1
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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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2
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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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3
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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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4
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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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5
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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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6
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Identification of crizotinib derivatives as potent SHIP2 inhibitors for the treatment of Alzheimer's disease. Eur J Med Chem 2018; 157:405-422. [PMID: 30103190 DOI: 10.1016/j.ejmech.2018.07.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/25/2018] [Accepted: 07/29/2018] [Indexed: 11/24/2022]
Abstract
SH2 domain-containing inositol 5'-phosphatase 2 (SHIP2) is a lipid phosphatase that produce phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) from phosphatidylinositol 3,4,5-triphosphate (PI(3,4,5)P3), and is involved in many diseases such as neurodegenerative diseases. A recent report demonstrating that SHIP2 inhibition decreased tau hyperphosphorylation induced by amyloid β and rescued memory impairment in a transgenic Alzheimer's disease mouse model indicates SHIP2 can be a promising therapeutic target for Alzheimer's disease. In the present study, we have developed novel, potent SHIP2 inhibitors by extensive structural elaboration of crizotinib discovered from a high-throughput screening. Our representative compound 43 potently inhibited SHIP2 activity as well as GSK3β activation in HT22 neuronal cells. It was also shown that 43 has favorable physicochemical properties, especially high brain penetration. Considering SHIP2 is one of key signal mediators for tau hyperphosphorylation, our potent SHIP2 inhibitor 43 may function as a promising lead compound for the treatment of Alzheimer's disease.
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7
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Neuwald AF, Aravind L, Altschul SF. Inferring joint sequence-structural determinants of protein functional specificity. eLife 2018; 7. [PMID: 29336305 PMCID: PMC5770160 DOI: 10.7554/elife.29880] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/22/2017] [Indexed: 01/05/2023] Open
Abstract
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns. For each subgroup, a second measure identifies structural interactions involving pattern residues. Such interactions are derived either from atomic coordinates or from Direct Coupling Analysis scores, used as surrogates for structural distances. Applying this approach to N-acetyltransferases, P-loop GTPases, RNA helicases, synaptojanin-superfamily phosphatases and nucleases, and thymine/uracil DNA glycosylases yielded results congruent with biochemical understanding of these proteins, and also revealed striking sequence-structural features overlooked by other methods. These and similar analyses can aid the design of drugs targeting allosteric sites.
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Affiliation(s)
- Andrew F Neuwald
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, United States
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Stephen F Altschul
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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8
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Abdalla E, El‐Beheiry A, Dieterich K, Thevenon J, Fauré J, Rendu J. “Lowe syndrome: A particularly severe phenotype without clinical kidney involvement”. Am J Med Genet A 2017; 176:460-464. [DOI: 10.1002/ajmg.a.38572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 11/02/2017] [Accepted: 11/13/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Ebtesam Abdalla
- Department of Human GeneticsMedical Research InstituteAlexandria UniversityAlexandriaEgypt
| | - Ahmed El‐Beheiry
- Department of RadiologyAlexandria Faculty of MedicineAlexandria UniversityAlexandriaEgypt
| | - Klaus Dieterich
- Département de Génétique et ProcréationCHU Grenoble AlpesUniversité Grenoble AlpesGrenobleFrance
| | - Julien Thevenon
- Département de Génétique et ProcréationCHU Grenoble AlpesUniversité Grenoble AlpesGrenobleFrance
| | - Julien Fauré
- Département de Biochimie Pharmacologie ToxicologieBiochimie et Génétique MoléculaireCentre Hospitalier Universitaire Grenoble AlpesUniversité Grenoble AlpesGrenobleFrance
- Grenoble Institut des NeurosciencesInserm U1216–Eq. 4 C‐MyPathLaTroncheFrance
| | - John Rendu
- Département de Biochimie Pharmacologie ToxicologieBiochimie et Génétique MoléculaireCentre Hospitalier Universitaire Grenoble AlpesUniversité Grenoble AlpesGrenobleFrance
- Grenoble Institut des NeurosciencesInserm U1216–Eq. 4 C‐MyPathLaTroncheFrance
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9
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Le Coq J, Camacho-Artacho M, Velázquez JV, Santiveri CM, Gallego LH, Campos-Olivas R, Dölker N, Lietha D. Structural basis for interdomain communication in SHIP2 providing high phosphatase activity. eLife 2017; 6. [PMID: 28792888 PMCID: PMC5550278 DOI: 10.7554/elife.26640] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022] Open
Abstract
SH2-containing-inositol-5-phosphatases (SHIPs) dephosphorylate the 5-phosphate of phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3) and play important roles in regulating the PI3K/Akt pathway in physiology and disease. Aiming to uncover interdomain regulatory mechanisms in SHIP2, we determined crystal structures containing the 5-phosphatase and a proximal region adopting a C2 fold. This reveals an extensive interface between the two domains, which results in significant structural changes in the phosphatase domain. Both the phosphatase and C2 domains bind phosphatidylserine lipids, which likely helps to position the active site towards its substrate. Although located distant to the active site, the C2 domain greatly enhances catalytic turnover. Employing molecular dynamics, mutagenesis and cell biology, we identify two distinct allosteric signaling pathways, emanating from hydrophobic or polar interdomain interactions, differentially affecting lipid chain or headgroup moieties of PI(3,4,5)P3. Together, this study reveals details of multilayered C2-mediated effects important for SHIP2 activity and points towards interesting new possibilities for therapeutic interventions. DOI:http://dx.doi.org/10.7554/eLife.26640.001
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Affiliation(s)
- Johanne Le Coq
- Cell Signalling and Adhesion Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Marta Camacho-Artacho
- Cell Signalling and Adhesion Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - José Vicente Velázquez
- Cell Signalling and Adhesion Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Clara M Santiveri
- Spectroscopy and Nuclear Magnetic Resonance Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Luis Heredia Gallego
- Cell Signalling and Adhesion Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Ramón Campos-Olivas
- Spectroscopy and Nuclear Magnetic Resonance Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Nicole Dölker
- Structural Computational Biology Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Daniel Lietha
- Cell Signalling and Adhesion Group, Spanish National Cancer Research Centre, Madrid, Spain
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