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Lim PC, Yap BK, Tay YJ, Hanapi NA, Yusof SR, Lee CY. Discovery of aurones bearing two amine functionalities as SHIP2 inhibitors with insulin-sensitizing effect in rat myotubes. RSC Med Chem 2024; 15:2179-2195. [PMID: 38911152 PMCID: PMC11187551 DOI: 10.1039/d3md00360d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/25/2023] [Indexed: 06/25/2024] Open
Abstract
Pharmacological inhibition of the SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) by small-molecule compounds presents an attractive approach to modulate insulin sensitivity. Few drug-like SHIP2 inhibitors have been discovered to date. A series of aurones incorporating key motifs from known SHIP2 inhibitors were synthesized and evaluated for SHIP2-inhibiting activity against a recombinant SHIP2 protein in vitro. Three aurones that inhibited SHIP2 at 15-50 μM were identified. These aurone inhibitors required two amine functionalities, one at ring A and a second at ring B for good inhibitory activity as exemplified by 12a. Mechanistically, molecular dynamics simulations revealed 12a to preferably bind to an allosteric site, restricting the motion of the flexible L4 loop required for SHIP2 phosphatase activity. Additionally, a basic piperidine moiety of 12a interacted with an aspartate residue proximal to the site. At 20-40 μM, 12a significantly enhanced glucose uptake in rat myotubes via increased Akt phosphorylation. 12a showed good permeability across the Caco-2 cell monolayer supporting the aurone chemotype as a new lead to develop drug-like, oral insulin sensitizers.
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Affiliation(s)
- Phei Ching Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia Minden 11800 Penang Malaysia +604 653 4086
| | - Beow Keat Yap
- School of Pharmaceutical Sciences, Universiti Sains Malaysia Minden 11800 Penang Malaysia +604 653 4086
| | - Yi Juin Tay
- School of Pharmaceutical Sciences, Universiti Sains Malaysia Minden 11800 Penang Malaysia +604 653 4086
| | - Nur Aziah Hanapi
- Centre for Drug Research, Universiti Sains Malaysia Minden 11800 Penang Malaysia
| | - Siti Rafidah Yusof
- Centre for Drug Research, Universiti Sains Malaysia Minden 11800 Penang Malaysia
| | - Chong-Yew Lee
- School of Pharmaceutical Sciences, Universiti Sains Malaysia Minden 11800 Penang Malaysia +604 653 4086
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2
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Bradshaw WJ, Kennedy EC, Moreira T, Smith LA, Chalk R, Katis VL, Benesch JLP, Brennan PE, Murphy EJ, Gileadi O. Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2. Structure 2024; 32:453-466.e6. [PMID: 38309262 PMCID: PMC10997489 DOI: 10.1016/j.str.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
SHIP1, an inositol 5-phosphatase, plays a central role in cellular signaling. As such, it has been implicated in many conditions. Exploiting SHIP1 as a drug target will require structural knowledge and the design of selective small molecules. We have determined apo, and magnesium and phosphate-bound structures of the phosphatase and C2 domains of SHIP1. The C2 domains of SHIP1 and the related SHIP2 modulate the activity of the phosphatase domain. To understand the mechanism, we performed activity assays, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics on SHIP1 and SHIP2. Our findings demonstrate that the influence of the C2 domain is more pronounced for SHIP2 than SHIP1. We determined 91 structures of SHIP1 with fragments bound, with some near the interface between the two domains. We performed a mass spectrometry screen and determined four structures with covalent fragments. These structures could act as starting points for the development of potent, selective probes.
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Affiliation(s)
- William J Bradshaw
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
| | - Emma C Kennedy
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Tiago Moreira
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Luke A Smith
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Rod Chalk
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Vittorio L Katis
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Justin L P Benesch
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Paul E Brennan
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Emma J Murphy
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Opher Gileadi
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
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Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [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: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
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Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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Terzioglu G, Young-Pearse TL. Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer's disease. Mol Neurodegener 2023; 18:89. [PMID: 38017562 PMCID: PMC10685641 DOI: 10.1186/s13024-023-00674-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023] Open
Abstract
Recent genetic studies on Alzheimer's disease (AD) have brought microglia under the spotlight, as loci associated with AD risk are enriched in genes expressed in microglia. Several of these genes have been recognized for their central roles in microglial functions. Increasing evidence suggests that SHIP1, the protein encoded by the AD-associated gene INPP5D, is an important regulator of microglial phagocytosis and immune response. A recent study from our group identified SHIP1 as a negative regulator of the NLRP3 inflammasome in human iPSC-derived microglial cells (iMGs). In addition, we found evidence for a connection between SHIP1 activity and inflammasome activation in the AD brain. The NLRP3 inflammasome is a multiprotein complex that induces the secretion of pro-inflammatory cytokines as part of innate immune responses against pathogens and endogenous damage signals. Previously published studies have suggested that the NLRP3 inflammasome is activated in AD and contributes to AD-related pathology. Here, we provide an overview of the current understanding of the microglial NLRP3 inflammasome in the context of AD-related inflammation. We then review the known intracellular functions of SHIP1, including its role in phosphoinositide signaling, interactions with microglial phagocytic receptors such as TREM2 and evidence for its intersection with NLRP3 inflammasome signaling. Through rigorous examination of the intricate connections between microglial signaling pathways across several experimental systems and postmortem analyses, the field will be better equipped to tailor newly emerging therapeutic strategies targeting microglia in neurodegenerative diseases.
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Affiliation(s)
- Gizem Terzioglu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA.
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Jesudason CD, Mason ER, Chu S, Oblak AL, Javens‐Wolfe J, Moussaif M, Durst G, Hipskind P, Beck DE, Dong J, Amarasinghe O, Zhang Z, Hamdani AK, Singhal K, Mesecar AD, Souza S, Jacobson M, Salvo JD, Soni DM, Kandasamy M, Masters AR, Quinney SK, Doolen S, Huhe H, Rizzo SJS, Lamb BT, Palkowitz AD, Richardson TI. SHIP1 therapeutic target enablement: Identification and evaluation of inhibitors for the treatment of late-onset Alzheimer's disease. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2023; 9:e12429. [PMID: 38023622 PMCID: PMC10655782 DOI: 10.1002/trc2.12429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 09/17/2023] [Indexed: 12/01/2023]
Abstract
INTRODUCTION The risk of developing Alzheimer's disease is associated with genes involved in microglial function. Inositol polyphosphate-5-phosphatase (INPP5D), which encodes Src homology 2 (SH2) domain-containing inositol polyphosphate 5-phosphatase 1 (SHIP1), is a risk gene expressed in microglia. Because SHIP1 binds receptor immunoreceptor tyrosine-based inhibitory motifs (ITIMs), competes with kinases, and converts PI(3,4,5)P3 to PI(3,4)P2, it is a negative regulator of microglia function. Validated inhibitors are needed to evaluate SHIP1 as a potential therapeutic target. METHODS We identified inhibitors and screened the enzymatic domain of SHIP1. A protein construct containing two domains was used to evaluate enzyme inhibitor potency and selectivity versus SHIP2. Inhibitors were tested against a construct containing all ordered domains of the human and mouse proteins. A cellular thermal shift assay (CETSA) provided evidence of target engagement in cells. Phospho-AKT levels provided further evidence of on-target pharmacology. A high-content imaging assay was used to study the pharmacology of SHIP1 inhibition while monitoring cell health. Physicochemical and absorption, distribution, metabolism, and excretion (ADME) properties were evaluated to select a compound suitable for in vivo studies. RESULTS SHIP1 inhibitors displayed a remarkable array of activities and cellular pharmacology. Inhibitory potency was dependent on the protein construct used to assess enzymatic activity. Some inhibitors failed to engage the target in cells. Inhibitors that were active in the CETSA consistently destabilized the protein and reduced pAKT levels. Many SHIP1 inhibitors were cytotoxic either at high concentration due to cell stress or they potently induced cell death depending on the compound and cell type. One compound activated microglia, inducing phagocytosis at concentrations that did not result in significant cell death. A pharmacokinetic study demonstrated brain exposures in mice upon oral administration. DISCUSSION 3-((2,4-Dichlorobenzyl)oxy)-5-(1-(piperidin-4-yl)-1H-pyrazol-4-yl) pyridine activated primary mouse microglia and demonstrated exposures in mouse brain upon oral dosing. Although this compound is our recommended chemical probe for investigating the pharmacology of SHIP1 inhibition at this time, further optimization is required for clinical studies. Highlights Cellular thermal shift assay (CETSA) and signaling (pAKT) assays were developed to provide evidence of src homology 2 (SH2) domain-contaning inositol phosphatase 1 (SHIP1) target engagement and on-target activity in cellular assays.A phenotypic high-content imaging assay with simultaneous measures of phagocytosis, cell number, and nuclear intensity was developed to explore cellular pharmacology and monitor cell health.SHIP1 inhibitors demonstrate a wide range of activity and cellular pharmacology, and many reported inhibitors are cytotoxic.The chemical probe 3-((2,4-dichlorobenzyl)oxy)-5-(1-(piperidin-4-yl)-1H-pyrazol-4-yl) pyridine is recommended to explore SHIP1 pharmacology.
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Affiliation(s)
| | - Emily R. Mason
- Indiana University School of MedicineIndianapolisIndianaUSA
| | - Shaoyou Chu
- Indiana University School of MedicineIndianapolisIndianaUSA
| | - Adrian L. Oblak
- Indiana University School of MedicineIndianapolisIndianaUSA
- Stark Neurosciences Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
| | | | | | | | | | - Daniel E. Beck
- Institute for Drug DiscoveryPurdue UniversityWest LafayetteIndianaUSA
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityWest LafayetteIndianaUSA
| | - Ovini Amarasinghe
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityWest LafayetteIndianaUSA
| | - Zhong‐Yin Zhang
- Institute for Drug DiscoveryPurdue UniversityWest LafayetteIndianaUSA
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityWest LafayetteIndianaUSA
| | - Adam K. Hamdani
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
| | - Kratika Singhal
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
| | | | | | | | | | - Disha M. Soni
- Indiana University School of MedicineIndianapolisIndianaUSA
| | | | | | - Sara K Quinney
- Indiana University School of MedicineIndianapolisIndianaUSA
| | - Suzanne Doolen
- University of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Hasi Huhe
- University of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | | | - Bruce T. Lamb
- Indiana University School of MedicineIndianapolisIndianaUSA
- Stark Neurosciences Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
| | - Alan D. Palkowitz
- Indiana University School of MedicineIndianapolisIndianaUSA
- Indiana Biosciences Research InstituteIndianapolisIndianaUSA
| | - Timothy I. Richardson
- Indiana University School of MedicineIndianapolisIndianaUSA
- Stark Neurosciences Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
- Indiana Biosciences Research InstituteIndianapolisIndianaUSA
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6
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Serwanja J, Brandstetter H, Schönauer E. Quantitative cross-linking via engineered cysteines to study inter-domain interactions in bacterial collagenases. STAR Protoc 2023; 4:102519. [PMID: 37605531 PMCID: PMC10458335 DOI: 10.1016/j.xpro.2023.102519] [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: 05/25/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/23/2023] Open
Abstract
Inter-domain movements act as important activity modulators in multi-domain proteins. Here, we present a protocol for inter-domain cross-linking via engineered cysteines. Using collagenase G (ColG) from Hathewaya histolytica as a model, we describe steps for the design, expression, purification, and cross-linking of the target protein. We detail a system to monitor the progress of the cross-linking reaction and to confirm the structural integrity of the purified cross-linked proteins. We anticipate this protocol to be readily adaptable to other multi-domain enzymes. For complete details on the use and execution of this protocol, please refer to Serwanja et al.1.
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Affiliation(s)
- Jamil Serwanja
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Esther Schönauer
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria.
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7
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of the autoinhibited SHIP1 inositol 5-phosphatase. J Biol Chem 2023; 299:105022. [PMID: 37423304 PMCID: PMC10448276 DOI: 10.1016/j.jbc.2023.105022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023] Open
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P3) lipids by PI3K. Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P3 to generate phosphatidylinositol-(3,4)-bisphosphate. Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single-molecule total internal reflection fluorescence microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that localization of the central catalytic domain of SHIP1 is insensitive to dynamic changes in PI(3,4,5)P3 and phosphatidylinositol-(3,4)-bisphosphate both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine and PI(3,4,5)P3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal Src homology 2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor-derived phosphopeptides presented either in solution or conjugated to a membrane. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid-binding specificity, protein-protein interactions, and the activation of autoinhibited SHIP1.
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Affiliation(s)
- Grace L Waddell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Emma E Drew
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Henry P Rupp
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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8
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of autoinhibited SHIP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.30.538895. [PMID: 37205499 PMCID: PMC10187190 DOI: 10.1101/2023.04.30.538895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P 3 ) lipids by phosphoinositide-3-kinase (PI3K). Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P 3 to generate PI(3,4)P 2 . Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single molecule TIRF microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that SHIP1's interactions with lipids are insensitive to dynamic changes in PI(3,4,5)P 3 both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine (PS) and PI(3,4,5)P 3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal SH2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor derived phosphopeptides presented either in solution or conjugated to supported membranes. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid binding specificity, protein-protein interactions, and activation of autoinhibited SHIP1.
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9
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Wei W, Geer MJ, Guo X, Dolgalev I, Sanjana NE, Neel BG. Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition. J Exp Med 2023; 220:e20221563. [PMID: 36820830 PMCID: PMC9998968 DOI: 10.1084/jem.20221563] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/14/2022] [Accepted: 01/20/2023] [Indexed: 02/24/2023] Open
Abstract
SHP2 (PTPN11) acts upstream of SOS1/2 to enable RAS activation. Allosteric SHP2 inhibitors (SHP2i) in the clinic prevent SHP2 activation, block proliferation of RTK- or cycling RAS mutant-driven cancers, and overcome "adaptive resistance." To identify SHP2i resistance mechanisms, we performed genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive cell lines, recovering genes expected to cause resistance (NF1, PTEN, CDKN1B, LZTR1, and RASA2) and novel targets (INPPL1, MAP4K5, epigenetic modifiers). We screened 14 additional lines with a focused CRISPR library targeting common "hits" from the genome-wide screens. LZTR1 deletion conferred resistance in 12/14 lines, followed by MAP4K5 (8/14), SPRED2/STK40 (6/14), and INPPL1 (5/14). INPPL1, MAP4K5, or LZTR1 deletion reactivated ERK signaling. INPPL1-mediated sensitization to SHP2i required its NPXY motif but not lipid phosphatase activity. MAP4K5 acted upstream of MEK through a kinase-dependent target(s); LZTR1 had cell-dependent effects on RIT and RAS stability. INPPL1, MAP4K5, or LZTR1 deletion also conferred SHP2i resistance in vivo. Defining the SHP2i resistance landscape could suggest effective combination approaches.
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Affiliation(s)
- Wei Wei
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Mitchell J. Geer
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Xinyi Guo
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Neville E. Sanjana
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
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John LH, Naughton FB, Sansom MSP, Larsen AH. The Role of C2 Domains in Two Different Phosphatases: PTEN and SHIP2. MEMBRANES 2023; 13:408. [PMID: 37103835 PMCID: PMC10146288 DOI: 10.3390/membranes13040408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Phosphatase and tensin homologue (PTEN) and SH2-containing inositol 5'-phosphatase 2 (SHIP2) are structurally and functionally similar. They both consist of a phosphatase (Ptase) domain and an adjacent C2 domain, and both proteins dephosphorylate phosphoinositol-tri(3,4,5)phosphate, PI(3,4,5)P3; PTEN at the 3-phophate and SHIP2 at the 5-phosphate. Therefore, they play pivotal roles in the PI3K/Akt pathway. Here, we investigate the role of the C2 domain in membrane interactions of PTEN and SHIP2, using molecular dynamics simulations and free energy calculations. It is generally accepted that for PTEN, the C2 domain interacts strongly with anionic lipids and therefore significantly contributes to membrane recruitment. In contrast, for the C2 domain in SHIP2, we previously found much weaker binding affinity for anionic membranes. Our simulations confirm the membrane anchor role of the C2 domain in PTEN, as well as its necessity for the Ptase domain in gaining its productive membrane-binding conformation. In contrast, we identified that the C2 domain in SHIP2 undertakes neither of these roles, which are generally proposed for C2 domains. Our data support a model in which the main role of the C2 domain in SHIP2 is to introduce allosteric interdomain changes that enhance catalytic activity of the Ptase domain.
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Affiliation(s)
- Laura H. John
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Fiona B. Naughton
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark
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11
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Structural Insights into the Binding Propensity of Human SHIP2 SH2 to Oncogenic CagA Isoforms from Helicobacter pylori. Int J Mol Sci 2022; 23:ijms231911299. [PMID: 36232599 PMCID: PMC9569640 DOI: 10.3390/ijms231911299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
SHIP2 is a multi-domain inositol 5-phosphatase binding to a variety of phosphotyrosine (pY)-containing proteins through its SH2 domain, so as to regulate various cell signaling pathways by modulating the phosphatidylinositol level in the plasma membrane. Unfavorably, Helicobacter pylori can hijack SHIP2 through the CagA protein to induce gastric cell carcinogenesis. To date, the interaction between SHIP2 and CagA was not analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Tyr-phosphorylated peptides from four EPIYA motifs (A/B/C/D) in CagA was studied using NMR spectroscopy. The results showed that EPIYA-C and -D bind to a similar interface of SHIP2-SH2, including a pY-binding pocket and a hydrophobic pocket, to achieve high affinity, while EPIYA-A and -B bind to a smaller interface of SHIP2-SH2 with weak affinity. By summarizing the interface and affinity of SHIP2-SH2 for CagA EPIYA-A/B/C/D, c-MET and FcgR2B ITIM, it was proposed that, potentially, SHIP2-SH2 has a selective preference for L > I > V for the aliphatic residues at the pY+3 position in its ligand. This study reveals the rule of the ligand sequence bound by SHIP2-SH2 and the mechanism by which CagA protein hijacks SHIP2, which will help design a peptide inhibitor against SHIP2-SH2.
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12
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Pedicone C, Fernandes S, Matera A, Meyer ST, Loh S, Ha JH, Bernard D, Chisholm JD, Paolicelli RC, Kerr WG. Discovery of a novel SHIP1 agonist that promotes degradation of lipid-laden phagocytic cargo by microglia. iScience 2022; 25:104170. [PMID: 35465359 PMCID: PMC9020084 DOI: 10.1016/j.isci.2022.104170] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/31/2021] [Accepted: 03/24/2022] [Indexed: 12/01/2022] Open
Abstract
Here, we describe the use of artificial intelligence to identify novel agonists of the SH2-containing 5′ inositol phosphatase 1 (SHIP1). One of the compounds, K306, represents the most potent agonist identified to date. We find that K306 exhibits selectivity for SHIP1 vs. the paralog enzyme SHIP2, and this activation does not require the C2 domain of SHIP1 which other known SHIP1 agonists require. Thus, K306 represents a new class of SHIP1 agonists with a novel mode of agonism. Importantly, we find that K306 can suppress induction of inflammatory cytokines and iNOS in macrophages or microglia, but not by their SHIP1-deficient counterparts. K306 also reduces TNF-α production in vivo in an LPS-induced endotoxemia assay. Finally, we show that K306 enhances phagolysosomal degradation of synaptosomes and dead neurons by microglia revealing a novel function for SHIP1 that might be exploited therapeutically in dementia. Discovery of a potent SHIP1 selective agonist (K306) via artificial intelligence SHIP1 agonism via K306 is independent of the C2 domain and increases PI(3,4)P2 levels K306 reduces IL-6, TNF-α, and iNOS induction in microglia and macrophages K306 promotes phagocytic degradation of lipid-laden but not protein cargo in microglia
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Affiliation(s)
- Chiara Pedicone
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sandra Fernandes
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Alessandro Matera
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Shea T Meyer
- Chemistry Department, Syracuse University, Syracuse, NY 13210, USA
| | - Stewart Loh
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - John D Chisholm
- Chemistry Department, Syracuse University, Syracuse, NY 13210, USA
| | | | - William G Kerr
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.,Chemistry Department, Syracuse University, Syracuse, NY 13210, USA
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13
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Le Coq J, López Navajas P, Rodrigo Martin B, Alfonso C, Lietha D. A new layer of phosphoinositide-mediated allosteric regulation uncovered for SHIP2. FASEB J 2021; 35:e21815. [PMID: 34314064 DOI: 10.1096/fj.202100561r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/26/2021] [Accepted: 07/08/2021] [Indexed: 11/11/2022]
Abstract
The Src homology 2 containing inositol 5-phosphatase 2 (SHIP2) is a large multidomain enzyme that catalyzes the dephosphorylation of the phospholipid phosphatidylinositol 3,4,5-triphosphate (PI(3,4,5)P3 ) to form PI(3,4)P2 . PI(3,4,5)P3 is a key lipid second messenger controlling the recruitment of signaling proteins to the plasma membrane, thereby regulating a plethora of cellular events, including proliferation, growth, apoptosis, and cytoskeletal rearrangements. SHIP2, alongside PI3K and PTEN, regulates PI(3,4,5)P3 levels at the plasma membrane and has been heavily implicated in serious diseases such as cancer and type 2 diabetes; however, many aspects of its regulation mechanism remain elusive. We recently reported an activating effect of the SHIP2 C2 domain and here we describe an additional layer of regulation via the pleckstrin homology-related (PHR) domain. We show a phosphoinositide-induced transition to a high activity state of the enzyme that increases phosphatase activity up to 10-15 fold. We further show that PI(3,4)P2 directly interacts with the PHR domain to trigger this allosteric activation. Modeling of the PHR-phosphatase-C2 region of SHIP2 on the membrane suggests no major inter-domain interactions with the PHR domain, but close contacts between the two linkers offer a possible path of allosteric communication. Together, our data show that the PHR domain acts as an allosteric module regulating the catalytic activity of SHIP2 in response to specific phosphoinositide levels in the cell membrane.
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Affiliation(s)
- Johanne Le Coq
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pilar López Navajas
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Bárbara Rodrigo Martin
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Carlos Alfonso
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Daniel Lietha
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
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14
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Larsen AH, Sansom MSP. Binding of Ca 2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study. Structure 2021; 29:1200-1213.e2. [PMID: 34081910 PMCID: PMC8507603 DOI: 10.1016/j.str.2021.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 01/17/2023]
Abstract
C2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins. Binding of Ca2+-independent C2 domains to membranes was explored by MD simulation C2 domains from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2 were compared C2 domains formed longer-lived interactions with lipid bilayers containing PIP2 For PTEN and SHIP2, simulations of their phosphatase plus C2 domains were performed
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Affiliation(s)
- Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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15
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Wang Z, Zhou H, Yue X, Zhu J, Yang Y, Liu M. An auxiliary binding interface of SHIP2-SH2 for Y292-phosphorylated FcγRIIB reveals diverse recognition mechanisms for tyrosine-phosphorylated receptors involved in different cell signaling pathways. Anal Bioanal Chem 2021; 414:497-506. [PMID: 34021368 DOI: 10.1007/s00216-021-03373-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 12/27/2022]
Abstract
SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) plays an essential role in regulating phosphatidylinositol level in human cell, and is recruited to many phosphotyrosine (pY)-dependent signal transduction pathways by the SH2 domain. In immunity signaling, immunoreceptor FcγRIIB binds to SHIP2-SH2 via its Y292-phosphorylated immunoreceptor tyrosine-based inhibitory motif (ITIM) and transmits inhibitory signal, which regulates B cell and neuronal cell activity and is associated with immune diseases and Alzheimer's disease. To date, the interaction between SHIP2 and FcγRIIB has not been analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Y292-phosphorylated FcγRIIB-ITIM was analyzed using NMR spectroscopy. The results demonstrated that SHIP2-SH2 mainly utilizes two regions including a pY-binding pocket and a specificity pocket formed by βD, βE, and EF-loop, to bind with FcγRIIB-ITIM in high affinity. In addition to the two regions, the BG-loop of SHIP2-SH2 functions as an auxiliary interface enhancing affinity. By comparing the binding of SHIP2-SH2 with ligands from FcγRIIB and c-MET, a hepatocyte growth factor receptor associated with tumorigenesis, significant differences in interface and affinity were found, suggesting that SHIP2-SH2 applies diverse patterns for binding to different ligand proteins. Moreover, S49, S51, and R70 of SHIP2 were identified to mediate the binding of both FcγRIIB and c-MET, while R28 and Q107 were found to only participate in the binding of c-MET and FcγRIIB respectively. Taken together, this study reveals the diverse mechanisms of SHIP2-SH2 for recognizing different ligands, and provides important clues for selectively manipulating various signaling pathways and specific drug design.
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Affiliation(s)
- Zi Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Zhou
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, Hubei, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiali Yue
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, Hubei, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, Hubei, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, Hubei, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Whitfield H, Hemmings AM, Mills SJ, Baker K, White G, Rushworth S, Riley AM, Potter BVL, Brearley CA. Allosteric Site on SHIP2 Identified Through Fluorescent Ligand Screening and Crystallography: A Potential New Target for Intervention. J Med Chem 2021; 64:3813-3826. [PMID: 33724834 PMCID: PMC7610569 DOI: 10.1021/acs.jmedchem.0c01944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Src homology 2 domain-containing inositol phosphate phosphatase 2 (SHIP2) is one of the 10 human inositol phosphate 5-phosphatases. One of its physiological functions is dephosphorylation of phosphatidylinositol 3,4,5-trisphosphate, PtdIns(3,4,5)P3. It is therefore a therapeutic target for pathophysiologies dependent on PtdIns(3,4,5)P3 and PtdIns(3,4)P2. Therapeutic interventions are limited by the dearth of crystallographic data describing ligand/inhibitor binding. An active site-directed fluorescent probe facilitated screening of compound libraries for SHIP2 ligands. With two additional orthogonal assays, several ligands including galloflavin were identified as low micromolar Ki inhibitors. One ligand, an oxo-linked ethylene-bridged dimer of benzene 1,2,4-trisphosphate, was shown to be an uncompetitive inhibitor that binds to a regulatory site on the catalytic domain. We posit that binding of ligands to this site restrains L4 loop motions that are key to interdomain communications that accompany high catalytic activity with phosphoinositide substrate. This site may, therefore, be a future druggable target for medicinal chemistry.
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Affiliation(s)
- Hayley Whitfield
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Andrew M Hemmings
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Stephen J Mills
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Kendall Baker
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Gaye White
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Stuart Rushworth
- Department of Molecular Haematology; Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Andrew M Riley
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Barry V L Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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17
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Targeting SHIP1 and SHIP2 in Cancer. Cancers (Basel) 2021; 13:cancers13040890. [PMID: 33672717 PMCID: PMC7924360 DOI: 10.3390/cancers13040890] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Phosphoinositol signaling pathways and their dysregulation have been shown to have a fundamental role in health and disease, respectively. The SH2-containing 5′ inositol phosphatases, SHIP1 and SHIP2, are regulators of the PI3K/AKT pathway that have crucial roles in cancer progression. This review aims to summarize the role of SHIP1 and SHIP2 in cancer signaling and the immune response to cancer, the discovery and use of SHIP inhibitors and agonists as possible cancer therapeutics. Abstract Membrane-anchored and soluble inositol phospholipid species are critical mediators of intracellular cell signaling cascades. Alterations in their normal production or degradation are implicated in the pathology of a number of disorders including cancer and pro-inflammatory conditions. The SH2-containing 5′ inositol phosphatases, SHIP1 and SHIP2, play a fundamental role in these processes by depleting PI(3,4,5)P3, but also by producing PI(3,4)P2 at the inner leaflet of the plasma membrane. With the intent of targeting SHIP1 or SHIP2 selectively, or both paralogs simultaneously, small molecule inhibitors and agonists have been developed and tested in vitro and in vivo over the last decade in various disease models. These studies have shown promising results in various pre-clinical models of disease including cancer and tumor immunotherapy. In this review the potential use of SHIP inhibitors in cancer is discussed with particular attention to the molecular structure, binding site and efficacy of these SHIP inhibitors.
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18
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Ramadesikan S, Skiba L, Lee J, Madhivanan K, Sarkar D, De La Fuente A, Hanna CB, Terashi G, Hazbun T, Kihara D, Aguilar RC. Genotype & phenotype in Lowe Syndrome: specific OCRL1 patient mutations differentially impact cellular phenotypes. Hum Mol Genet 2021; 30:198-212. [PMID: 33517444 DOI: 10.1093/hmg/ddab025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Lowe Syndrome (LS) is a lethal genetic disorder caused by mutations in the OCRL1 gene which encodes the lipid 5' phosphatase Ocrl1. Patients exhibit a characteristic triad of symptoms including eye, brain and kidney abnormalities with renal failure as the most common cause of premature death. Over 200 OCRL1 mutations have been identified in LS, but their specific impact on cellular processes is unknown. Despite observations of heterogeneity in patient symptom severity, there is little understanding of the correlation between genotype and its impact on phenotype. Here, we show that different mutations had diverse effects on protein localization and on triggering LS cellular phenotypes. In addition, some mutations affecting specific domains imparted unique characteristics to the resulting mutated protein. We also propose that certain mutations conformationally affect the 5'-phosphatase domain of the protein, resulting in loss of enzymatic activity and causing common and specific phenotypes (a conformational disease scenario). This study is the first to show the differential effect of patient 5'-phosphatase mutations on cellular phenotypes and introduces a conformational disease component in LS. This work provides a framework that explains symptom heterogeneity and can help stratify patients as well as to produce a more accurate prognosis depending on the nature and location of the mutation within the OCRL1 gene.
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Affiliation(s)
- Swetha Ramadesikan
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Lisette Skiba
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Claudia B Hanna
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Tony Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.,Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - R Claudio Aguilar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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19
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Zhou H, Yue X, Wang Z, Li S, Zhu J, Yang Y, Liu M. Expression, purification and characterization of the RhoA-binding domain of human SHIP2 in E.coli. Protein Expr Purif 2021; 180:105821. [PMID: 33421554 DOI: 10.1016/j.pep.2021.105821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/02/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
Human SH2-containing inositol 5-phosphatase 2 (SHIP2) is a multi-domain protein playing essential roles in various physiological and pathological processes. In cell polarization and migration, SHIP2 serves as a RhoA effector for manipulating the level of phosphatidylinositol 3,4,5-trisphosphate. The domain between SH2 and a potential PH-R domain of SHIP2 was suggested to bind with GTP-bound form of RhoA. However, the structure of this RhoA-binding domain (RBD) of SHIP2 and the mechanism for its binding with RhoA remain unknown. In this study, SHIP2118-298 and SHIP2176-298, two truncated proteins harboring the RBD were designed, expressed, and purified successfully in E. coli. Unexpectedly, both SHIP2118-298 and SHIP2176-298 were determined to exist as homo-dimers in solution by multi-angle light scattering. Circular dichroism spectra indicated that both proteins predominantly consisted of α-helix structure. Moreover, in pull-down experiments, both proteins could bind with GTP-bound RhoA and RhoAQ63L, a mutant mimicing the state of GTP-bound RhoA. Importantly, in silico analysis showed that the shorter truncation, SHIP2176-298, contained all ordered residues between the SH2 and the PH-R domain, and matched the RhoA effector motif 1 of PKN1 well in sequence alignment, suggesting that SHIP2176-298 is sufficient for further studies on the structure and RhoA binding of SHIP2. This work shortens and confirms the main region of SHIP2 interacting with RhoA, provides the method for sample preparation, and presents preliminary information for SHIP2-RBD structure, which will facilitate the comprehensive understanding of the structure and function of SHIP2.
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Affiliation(s)
- Heng Zhou
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Xiali Yue
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zi Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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20
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Paesmans J, Martin E, Deckers B, Berghmans M, Sethi R, Loeys Y, Pardon E, Steyaert J, Verstreken P, Galicia C, Versées W. A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations. eLife 2020; 9:64922. [PMID: 33349335 PMCID: PMC7781601 DOI: 10.7554/elife.64922] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Synaptojanin1 (Synj1) is a phosphoinositide phosphatase, important in clathrin uncoating during endocytosis of presynaptic vesicles. It was identified as a potential drug target for Alzheimer's disease, Down syndrome, and TBC1D24-associated epilepsy, while also loss-of-function mutations in Synj1 are associated with epilepsy and Parkinson's disease. Despite its involvement in a range of disorders, structural, and detailed mechanistic information regarding the enzyme is lacking. Here, we report the crystal structure of the 5-phosphatase domain of Synj1. Moreover, we also present a structure of this domain bound to the substrate diC8-PI(3,4,5)P3, providing the first image of a 5-phosphatase with a trapped substrate in its active site. Together with an analysis of the contribution of the different inositide phosphate groups to catalysis, these structures provide new insights in the Synj1 mechanism. Finally, we analysed the effect of three clinical missense mutations (Y793C, R800C, Y849C) on catalysis, unveiling the molecular mechanisms underlying Synj1-associated disease.
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Affiliation(s)
- Jone Paesmans
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ella Martin
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Babette Deckers
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marjolijn Berghmans
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ritika Sethi
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yannick Loeys
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Els Pardon
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Christian Galicia
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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21
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Nelson N, Wundenberg T, Lin H, Rehbach C, Horn S, Windhorst S, Jücker M. Characterization of the substrate specificity of the inositol 5-phosphatase SHIP1. Biochem Biophys Res Commun 2020; 524:366-370. [PMID: 32005521 DOI: 10.1016/j.bbrc.2020.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 01/02/2020] [Indexed: 10/25/2022]
Abstract
SHIP1 is an inositol 5-phosphatase which is well established for its tumour suppressor potential in leukaemia. Enzymatically, two SHIP1 substrates, PtdIns(3,4,5)P3 and Ins(1,3,4,5)P4 have been identified to date. Additional substrates were found for the homologue SHIP2. In this study, we identified new inositol phosphate (InsP) substrates of SHIP1 by metal dye detection high-performance liquid chromatography and compared the substrate profiles of SHIP1 and SHIP2. We were able to verify Ins(1,3,4,5)P4 as a substrate of SHIP1 and interestingly found Ins(1,2,3,4,5)P5 and Ins(2,3,4,5)P4 to be preferably used as substrates and Ins(1,4,5,6)P4 and Ins(2,4,5,6)P4 to be weak substrates. All of those except Ins(2,3,4,5)P4 are also known substrates of SHIP2 indicating a possible exclusive role of Ins(2,3,4,5)P4 hydrolysis for SHIP1 but not SHIP2 function.
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Affiliation(s)
- Nina Nelson
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Torsten Wundenberg
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | | | - Christoph Rehbach
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Stefan Horn
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany; Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Sabine Windhorst
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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22
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White G, Prior C, Mills SJ, Baker K, Whitfield H, Riley AM, Oganesyan VS, Potter BVL, Brearley CA. Regioisomeric Family of Novel Fluorescent Substrates for SHIP2. ACS Med Chem Lett 2020; 11:309-315. [PMID: 32184962 PMCID: PMC7073872 DOI: 10.1021/acsmedchemlett.9b00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022] Open
Abstract
SHIP2 (SH2-domain containing inositol 5-phosphatase type 2) is a canonical 5-phosphatase, which, through its catalytic action on PtdInsP3, regulates the PI3K/Akt pathway and metabolic action of insulin. It is a drug target, but there is limited evidence of inhibition of SHIP2 by small molecules in the literature. With the goal to investigate inhibition, we report a homologous family of synthetic, chromophoric benzene phosphate substrates of SHIP2 that display the headgroup regiochemical hallmarks of the physiological inositide substrates that have proved difficult to crystallize with 5-phosphatases. Using time-dependent density functional theory (TD-DFT), we explore the intrinsic fluorescence of these novel substrates and show how fluorescence can be used to assay enzyme activity. The TD-DFT approach promises to inform rational design of enhanced active site probes for the broadest family of inositide-binding/metabolizing proteins, while maintaining the regiochemical properties of bona fide inositide substrates.
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Affiliation(s)
- Gaye White
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Christopher Prior
- School of Chemistry, UEA, Norwich Research Park, Norwich NR47TJ, U.K
| | - Stephen J. Mills
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Kendall Baker
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Hayley Whitfield
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Andrew M. Riley
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | | | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Charles A. Brearley
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
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23
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Small molecule targeting of SHIP1 and SHIP2. Biochem Soc Trans 2020; 48:291-300. [DOI: 10.1042/bst20190775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Modulating the activity of the Src Homology 2 (SH2) — containing Inositol 5′-Phosphatase (SHIP) enzyme family with small molecule inhibitors provides a useful and unconventional method of influencing cell signaling in the PI3K pathway. The development of small molecules that selectively target one of the SHIP paralogs (SHIP1 or SHIP2) as well as inhibitors that simultaneously target both enzymes have provided promising data linking the phosphatase activity of the SHIP enzymes to disorders and disease states that are in dire need of new therapeutic targets. These include cancer, immunotherapy, diabetes, obesity, and Alzheimer's disease. In this mini-review, we will provide a brief overview of research in these areas that support targeting SHIP1, SHIP2 or both enzymes for therapeutic purposes.
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24
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Aβ modulates actin cytoskeleton via SHIP2-mediated phosphoinositide metabolism. Sci Rep 2019; 9:15557. [PMID: 31664099 PMCID: PMC6820556 DOI: 10.1038/s41598-019-51914-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
Emerging evidences suggest that phospholipid metabolism is altered in Alzheimer’s disease (AD), but molecular mechanisms on how this affects neurodegeneration in AD is poorly understood. SHIP2 is a phosphoinositide-metabolizing enzyme, which dephosphorylates PI(3,4,5)P3 resulting to PI(3,4)P2, and it has been recently shown that Aβ directly increases the activity of SHIP2. Here we monitored, utilizing fluorescent SHIP2 biosensor, real-time increase of PI(3,4)P2-containing vesicles in HT22 cells treated with Aβ. Interestingly, PI(3,4)P2 is accumulated at late endosomes and lysosomal vesicles. We further discovered that ARAP3 can be attracted to PI(3,4)P2-positive mature endosomes via its PH domain and this facilitates the degradation of ARAP3. The reduced level of ARAP3 then causes RhoA hyperactivation and filamentous actin, which are critical for neurodegeneration in AD. These results provide a novel molecular link between Aβ and actin disruption through dysregulated phosphoinositide metabolism, and the SHIP2-PI(3,4)P2-ARAP3-RhoA signaling pathway can be considered as new therapeutic targets for synaptic dysfunctions in Alzheimer’s disease.
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25
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Goulden BD, Pacheco J, Dull A, Zewe JP, Deiters A, Hammond GRV. A high-avidity biosensor reveals plasma membrane PI(3,4)P 2 is predominantly a class I PI3K signaling product. J Cell Biol 2018; 218:1066-1079. [PMID: 30591513 PMCID: PMC6400549 DOI: 10.1083/jcb.201809026] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/20/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022] Open
Abstract
Class I phosphoinositide 3-OH kinase (PI3K) signaling is central to animal growth and metabolism, and pathological disruption of this pathway affects cancer and diabetes. However, the specific spatial/temporal dynamics and signaling roles of its minor lipid messenger, phosphatidylinositol (3,4)-bisphosphate (PI(3,4)P2), are not well understood. This owes principally to a lack of tools to study this scarce lipid. Here we developed a high-sensitivity genetically encoded biosensor for PI(3,4)P2, demonstrating high selectivity and specificity of the sensor for the lipid. We show that despite clear evidence for class II PI3K in PI(3,4)P2-driven function, the overwhelming majority of the lipid accumulates through degradation of class I PI3K-produced PIP3 However, we show that PI(3,4)P2 is also subject to hydrolysis by the tumor suppressor lipid phosphatase PTEN. Collectively, our results show that PI(3,4)P2 is potentially an important driver of class I PI3K-driven signaling and provides powerful new tools to begin to resolve the biological functions of this lipid downstream of class I and II PI3K.
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Affiliation(s)
- Brady D Goulden
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Allyson Dull
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - James P Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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26
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Ramos AR, Ghosh S, Erneux C. The impact of phosphoinositide 5-phosphatases on phosphoinositides in cell function and human disease. J Lipid Res 2018; 60:276-286. [PMID: 30194087 DOI: 10.1194/jlr.r087908] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/01/2018] [Indexed: 02/06/2023] Open
Abstract
Phosphoinositides (PIs) are recognized as major signaling molecules in many different functions of eukaryotic cells. PIs can be dephosphorylated by multiple phosphatase activities at the 5-, 4-, and 3- positions. Human PI 5-phosphatases belong to a family of 10 members. Except for inositol polyphosphate 5-phosphatase A, they all catalyze the dephosphorylation of PI(4,5)P2 and/or PI(3,4,5)P3 at the 5- position. PI 5-phosphatases thus directly control the levels of PI(3,4,5)P3 and participate in the fine-tuning regulatory mechanisms of PI(3,4)P2 and PI(4,5)P2 Second messenger functions have been demonstrated for PI(3,4)P2 in invadopodium maturation and lamellipodia formation. PI 5-phosphatases can use several substrates on isolated enzymes, and it has been challenging to establish their real substrate in vivo. PI(4,5)P2 has multiple functions in signaling, including interacting with scaffold proteins, ion channels, and cytoskeleton proteins. PI 5-phosphatase isoenzymes have been individually implicated in human diseases, such as the oculocerebrorenal syndrome of Lowe, through mechanisms that include lipid control. Oncogenic and tumor-suppressive functions of PI 5-phosphatases have also been reported in different cell contexts. The mechanisms responsible for genetic diseases and for oncogenic or tumor-suppressive functions are not fully understood. The regulation of PI 5-phosphatases is thus crucial in understanding cell functions.
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Affiliation(s)
- Ana Raquel Ramos
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Somadri Ghosh
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Christophe Erneux
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium
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27
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Wang Z, Nie Y, Zhang K, Xu H, Ramelot TA, Kennedy MA, Liu M, Zhu J, Yang Y. Solution structure of SHIP2 SH2 domain and its interaction with a phosphotyrosine peptide from c-MET. Arch Biochem Biophys 2018; 656:31-37. [PMID: 30165040 DOI: 10.1016/j.abb.2018.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/10/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022]
Abstract
SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) binds with the Y1356-phosphorylated hepatocyte growth factor (HGF) receptor, c-MET, through its SH2 domain, which is essential for the role of SHIP2 in HGF-induced cell scattering and cell spreading. Previously, the experimental structure of the SH2 domain from SHIP2 (SHIP2-SH2) had not been reported, and its interaction with the Y1356-phosphorylated c-MET had not been investigated from a structural point of view. In this study, the solution structure of SHIP2-SH2 was determined by NMR spectroscopy, where it was found to adopt a typical SH2-domain fold that contains a positively-charged pocket for binding to phosphotyrosine (pY). The interaction between SHIP2-SH2 and a pY-containing peptide from c-MET (Y1356 phosphorylated) was investigated through NMR titrations. The results showed that the binding affinity of SHIP2-SH2 with the phosphopeptide is at low micromolar level, and the binding interface consists of the positively-charged pocket and its surrounding regions. Furthermore, R28, S49 and R70 were identified as key residues for the binding and may directly interact with the pY. Taken together, these findings provide structural insights into the binding of SHIP2-SH2 with the Y1356-phosphorylated c-MET, and lay a foundation for further studies of the interactions between SHIP2-SH2 and its various binding partners.
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Affiliation(s)
- Zi Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunxiao Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Henghao Xu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
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28
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Ramos AR, Elong Edimo W, Erneux C. Phosphoinositide 5-phosphatase activities control cell motility in glioblastoma: Two phosphoinositides PI(4,5)P2 and PI(3,4)P2 are involved. Adv Biol Regul 2018; 67:40-48. [PMID: 28916189 DOI: 10.1016/j.jbior.2017.09.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/01/2017] [Accepted: 09/01/2017] [Indexed: 05/15/2023]
Abstract
Inositol polyphosphate 5-phosphatases or phosphoinositide 5-phosphatases (PI 5-phosphatases) are enzymes that can act on soluble inositol phosphates and/or phosphoinositides (PIs). Several PI 5-phosphatases have been linked to human genetic diseases, in particular the Lowe protein or OCRL which is mutated in the Lowe syndrome. There are 10 different members of this family and 9 of them can use PIs as substrate. One of these substrates, PI(3,4,5)P3 binds to specific PH domains and recruits as effectors specific proteins to signaling complexes. Protein kinase B is one target protein and activation of the kinase will have a major impact on cell proliferation, survival and cell metabolism. Two other PIs, PI(4,5)P2 and PI(3,4)P2, are produced or used as substrates of PI 5-phosphatases (OCRL, INPP5B, SHIP1/2, SYNJ1/2, INPP5K, INPP5J, INPP5E). The inositol lipids may influence many aspects of cytoskeletal organization, lamellipodia formation and F-actin polymerization. PI 5-phosphatases have been reported to control cell migration, adhesion, polarity and cell invasion particularly in cancer cells. In glioblastoma, reducing SHIP2 expression can positively or negatively affect the speed of cell migration depending on the glioblastoma cell type. The two PI 5-phosphatases SHIP2 or SKIP could be localized at the plasma membrane and can reduce either PI(3,4,5)P3 or PI(4,5)P2 abundance. In the glioblastoma 1321 N1 cells, SHIP2 controls plasma membrane PI(4,5)P2 thereby participating in the control of cell migration.
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Affiliation(s)
- Ana Raquel Ramos
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, Campus Erasme, Bldg C, 808 Route de Lennik, 1070 Brussels, Belgium
| | - William's Elong Edimo
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, Campus Erasme, Bldg C, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Christophe Erneux
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, Campus Erasme, Bldg C, 808 Route de Lennik, 1070 Brussels, Belgium.
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