1
|
Hostachy S, Wang H, Zong G, Franke K, Riley AM, Schmieder P, Potter BVL, Shears SB, Fiedler D. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry 2023; 29:e202302426. [PMID: 37773020 PMCID: PMC7615343 DOI: 10.1002/chem.202302426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP5 is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP5 . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations.
Collapse
Affiliation(s)
- Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Huanchen Wang
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Guangning Zong
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Katy Franke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Andrew M. Riley
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Stephen B. Shears
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| |
Collapse
|
2
|
Pipercevic J, Kohl B, Gerasimaite R, Comte-Miserez V, Hostachy S, Müntener T, Agustoni E, Jessen HJ, Fiedler D, Mayer A, Hiller S. Inositol pyrophosphates activate the vacuolar transport chaperone complex in yeast by disrupting a homotypic SPX domain interaction. Nat Commun 2023; 14:2645. [PMID: 37156835 PMCID: PMC10167327 DOI: 10.1038/s41467-023-38315-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Many proteins involved in eukaryotic phosphate homeostasis are regulated by SPX domains. In yeast, the vacuolar transporter chaperone (VTC) complex contains two such domains, but mechanistic details of its regulation are not well understood. Here, we show at the atomic level how inositol pyrophosphates interact with SPX domains of subunits Vtc2 and Vtc3 to control the activity of the VTC complex. Vtc2 inhibits the catalytically active VTC subunit Vtc4 by homotypic SPX-SPX interactions via the conserved helix α1 and the previously undescribed helix α7. Binding of inositol pyrophosphates to Vtc2 abrogates this interaction, thus activating the VTC complex. Accordingly, VTC activation is also achieved by site-specific point mutations that disrupt the SPX-SPX interface. Structural data suggest that ligand binding induces reorientation of helix α1 and exposes the modifiable helix α7, which might facilitate its post-translational modification in vivo. The variable composition of these regions within the SPX domain family might contribute to the diversified SPX functions in eukaryotic phosphate homeostasis.
Collapse
Affiliation(s)
- Joka Pipercevic
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Bastian Kohl
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Ruta Gerasimaite
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
- Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Véronique Comte-Miserez
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sarah Hostachy
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Elia Agustoni
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Henning Jacob Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorothea Fiedler
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| |
Collapse
|
3
|
Benjamin B, Goldgur Y, Jork N, Jessen HJ, Schwer B, Shuman S. Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States. mBio 2022; 13:e0308722. [PMID: 36468882 PMCID: PMC9765450 DOI: 10.1128/mbio.03087-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Expression of the fission yeast Schizosaccharomyces pombe phosphate regulon is sensitive to the intracellular level of the inositol pyrophosphate signaling molecule 1,5-IP8. IP8 dynamics are determined by Asp1, a bifunctional enzyme consisting of an N-terminal kinase domain and a C-terminal pyrophosphatase domain that catalyze IP8 synthesis and catabolism, respectively. Here, we report structures of the Asp1 kinase domain, crystallized with two protomers in the asymmetric unit, one of which was complexed with ligands (ADPNP, ADP, or ATP; Mg2+ or Mn2+; IP6, 5-IP7, or 1,5-IP8) and the other which was ligand-free. The ligand-free enzyme adopts an "open" conformation that allows ingress of substrates and egress of products. ADPNP, ADP, and ATP and associated metal ions occupy a deep phospho-donor pocket in the active site. IP6 or 5-IP7 engagement above the nucleotide favors adoption of a "closed" conformation, in which surface protein segments undergo movement and a disordered-to-ordered transition to form an inositol polyphosphate-binding site. In a structure mimetic of the kinase Michaelis complex, the anionic 5-IP7 phosphates are encaged by an ensemble of nine cationic amino acids: Lys43, Arg223, Lys224, Lys260, Arg274, Arg285, Lys290, Arg293, and Lys341. Alanine mutagenesis of amino acids that contact the adenosine nucleoside of the ATP donor underscored the contributions of Asp258 interaction with the ribose 3'-OH and of Glu248 with adenine-N6. Changing Glu248 to Gln elicited a gain of function whereby the kinase became adept at using GTP as phosphate donor. Wild-type Asp1 kinase can utilize N6-benzyl-ATP as phosphate donor. IMPORTANCE The inositol pyrophosphate signaling molecule 1,5-IP8 modulates fission yeast phosphate homeostasis via its action as an agonist of RNA 3'-processing and transcription termination. Cellular IP8 levels are determined by Asp1, a bifunctional enzyme composed of an N-terminal kinase and a C-terminal pyrophosphatase domain. Here, we present a series of crystal structures of the Asp1 kinase domain, in a ligand-free state and in complexes with nucleotides ADPNP, ADP, and ATP, divalent cations magnesium and manganese, and inositol polyphosphates IP6, 5-IP7, and 1,5-IP8. Substrate binding elicits a switch from open to closed conformations, entailing a disordered-to-ordered transition and a rearrangement or movement of two peptide segments that form a binding site for the phospho-acceptor. Our structures, along with structure-guided mutagenesis, fortify understanding of the mechanism and substrate specificity of Asp1 kinase, and they extend and complement structural and functional studies of the orthologous human kinase PPIP5K2.
Collapse
Affiliation(s)
- Bradley Benjamin
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Yehuda Goldgur
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
4
|
Couto D, Richter A, Walter H, Furkert D, Hothorn M, Fiedler D. Using Biotinylated myo-Inositol Hexakisphosphate to Investigate Inositol Pyrophosphate-Protein Interactions with Surface-Based Biosensors. Biochemistry 2021; 60:2739-2748. [PMID: 34499474 DOI: 10.1021/acs.biochem.1c00497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inositol pyrophosphates (PP-InsPs) are highly phosphorylated molecules that have emerged as central nutrient messengers in eukaryotic organisms. They can bind to structurally diverse target proteins to regulate biological functions, such as protein-protein interactions. PP-InsPs are strongly negatively charged and interact with highly basic surface patches in proteins, making their quantitative biochemical analysis challenging. Here, we present the synthesis of biotinylated myo-inositol hexakisphosphates and their application in surface plasmon resonance and grating-coupled interferometry assays, to enable the rapid identification, validation, and kinetic characterization of InsP- and PP-InsP-protein interactions.
Collapse
Affiliation(s)
- Daniel Couto
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Annika Richter
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Henriette Walter
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| |
Collapse
|
5
|
Hostachy S, Utesch T, Franke K, Dornan GL, Furkert D, Türkaydin B, Haucke V, Sun H, Fiedler D. Dissecting the activation of insulin degrading enzyme by inositol pyrophosphates and their bisphosphonate analogs. Chem Sci 2021; 12:10696-10702. [PMID: 34476054 PMCID: PMC8372538 DOI: 10.1039/d1sc02975d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/06/2021] [Indexed: 11/21/2022] Open
Abstract
Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are densely phosphorylated eukaryotic messengers, which are involved in numerous cellular processes. To elucidate their signaling functions at the molecular level, non-hydrolyzable bisphosphonate analogs of inositol pyrophosphates, PCP-InsPs, have been instrumental. Here, an efficient synthetic strategy to obtain these analogs in unprecedented quantities is described - relying on the use of combined phosphate ester-phosphoramidite reagents. The PCP-analogs, alongside their natural counterparts, were applied to investigate their regulatory effect on insulin-degrading enzyme (IDE), using a range of biochemical, biophysical and computational methods. A unique interplay between IDE, its substrates and the PP-InsPs was uncovered, in which the PP-InsPs differentially modulated the activity of the enzyme towards short peptide substrates. Aided by molecular docking and molecular dynamics simulations, a flexible binding mode for the InsPs/PP-InsPs was identified at the anion binding site of IDE. Targeting IDE for therapeutic purposes should thus take regulation by endogenous PP-InsP metabolites into account.
Collapse
Affiliation(s)
- Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Tillmann Utesch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Katy Franke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Gillian Leigh Dornan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Berke Türkaydin
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| |
Collapse
|
6
|
Márquez-Moñino MÁ, Ortega-García R, Shipton ML, Franco-Echevarría E, Riley AM, Sanz-Aparicio J, Potter BVL, González B. Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping. SCIENCE ADVANCES 2021; 7:7/17/eabf6744. [PMID: 33893105 PMCID: PMC8064635 DOI: 10.1126/sciadv.abf6744] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase DDP1 is a Nudix enzyme with pyrophosphatase activity on diphosphoinositides, dinucleotides, and polyphosphates. These substrates bind to diverse protein targets and participate in signaling and metabolism, being essential for energy and phosphate homeostasis, ATPase pump regulation, or protein phosphorylation. An exhaustive structural study of DDP1 in complex with multiple ligands related to its three diverse substrate classes is reported. This allowed full characterization of the DDP1 active site depicting the molecular basis for endowing multisubstrate abilities to a Nudix enzyme, driven by phosphate anchoring following a defined path. This study, combined with multiple enzyme variants, reveals the different substrate binding modes, preferences, and selection. Our findings expand current knowledge on this important structural superfamily with implications extending beyond inositide research. This work represents a valuable tool for inhibitor/substrate design for ScDDP1 and orthologs as potential targets to address fungal infections and other health concerns.
Collapse
Affiliation(s)
- María Ángeles Márquez-Moñino
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Raquel Ortega-García
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Megan L Shipton
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK
| | - Elsa Franco-Echevarría
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK
| | - Beatriz González
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.
| |
Collapse
|
7
|
Shears SB, Wang H. Metabolism and Functions of Inositol Pyrophosphates: Insights Gained from the Application of Synthetic Analogues. Molecules 2020; 25:E4515. [PMID: 33023101 PMCID: PMC7583957 DOI: 10.3390/molecules25194515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Inositol pyrophosphates (PP-InsPs) comprise an important group of intracellular, diffusible cellular signals that a wide range of biological processes throughout the yeast, plant, and animal kingdoms. It has been difficult to gain a molecular-level mechanistic understanding of the actions of these molecules, due to their highly phosphorylated nature, their low levels, and their rapid metabolic turnover. More recently, these obstacles to success are being surmounted by the chemical synthesis of a number of insightful PP-InsP analogs. This review will describe these analogs and will indicate the important chemical and biological information gained by using them.
Collapse
Affiliation(s)
- Stephen B. Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA;
| | | |
Collapse
|
8
|
Chin AC, Gao Z, Riley AM, Furkert D, Wittwer C, Dutta A, Rojas T, Semenza ER, Felder RA, Pluznick JL, Jessen HJ, Fiedler D, Potter BVL, Snyder SH, Fu C. The inositol pyrophosphate 5-InsP 7 drives sodium-potassium pump degradation by relieving an autoinhibitory domain of PI3K p85α. SCIENCE ADVANCES 2020; 6:6/44/eabb8542. [PMID: 33115740 PMCID: PMC7608788 DOI: 10.1126/sciadv.abb8542] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/14/2020] [Indexed: 05/10/2023]
Abstract
Sodium/potassium-transporting adenosine triphosphatase (Na+/K+-ATPase) is one of the most abundant cell membrane proteins and is essential for eukaryotes. Endogenous negative regulators have long been postulated to play an important role in regulating the activity and stability of Na+/K+-ATPase, but characterization of these regulators has been elusive. Mechanisms of regulating Na+/K+-ATPase homeostatic turnover are unknown. Here, we report that 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7), generated by inositol hexakisphosphate kinase 1 (IP6K1), promotes physiological endocytosis and downstream degradation of Na+/K+-ATPase-α1. Deletion of IP6K1 elicits a twofold enrichment of Na+/K+-ATPase-α1 in plasma membranes of multiple tissues and cell types. Using a suite of synthetic chemical biology tools, we found that 5-InsP7 binds the RhoGAP domain of phosphatidylinositol 3-kinase (PI3K) p85α to disinhibit its interaction with Na+/K+-ATPase-α1. This recruits adaptor protein 2 (AP2) and triggers the clathrin-mediated endocytosis of Na+/K+-ATPase-α1. Our study identifies 5-InsP7 as an endogenous negative regulator of Na+/K+-ATPase-α1.
Collapse
Affiliation(s)
- Alfred C Chin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhe Gao
- Tianjin Key Laboratory of Metabolic Diseases, Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Andrew M Riley
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Oxford, UK
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Christopher Wittwer
- Institute of Organic Chemistry and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Amit Dutta
- Institute of Organic Chemistry and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Tomas Rojas
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evan R Semenza
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robin A Felder
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Jennifer L Pluznick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Henning J Jessen
- Institute of Organic Chemistry and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Oxford, UK
| | - Solomon H Snyder
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chenglai Fu
- Tianjin Key Laboratory of Metabolic Diseases, Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China.
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| |
Collapse
|
9
|
Riley AM, Wang H, Shears SB, Potter BVL. Synthesis of an α-phosphono-α,α-difluoroacetamide analogue of the diphosphoinositol pentakisphosphate 5-InsP 7. MEDCHEMCOMM 2019; 10:1165-1172. [PMID: 31391889 PMCID: PMC6657673 DOI: 10.1039/c9md00163h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022]
Abstract
Diphosphoinositol phosphates (PP-InsPs) are an evolutionarily ancient group of signalling molecules that are essential to cellular and organismal homeostasis. As the detailed mechanisms of PP-InsP signalling begin to emerge, synthetic analogues of PP-InsPs containing stabilised mimics of the labile diphosphate group can provide valuable investigational tools. We synthesised 5-PCF2Am-InsP5 (1), a novel fluorinated phosphonate analogue of 5-PP-InsP5, and obtained an X-ray crystal structure of 1 in complex with diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2). 5-PCF2Am-InsP5 binds to the kinase domain of PPIP5K2 in a similar orientation to that of the natural substrate 5-PP-InsP5 and the PCF2Am structure can mimic many aspects of the diphosphate group in 5-PP-InsP5. We propose that 1, the structural and electronic properties of which are in some ways complementary to those of existing phosphonoacetate and methylenebisphosphonate analogues of 5-PP-InsP5, may be a useful addition to the expanding array of chemical tools for the investigation of signalling by PP-InsPs. The PCF2Am group may also deserve attention for wider application as a diphosphate mimic.
Collapse
Affiliation(s)
- Andrew M Riley
- Medicinal Chemistry and Drug Discovery , Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK . ; ; Tel: +44 (0)1865 271945
| | - Huanchen Wang
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Stephen B Shears
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery , Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK . ; ; Tel: +44 (0)1865 271945
| |
Collapse
|
10
|
Dohle W, Su X, Mills SJ, Rossi A, Taylor CW, Potter BVL. A synthetic cyclitol-nucleoside conjugate polyphosphate is a highly potent second messenger mimic. Chem Sci 2019; 10:5382-5390. [PMID: 31171961 PMCID: PMC6540904 DOI: 10.1039/c9sc00445a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Reactions that form sec-sec ethers are well known, but few lead to compounds with dense functionality around the O-linkage. Replacement of the α-glucopyranosyl unit of adenophostin A, a potent d-myo-inositol 1,4,5-trisphosphate (IP3R) agonist, with a d-chiro-inositol surrogate acting substantially as a pseudosugar, leads to "d-chiro-inositol adenophostin". At its core, this cyclitol-nucleoside trisphosphate comprises a nucleoside sugar linked via an axial d-chiro-inositol 1-hydroxyl-adenosine 3'-ribose ether linkage. A divergent synthesis of d-chiro-inositol adenophostin has been achieved. Key features of the synthetic strategy to produce a triol for phosphorylation include a new selective mono-tosylation of racemic 1,2:4,5-di-O-isopropylidene-myo-inositol using tosyl imidazole; subsequent conversion of the product into separable camphanate ester derivatives, one leading to a chiral myo-inositol triflate used as a synthetic building block and the other to l-5-O-methyl-myo-inositol [l-(+)-bornesitol] to assign the absolute configuration; the nucleophilic coupling of an alkoxide of a ribose pent-4-ene orthoester unit with a structurally rigid chiral myo-inositol triflate derivative, representing the first sec-sec ether formation between a cyclitol and ribose. Reaction of the coupled product with a silylated nucleobase completes the assembly of the core structure. Further protecting group manipulation, mixed O- and N-phosphorylation, and subsequent removal of all protecting groups in a single step achieves the final product, avoiding a separate N6 protection/deprotection strategy. d-chiro-Inositol adenophostin evoked Ca2+ release through IP3Rs at lower concentrations than adenophostin A, hitherto the most potent known agonist of IP3Rs.
Collapse
Affiliation(s)
- Wolfgang Dohle
- Medicinal Chemistry & Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford
, OX1 3QT
, UK
.
; Tel: +44-1865-271945
| | - Xiangdong Su
- Medicinal Chemistry & Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford
, OX1 3QT
, UK
.
; Tel: +44-1865-271945
| | - Stephen J. Mills
- Medicinal Chemistry & Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford
, OX1 3QT
, UK
.
; Tel: +44-1865-271945
| | - Ana M. Rossi
- Department of Pharmacology
, University of Cambridge
,
Tennis Court Road
, Cambridge
, CB2 1PD
, UK
| | - Colin W. Taylor
- Department of Pharmacology
, University of Cambridge
,
Tennis Court Road
, Cambridge
, CB2 1PD
, UK
| | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford
, OX1 3QT
, UK
.
; Tel: +44-1865-271945
| |
Collapse
|
11
|
Riley AM, Unterlass JE, Konieczny V, Taylor CW, Helleday T, Potter BVL. A synthetic diphosphoinositol phosphate analogue of inositol trisphosphate. MEDCHEMCOMM 2018; 9:1105-1113. [PMID: 30079174 PMCID: PMC6071853 DOI: 10.1039/c8md00149a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/01/2018] [Indexed: 01/17/2023]
Abstract
Diphosphoinositol phosphates (PP-InsPs) are inositol phosphates (InsPs) that contain PP (diphosphate) groups. Converting a phosphate group in an InsP into a diphosphate has been reported to enhance affinity for some binding proteins. We synthesised 1-PP-Ins(4,5)P2, the first diphosphate analogue of the intracellular signalling molecule InsP3, and examined its effects on InsP3 receptors, which are intracellular Ca2+ channels. 1-PP-Ins(4,5)P2 was indistinguishable from InsP3 in its ability to bind to and activate type 1 InsP3 receptors, indicating that the diphosphate modification of InsP3 affected neither affinity nor efficacy. Nevertheless, 1-PP-Ins(4,5)P2 is the most potent 1-phosphate modified analogue of InsP3 yet identified. PP-InsPs are generally hydrolysed by diphosphoinositol phosphate phosphohydrolases (DIPPs), but 1-PP-Ins(4,5)P2 was not readily metabolised by human DIPPs. Differential scanning fluorimetry showed that 1-PP-Ins(4,5)P2 stabilises DIPP proteins, but to a lesser extent than naturally occurring substrates 1-PP-InsP5 and 5-PP-InsP5. The non-hydrolysable InsP7 analogues 1-PCP-InsP5 and 5-PCP-InsP5 showed comparable stabilising abilities to their natural counterparts and may therefore be promising substrate analogues for co-crystallisation with DIPPs.
Collapse
Affiliation(s)
- Andrew M. Riley
- Medicinal Chemistry and Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford OX1 3QT
, UK
.
; Fax: +44 (0)1865 271853
; Tel: +44 (0)1865 271945
| | - Judith E. Unterlass
- Science for Life Laboratory
, Department of Oncology-Pathology
, Karolinska Institutet
,
SE-171 21 Solna
, Sweden
| | - Vera Konieczny
- Department of Pharmacology
, University of Cambridge
,
Tennis Court Road
, Cambridge CB2 1PD
, UK
| | - Colin W. Taylor
- Department of Pharmacology
, University of Cambridge
,
Tennis Court Road
, Cambridge CB2 1PD
, UK
| | - Thomas Helleday
- Science for Life Laboratory
, Department of Oncology-Pathology
, Karolinska Institutet
,
SE-171 21 Solna
, Sweden
| | - Barry V. L. Potter
- Medicinal Chemistry and Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford OX1 3QT
, UK
.
; Fax: +44 (0)1865 271853
; Tel: +44 (0)1865 271945
| |
Collapse
|
12
|
Brown NW, Marmelstein AM, Fiedler D. Chemical tools for interrogating inositol pyrophosphate structure and function. Chem Soc Rev 2018; 45:6311-6326. [PMID: 27462803 DOI: 10.1039/c6cs00193a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The inositol pyrophosphates (PP-InsPs) are a unique group of intracellular messengers that represent some of the most highly phosphorylated molecules in nature. Genetic perturbation of the PP-InsP biosynthetic network indicates a central role for these metabolites in maintaining cellular energy homeostasis and in controlling signal transduction networks. However, despite their discovery over two decades ago, elucidating their physiologically relevant isomers, the biochemical pathways connecting these molecules to their associated phenotypes, and their modes of signal transduction has often been stymied by technical challenges. Many of the advances in understanding these molecules to date have been facilitated by the total synthesis of the various PP-InsP isomers and by the development of new methods that are capable of identifying their downstream signalling partners. Chemical tools have also been developed to distinguish between the proposed PP-InsP signal transduction mechanisms: protein binding, and a covalent modification of proteins termed protein pyrophosphorylation. In this article, we review these recent developments, discuss how they have helped to illuminate PP-InsP structure and function, and highlight opportunities for future discovery.
Collapse
Affiliation(s)
- Nathaniel W Brown
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| | - Alan M Marmelstein
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| | - Dorothea Fiedler
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| |
Collapse
|
13
|
Dutta AK, Captain I, Jessen HJ. New Synthetic Methods for Phosphate Labeling. Top Curr Chem (Cham) 2017; 375:51. [DOI: 10.1007/s41061-017-0135-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/27/2017] [Indexed: 12/12/2022]
|
14
|
Shah A, Ganguli S, Sen J, Bhandari R. Inositol Pyrophosphates: Energetic, Omnipresent and Versatile Signalling Molecules. J Indian Inst Sci 2017; 97:23-40. [PMID: 32214696 PMCID: PMC7081659 DOI: 10.1007/s41745-016-0011-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy-rich signalling molecules found in all eukaryotic cells. These are derivatives of inositol that contain one or more diphosphate (or pyrophosphate) groups in addition to monophosphates. The more abundant and best studied PP-IPs are diphosphoinositol pentakisphosphate (IP7) and bis-diphosphoinositol tetrakisphosphate (IP8). These molecules can influence protein function by two mechanisms: binding and pyrophosphorylation. The former involves the specific interaction of a particular inositol pyrophosphate with a binding site on a protein, while the latter is a unique attribute of inositol pyrophosphates, wherein the β-phosphate moiety is transferred from a PP-IP to a pre-phosphorylated serine residue in a protein to generate pyrophosphoserine. Both these events can result in changes in the target protein’s activity, localisation or its interaction with other partners. As a consequence of their ubiquitous presence in all eukaryotic organisms and all cell types examined till date, and their ability to modify protein function, PP-IPs have been found to participate in a wide range of metabolic, developmental, and signalling pathways. This review highlights
many of the known functions of PP-IPs in the context of their temporal and spatial distribution in eukaryotic cells.
Collapse
Affiliation(s)
- Akruti Shah
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Jayraj Sen
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
| |
Collapse
|
15
|
Abstract
To help define the molecular basis of cellular signalling cascades, and their biological functions, there is considerable value in utilizing a high-quality chemical 'probe' that has a well-defined interaction with a specific cellular protein. Such reagents include inhibitors of protein kinases and small molecule kinases, as well as mimics or antagonists of intracellular signals. The purpose of this review is to consider recent progress and promising future directions for the development of novel molecules that can interrogate and manipulate the cellular actions of inositol pyrophosphates (PP-IPs)--a specialized, 'energetic' group of cell-signalling molecules in which multiple phosphate and diphosphate groups are crammed around a cyclohexane polyol scaffold.
Collapse
|
16
|
Yates LM, Fiedler D. A Stable Pyrophosphoserine Analog for Incorporation into Peptides and Proteins. ACS Chem Biol 2016; 11:1066-73. [PMID: 26760216 DOI: 10.1021/acschembio.5b00972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein pyrophosphorylation is a covalent modification of proteins, mediated by the inositol pyrophosphate messengers. Although the inositol pyrophosphates have been linked to a range of cellular processes, the role of protein pyrophosphorylation remains minimally characterized in vivo. The inherent instability of the phosphoanhydride bond has hampered the development of useful bioanalytical techniques to interrogate this novel signaling mechanism. Here, we describe the preparation of a pyrophosphoserine analog containing a stable methylene-bisphosphonate group that is compatible with solid-phase peptide synthesis. The resulting peptides demonstrate enhanced stability in Eukaryotic cell lysates and mammalian plasma and display resistance toward chemical degradation, when compared to the corresponding pyrophosphopeptides. In addition, the peptides containing the stable pyrophosphoserine analog are highly compatible with common ligation methods, such as native chemical ligation, maleimide conjugation, and glutaraldehyde ligation. The bisphosphonate-containing peptides will, therefore, be well-suited for future pyrophosphoserine antibody generation and affinity capture of pyrophosphoprotein binding partners and provide a key entry point to study the regulatory role of protein pyrophosphorylation.
Collapse
Affiliation(s)
- Lisa M. Yates
- Department
of Chemistry, Princeton University, Washington Rd, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Department
of Chemistry, Princeton University, Washington Rd, Princeton, New Jersey 08544, United States
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| |
Collapse
|
17
|
Pavlovic I, Thakor DT, Jessen HJ. Synthesis of 2-diphospho-myo-inositol 1,3,4,5,6-pentakisphosphate and a photocaged analogue. Org Biomol Chem 2016; 14:5559-62. [DOI: 10.1039/c6ob00094k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diphosphoinositol polyphosphates (inositol pyrophosphates, X-InsP7) are a family of second messengers with important roles in eukaryotic biology. A new approach targeting 2-InsP7 and a photocaged analogue is described.
Collapse
Affiliation(s)
- I. Pavlovic
- Department of Chemistry
- University of Zürich
- 8057 Zürich
- Switzerland
| | - D. T. Thakor
- Department of Chemistry
- University of Zürich
- 8057 Zürich
- Switzerland
| | - H. J. Jessen
- Department of Chemistry and Pharmacy
- Albert-Ludwigs University Freiburg
- 79104 Freiburg
- Germany
| |
Collapse
|