCD) cells which, we show, express PI5P4Kγ that increases when the cells grow to confluence and polarize. NIH-12848 inhibited the translocation of Na+/K+-ATPase to the plasma membrane that occurs when mpkCCD cells grow to confluence and also prevented reversibly their forming of ‘domes’ on the culture dish. Both these NIH-12848-induced effects were mimicked by specific RNAi knockdown of PI5P4Kγ, but not that of PI5P4Ks α or β. Overall, the data reveal a probable contribution of PI5P4Kγ to the development and maintenance of epithelial cell functional polarity and show that NIH-12848 is a potentially powerful tool for exploring the cell physiology of PI5P4Ks. We have characterised a specific inhibitor of the enzyme Phosphatidylinositol 5-phosphate 4-kinase γ, including establishing where on the enzyme the inhibitor binds, and then applied this inhibitor to a kidney cell line to elucidate the intracellular functions of the enzyme.
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42
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Fiume R, Stijf-Bultsma Y, Shah ZH, Keune WJ, Jones DR, Jude JG, Divecha N. PIP4K and the role of nuclear phosphoinositides in tumour suppression. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:898-910. [PMID: 25728392 DOI: 10.1016/j.bbalip.2015.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/03/2015] [Accepted: 02/17/2015] [Indexed: 12/27/2022]
Abstract
Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated lipid kinases that phosphorylate PtdIns5P to generate PtdIns(4,5)P₂. There are three isoforms of PIP4Ks: PIP4K2A, 2B and 2C, which localise to different subcellular compartments with the PIP4K2B isoform being localised predominantly in the nucleus. Suppression of PIP4K expression selectively prevents tumour cell growth in vitro and prevents tumour development in mice that have lost the tumour suppressor p53. p53 is lost or mutated in over 70% of all human tumours. These studies suggest that inhibition of PIP4K signalling constitutes a novel anti-cancer therapeutic target. In this review we will discuss the role of PIP4K in tumour suppression and speculate on how PIP4K modulates nuclear phosphoinositides (PPIns) and how this might impact on nuclear functions to regulate cell growth. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Roberta Fiume
- Cellular Signalling Laboratory, DIBINEM, University of Bologna, Bologna, Italy.
| | - Yvette Stijf-Bultsma
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Zahid H Shah
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Willem Jan Keune
- The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - David R Jones
- Oncology iMED, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, UK
| | - Julian Georg Jude
- IMP - Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Nullin Divecha
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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43
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Lacalle RA, de Karam JC, Martínez-Muñoz L, Artetxe I, Peregil RM, Sot J, Rojas AM, Goñi FM, Mellado M, Mañes S. Type I phosphatidylinositol 4-phosphate 5-kinase homo- and heterodimerization determines its membrane localization and activity. FASEB J 2015; 29:2371-85. [PMID: 25713054 DOI: 10.1096/fj.14-264606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/03/2015] [Indexed: 11/11/2022]
Abstract
Type I phosphatidylinositol 4-phosphate 5-kinases (PIP5KIs; α, β, and γ) are a family of isoenzymes that produce phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] using phosphatidylinositol 4-phosphate as substrate. Their structural homology with the class II lipid kinases [type II phosphatidylinositol 5-phosphate 4-kinase (PIP4KII)] suggests that PIP5KI dimerizes, although this has not been formally demonstrated. Neither the hypothetical structural dimerization determinants nor the functional consequences of dimerization have been studied. Here, we used Förster resonance energy transfer, coprecipitation, and ELISA to show that PIP5KIβ forms homo- and heterodimers with PIP5KIγ_i2 in vitro and in live human cells. Dimerization appears to be a general phenomenon for PIP5KI isoenzymes because PIP5KIβ/PIP5KIα heterodimers were also detected by mass spectrometry. Dimerization was independent of actin cytoskeleton remodeling and was also observed using purified proteins. Mutagenesis studies of PIP5KIβ located the dimerization motif at the N terminus, in a region homologous to that implicated in PIP4KII dimerization. PIP5KIβ mutants whose dimerization was impaired showed a severe decrease in PI(4,5)P2 production and plasma membrane delocalization, although their association to lipid monolayers was unaltered. Our results identify dimerization as an integral feature of PIP5K proteins and a central determinant of their enzyme activity.
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Affiliation(s)
- Rosa Ana Lacalle
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Juan C de Karam
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Laura Martínez-Muñoz
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Ibai Artetxe
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Rosa M Peregil
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Jesús Sot
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Ana M Rojas
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Félix M Goñi
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Mario Mellado
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Santos Mañes
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
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Mackey AM, Sarkes DA, Bettencourt I, Asara JM, Rameh LE. PIP4kγ is a substrate for mTORC1 that maintains basal mTORC1 signaling during starvation. Sci Signal 2014; 7:ra104. [PMID: 25372051 DOI: 10.1126/scisignal.2005191] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphatidylinositol-5-phosphate 4-kinases (PIP4ks) are a family of lipid kinases that specifically use phosphatidylinositol 5-monophosphate (PI-5-P) as a substrate to synthesize phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Suppression of PIP4k function in Drosophila results in smaller cells and reduced target of rapamycin complex 1 (TORC1) signaling. We showed that the γ isoform of PIP4k stimulated signaling through mammalian TORC1 (mTORC1). Knockdown of PIP4kγ reduced cell mass in cells in which mTORC1 is constitutively activated by Tsc2 deficiency. In Tsc2 null cells, mTORC1 activation was partially independent of amino acids or glucose and glutamine. PIP4kγ knockdown inhibited the nutrient-independent activation of mTORC1 in Tsc2 knockdown cells and reduced basal mTORC1 signaling in wild-type cells. PIP4kγ was phosphorylated by mTORC1 and associated with the complex. Phosphorylated PIP4kγ was enriched in light microsomal vesicles, whereas the unphosphorylated form was enriched in heavy microsomal vesicles associated with the Golgi. Furthermore, basal mTORC1 signaling was enhanced by overexpression of unphosphorylated wild-type PIP4kγ or a phosphorylation-defective mutant and decreased by overexpression of a phosphorylation-mimetic mutant. Together, these results demonstrate that PIP4kγ and mTORC1 interact in a self-regulated feedback loop to maintain low and tightly regulated mTORC1 activation during starvation.
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Affiliation(s)
- Ashley M Mackey
- Boston Biomedical Research Institute, Watertown, MA 02472, USA. Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Ian Bettencourt
- Boston Biomedical Research Institute, Watertown, MA 02472, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Lucia E Rameh
- Boston Biomedical Research Institute, Watertown, MA 02472, USA. Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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Bulley SJ, Clarke JH, Droubi A, Giudici ML, Irvine RF. Exploring phosphatidylinositol 5-phosphate 4-kinase function. Adv Biol Regul 2014; 57:193-202. [PMID: 25311266 PMCID: PMC4359101 DOI: 10.1016/j.jbior.2014.09.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
The family of phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) is emerging from a comparative backwater in inositide signalling into the mainstream, as is their substrate, phosphatidylinositol 5-phosphate (PI5P). Here we review some of the key questions about the PI5P4Ks, their localisation, interaction, and regulation and also we summarise our current understanding of how PI5P is synthesised and what its cellular functions might be. Finally, some of the evidence for the involvement of PI5P4Ks in pathology is discussed.
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Affiliation(s)
- Simon J Bulley
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Jonathan H Clarke
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Alaa Droubi
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Robin F Irvine
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK.
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Ueda Y. The Role of Phosphoinositides in Synapse Function. Mol Neurobiol 2014; 50:821-38. [DOI: 10.1007/s12035-014-8768-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 06/01/2014] [Indexed: 11/30/2022]
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Peter E, Dick B, Stambolic I, Baeurle SA. Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique. Proteins 2014; 82:2018-40. [PMID: 24623633 DOI: 10.1002/prot.24556] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/19/2014] [Accepted: 03/10/2014] [Indexed: 12/21/2022]
Abstract
Devising analysis tools for elucidating the regulatory mechanism of complex enzymes has been a challenging task for many decades. It generally requires the determination of the structural-dynamical information of protein solvent systems far from equilibrium over multiple length and time scales, which is still difficult both theoretically and experimentally. To cope with the problem, we introduce a full-residue space multiscale simulation method based on a combination of the kinetic Monte Carlo and molecular dynamics techniques, in which the rates of the rate-determining processes are evaluated from a biomolecular forcefield on the fly during the simulation run by taking into account the full space of residues. To demonstrate its reliability and efficiency, we explore the light-induced functional behavior of the full-length phototropin1 from Chlamydomonas reinhardtii (Cr-phot1) and its various subdomains. Our results demonstrate that in the dark state the light oxygen voltage-2-Jα (LOV2-Jα) photoswitch inhibits the enzymatic activity of the kinase, whereas the LOV1-Jα photoswitch controls the dimerization with the LOV2 domain. This leads to the repulsion of the LOV1-LOV2 linker out of the interface region between both LOV domains, which results in a positively charged surface suitable for cell-membrane interaction. By contrast, in the light state, we observe that the distance between both LOV domains is increased and the LOV1-LOV2 linker forms a helix-turn-helix (HTH) motif, which enables gene control through nucleotide binding. Finally, we find that the kinase is activated through the disruption of the Jα-helix from the LOV2 domain, which is followed by a stretching of the activation loop (A-loop) and broadening of the catalytic cleft of the kinase.
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Affiliation(s)
- Emanuel Peter
- Department of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93040, Regensburg, Germany
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Viaud J, Boal F, Tronchère H, Gaits-Iacovoni F, Payrastre B. Phosphatidylinositol 5-phosphate: A nuclear stress lipid and a tuner of membranes and cytoskeleton dynamics. Bioessays 2013; 36:260-72. [DOI: 10.1002/bies.201300132] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julien Viaud
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
| | - Frédéric Boal
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
| | - Hélène Tronchère
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
| | | | - Bernard Payrastre
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
- CHU de Toulouse; Laboratoire d'Hématologie; Toulouse France
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