1
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Kozakiewicz-Piekarz A, Grzegórska M, Ziemkiewicz K, Grab K, Baranowski MR, Zapadka M, Karpiel M, Kupcewicz B, Kowalska J, Wujak M. Synthesis, kinetic studies, and QSAR of dinucleoside polyphosphate derivatives as human AK1 inhibitors. Bioorg Chem 2024; 148:107432. [PMID: 38744169 DOI: 10.1016/j.bioorg.2024.107432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Adenylate kinase (AK) plays a crucial role in the metabolic monitoring of cellular adenine nucleotide homeostasis by catalyzing the reversible transfer of a phosphate group between ATP and AMP, yielding two ADP molecules. By regulating the nucleotide levels and energy metabolism, the enzyme is considered a disease modifier and potential therapeutic target for various human diseases, including malignancies and inflammatory and neurodegenerative disorders. However, lacking approved drugs targeting AK hinders broad studies on this enzyme's pathological importance and therapeutic potential. In this work, we determined the effect of a series of dinucleoside polyphosphate derivatives, commercially available (11 compounds) and newly synthesized (8 compounds), on the catalytic activity of human adenylate kinase isoenzyme 1 (hAK1). The tested compounds belonged to the following groups: (1) diadenosine polyphosphates with different phosphate chain lengths, (2) base-modified derivatives, and (3) phosphate-modified derivatives. We found that all the investigated compounds inhibited the catalytic activity of hAK1, yet with different efficiencies. Three dinucleoside polyphosphates showed IC50 values below 1 µM, and the most significant inhibitory effect was observed for P1-(5'-adenosyl) P5-(5'-adenosyl) pentaphosphate (Ap5A). To understand the observed differences in the inhibition efficiency of the tested dinucleoside polyphosphates, the molecular docking of these compounds to hAK1 was performed. Finally, we conducted a quantitative structure-activity relationship (QSAR) analysis to establish a computational prediction model for hAK1 modulators. Two PLS-regression-based models were built using kinetic data obtained from the AK1 activity analysis performed in both directions of the enzymatic reaction. Model 1 (AMP and ATP synthesis) had a good prediction power (R2 = 0.931, Q2 = 0.854, and MAE = 0.286), while Model 2 (ADP synthesis) exhibited a moderate quality (R2 = 0.913, Q2 = 0.848, and MAE = 0.370). These studies can help better understand the interactions between dinucleoside polyphosphates and adenylate kinase to attain more effective and selective inhibitors in the future.
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Affiliation(s)
| | - Magdalena Grzegórska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 87-100 Torun, Poland
| | - Kamil Ziemkiewicz
- Centre of New Technologies, University of Warsaw, Banacha 2C 02-097 Warsaw, Poland
| | - Katarzyna Grab
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 02-093 Warsaw, Poland
| | - Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 02-093 Warsaw, Poland
| | - Mariusz Zapadka
- Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2 85-089 Bydgoszcz, Poland
| | - Marta Karpiel
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2 30-387 Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11 30-348 Krakow, Poland
| | - Bogumiła Kupcewicz
- Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2 85-089 Bydgoszcz, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 02-093 Warsaw, Poland
| | - Magdalena Wujak
- Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2 85-089 Bydgoszcz, Poland.
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2
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Appy L, Peyrottes S, Roy B. Supported Synthesis of Adenosine Nucleotides and Derivatives on a Benzene‐Centered Tripodal Soluble Support. European J Org Chem 2022. [DOI: 10.1002/ejoc.202100544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lucie Appy
- Nucleosides & Phosphorylated Effectors Team Institute for Biomolecules Max Mousseron (IBMM) UMR 5247 CNRS University of Montpellier, ENSCM Campus Triolet cc 1705, Place Eugène Bataillon 34095 Montpellier France
| | - Suzanne Peyrottes
- Nucleosides & Phosphorylated Effectors Team Institute for Biomolecules Max Mousseron (IBMM) UMR 5247 CNRS University of Montpellier, ENSCM Campus Triolet cc 1705, Place Eugène Bataillon 34095 Montpellier France
| | - Béatrice Roy
- Nucleosides & Phosphorylated Effectors Team Institute for Biomolecules Max Mousseron (IBMM) UMR 5247 CNRS University of Montpellier, ENSCM Campus Triolet cc 1705, Place Eugène Bataillon 34095 Montpellier France
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3
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Appy L, Depaix A, Bantreil X, Lamaty F, Peyrottes S, Roy B. Alternative synthetic approaches for nucleotides and derivatives. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2021.1998050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lucie Appy
- Nucleosides & Phosphorylated Effectors Team, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Anaïs Depaix
- Nucleosides & Phosphorylated Effectors Team, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Xavier Bantreil
- Green Chemistry and Enabling Technologies, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Frédéric Lamaty
- Green Chemistry and Enabling Technologies, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Suzanne Peyrottes
- Nucleosides & Phosphorylated Effectors Team, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Béatrice Roy
- Nucleosides & Phosphorylated Effectors Team, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 CNRS, University of Montpellier, ENSCM, Montpellier, France
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4
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Krüger L, Albrecht CJ, Schammann HK, Stumpf FM, Niedermeier ML, Yuan Y, Stuber K, Wimmer J, Stengel F, Scheffner M, Marx A. Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate. Nat Commun 2021; 12:5808. [PMID: 34608152 PMCID: PMC8490401 DOI: 10.1038/s41467-021-26075-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/10/2021] [Indexed: 01/14/2023] Open
Abstract
The nucleotides diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) are formed in prokaryotic and eukaryotic cells. Since their concentrations increase significantly upon cellular stress, they are considered to be alarmones triggering stress adaptive processes. However, their cellular roles remain elusive. To elucidate the proteome-wide interactome of Ap3A and Ap4A and thereby gain insights into their cellular roles, we herein report the development of photoaffinity-labeling probes and their employment in chemical proteomics. We demonstrate that the identified ApnA interactors are involved in many fundamental cellular processes including carboxylic acid and nucleotide metabolism, gene expression, various regulatory processes and cellular response mechanisms and only around half of them are known nucleotide interactors. Our results highlight common functions of these ApnAs across the domains of life, but also identify those that are different for Ap3A or Ap4A. This study provides a rich source for further functional studies of these nucleotides and depicts useful tools for characterization of their regulatory mechanisms in cells. Diadenosine polyphosphates (ApAs) are involved in cellular stress signaling but only a few molecular targets have been characterized so far. Here, the authors develop ApnA-based photoaffinity-labeling probes and use them to identify Ap3A and Ap4A binding proteins in human cell lysates.
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Affiliation(s)
- Lena Krüger
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Christoph J Albrecht
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Florian M Stumpf
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Katrin Stuber
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Josua Wimmer
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.
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5
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Oliva P, Scortichini M, Dobelmann C, Jain S, Gopinatth V, Toti KS, Phung NB, Junker A, Jacobson KA. Structure-activity relationships of pyrimidine nucleotides containing a 5'-α,β-methylene diphosphonate at the P2Y 6 receptor. Bioorg Med Chem Lett 2021; 45:128137. [PMID: 34048882 PMCID: PMC8276771 DOI: 10.1016/j.bmcl.2021.128137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
The Gq-coupled P2Y6 receptor (P2Y6R) is a component of the purinergic signaling system and functions in inflammatory, cardiovascular and metabolic processes. UDP, the native P2Y6R agonist and P2Y14R partial agonist, is subject to hydrolysis by ectonucleotidases. Therefore, we have synthesized UDP/CDP analogues containing a stabilizing α,β-methylene bridge as P2Y6R agonists and identified compatible affinity-enhancing pyrimidine modifications. A distal binding region on the receptor was explored with 4-benzyloxyimino cytidine 5'-diphosphate analogues and their potency determined in a calcium mobilization assay. A 4-trifluoromethyl-benzyloxyimino substituent in 25 provided the highest human P2Y6R potency (MRS4554, 0.57 µM), and a 5-fluoro substitution of the cytosine ring in 28 similarly enhanced potency, with >175- and 39-fold selectivity over human P2Y14R, respectively. However, 3-alkyl (31-33, 37, 38), β-d-arabinofuranose (39) and 6-aza (40) substitution prevented P2Y6R activation. Thus, we have identified new α,β-methylene bridged N4-extended CDP analogues as P2Y6R agonists that are highly selective over the P2Y14R.
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Affiliation(s)
- Paola Oliva
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mirko Scortichini
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clemens Dobelmann
- University of Münster, European Institute for Molecular Imaging (EIMI), Waldeyerstraße 15, D-48149 Münster, Germany
| | - Shanu Jain
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Varun Gopinatth
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ngan B Phung
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Junker
- University of Münster, European Institute for Molecular Imaging (EIMI), Waldeyerstraße 15, D-48149 Münster, Germany
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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6
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Schmies CC, Rolshoven G, Idris RM, Losenkova K, Renn C, Schäkel L, Al-Hroub H, Wang Y, Garofano F, Schmidt-Wolf IGH, Zimmermann H, Yegutkin GG, Müller CE. Fluorescent Probes for Ecto-5'-nucleotidase (CD73). ACS Med Chem Lett 2020; 11:2253-2260. [PMID: 33214837 DOI: 10.1021/acsmedchemlett.0c00391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/03/2020] [Indexed: 12/22/2022] Open
Abstract
Ecto-5'-nucleotidase (CD73) catalyzes the hydrolysis of AMP to anti-inflammatory, immunosuppressive adenosine. It is expressed on vascular endothelial, epithelial, and also numerous cancer cells where it strongly contributes to an immunosuppressive microenvironment. In the present study we designed and synthesized fluorescent-labeled CD73 inhibitors with low nanomolar affinity and high selectivity based on N 6 -benzyl-α,β-methylene-ADP (PSB-12379) as a lead structure. Fluorescein was attached to the benzyl residue via different linkers resulting in PSB-19416 (14b, K i 12.6 nM) and PSB-18332 (14a, K i 2.98 nM) as fluorescent high-affinity probes for CD73. These compounds are anticipated to become useful tools for biological studies, drug screening, and diagnostic applications.
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Affiliation(s)
- Constanze C. Schmies
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Georg Rolshoven
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Riham M. Idris
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | | | - Christian Renn
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Laura Schäkel
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Haneen Al-Hroub
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Yulu Wang
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Bonn D-53127, Germany
| | - Francesca Garofano
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Bonn D-53127, Germany
| | - Ingo G. H. Schmidt-Wolf
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Bonn D-53127, Germany
| | - Herbert Zimmermann
- Institute of Cell Biology and Neuroscience, Goethe-University, D-60438 Frankfurt am Main, Germany
| | | | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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7
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Raimi OG, Hurtado-Guerrero R, Borodkin V, Ferenbach A, Urbaniak MD, Ferguson MAJ, van Aalten DMF. A mechanism-inspired UDP- N-acetylglucosamine pyrophosphorylase inhibitor. RSC Chem Biol 2020; 1:13-25. [PMID: 34458745 PMCID: PMC8386105 DOI: 10.1039/c9cb00017h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022] Open
Abstract
UDP-N-acetylglucosamine pyrophosphorylase (UAP1) catalyses the last step in eukaryotic biosynthesis of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), converting UTP and GlcNAc-1P to the sugar nucleotide. Gene disruption studies have shown that this gene is essential in eukaryotes and a possible antifungal target, yet no inhibitors of fungal UAP1 have so far been reported. Here we describe the crystal structures of substrate/product complexes of UAP1 from Aspergillus fumigatus that together provide snapshots of catalysis. A structure with UDP-GlcNAc, pyrophosphate and Mg2+ provides the first Michaelis complex trapped for this class of enzyme, revealing the structural basis of the previously reported Mg2+ dependence and direct observation of pyrophosphorolysis. We also show that a highly conserved lysine mimics the role of a second metal observed in structures of bacterial orthologues. A mechanism-inspired UTP α,β-methylenebisphosphonate analogue (meUTP) was designed and synthesized and was shown to be a micromolar inhibitor of the enzyme. The mechanistic insights and inhibitor described here will facilitate future studies towards the discovery of small molecule inhibitors of this currently unexploited potential antifungal drug target. UDP-N-acetylglucosamine pyrophosphorylase (UAP1) catalyses the last step in eukaryotic biosynthesis of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), converting UTP and GlcNAc-1P to the sugar nucleotide.![]()
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Affiliation(s)
- Olawale G Raimi
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Ramon Hurtado-Guerrero
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Vladimir Borodkin
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Andrew Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Michael D Urbaniak
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
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8
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Romanenko VD. α-Heteroatom-substituted gem-Bisphosphonates: Advances in the Synthesis and Prospects for Biomedical Application. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190401141844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Functionalized gem-bisphosphonic acid derivatives being pyrophosphate isosteres are of great synthetic and biological interest since they are currently the most important class of drugs developed for the treatment of diseases associated with the disorder of calcium metabolism, including osteoporosis, Paget’s disease, and hypercalcemia. In this article, we will try to give an in-depth overview of the methods for obtaining α- heteroatom-substituted methylenebisphosphonates and acquaint the reader with the synthetic strategies that are used to develop biologically important compounds of this type.
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Affiliation(s)
- Vadim D. Romanenko
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 1-Murmanska Street, Kyiv-94, 02660, Ukraine
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9
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Bednarek S, Madan V, Sikorski PJ, Bartenschlager R, Kowalska J, Jemielity J. mRNAs biotinylated within the 5' cap and protected against decapping: new tools to capture RNA-protein complexes. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0167. [PMID: 30397103 DOI: 10.1098/rstb.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
The 5'-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5'-5' triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2. The utility of such cap-biotinylated RNAs as molecular tool was demonstrated by ultraviolet-cross-linking and affinity capture of protein-RNA complexes. In conclusion, RNAs labelled with biotin via the 5' cap structure can be applied to a variety of biological experiments based on biotin-avidin interaction or by means of biotin-specific antibodies, including protein affinity purification, pull-down assays, in vivo visualization, cellular delivery and many others.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Sylwia Bednarek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Vanesa Madan
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Ralf Bartenschlager
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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10
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Toti KS, Jain S, Ciancetta A, Balasubramanian R, Chakraborty S, Surujdin R, Shi ZD, Jacobson KA. Pyrimidine Nucleotides Containing a (S)-Methanocarba Ring as P2Y 6 Receptor Agonists. MEDCHEMCOMM 2017; 8:1897-1908. [PMID: 29423136 DOI: 10.1039/c7md00397h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Both agonists and antagonists of the UDP-activated P2Y6 receptor (P2Y6R) have been proposed for therapeutic use, in conditions such as cancer, inflammation, neurodegeneration and diabetes. Uracil nucleotides containing a South-bicyclo[3.1.0]hexane ((S)-methanocarba) ring system in place of the ribose ring were synthesized and shown to be potent P2Y6R agonists in a calcium mobilization assay. The (S)-methanocarba modification was compatible with either a 5-iodo or 4-methoxyimino group on the pyrimidine, but not with a α,β-methylene 5´-diphosphate. (S)-Methanocarba dinucleotide potency was compatible with a N4-methoxy modification on the proximal nucleoside that is assumed to bind at the P2Y6R similarly to UDP; (N)-methanocarba was preferred on the distal nucleoside moiety. This suggests that the distal dinucleotide P2Y6R binding site prefers a ribose-like group that can attain a (N) conformation, rather than (S). Dinucleotide binding was modeled by homology modeling, docking and molecular dynamics simulations, which suggested the same ribose conformational preferences found empirically.
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Affiliation(s)
- Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Shanu Jain
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ramachandran Balasubramanian
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Saibal Chakraborty
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ryan Surujdin
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Zhen-Dan Shi
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850 USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
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11
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Analysis of mononucleotides by tandem mass spectrometry: investigation of fragmentation pathways for phosphate- and ribose-modified nucleotide analogues. Sci Rep 2017; 7:8931. [PMID: 28827558 PMCID: PMC5567097 DOI: 10.1038/s41598-017-09416-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/24/2017] [Indexed: 12/23/2022] Open
Abstract
Synthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5′-mono-, 5′-di-, and 5′-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination. While positive-ion mode yielded fragments derived mainly from nucleobases, negative-ion mode provided insight into the structures of phosphoryl and phosphoribosyl moieties, enabling the determination of structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. Based on these data, we proposed fragmentation pathways that were confirmed by experiments with [18O]-isotopologues. We demonstrated the utility of ESI(−)/MS/MS in the analysis of structurally related compounds by analysing isomeric and isobaric nucleotides and applying ESI(−)/MS/MS to rapid identification of nucleotide synthesis products. We formulated general rules regarding nucleotide structure–fragmentation pattern relationships and indicating characteristic fragmentation ions for the interpretation of ESI(−)/MS/MS spectra of nucleotides and their analogues. The ESI(−)/MS/MS spectra of all nucleotides are available in an on-line database, msTide, at www.msTide-db.com.
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12
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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13
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017; 56:2955-2959. [DOI: 10.1002/anie.201611878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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14
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Ziemniak M, Mugridge JS, Kowalska J, Rhoads RE, Gross JD, Jemielity J. Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex. RNA (NEW YORK, N.Y.) 2016; 22:518-29. [PMID: 26826132 PMCID: PMC4793208 DOI: 10.1261/rna.055152.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/10/2015] [Indexed: 05/08/2023]
Abstract
Dcp1/2 is the major eukaryotic RNA decapping complex, comprised of the enzyme Dcp2 and activator Dcp1, which removes the 5' m(7)G cap from mRNA, committing the transcript to degradation. Dcp1/2 activity is crucial for RNA quality control and turnover, and deregulation of these processes may lead to disease development. The molecular details of Dcp1/2 catalysis remain elusive, in part because both cap substrate (m(7)GpppN) and m(7)GDP product are bound by Dcp1/2 with weak (mM) affinity. In order to find inhibitors to use in elucidating the catalytic mechanism of Dcp2, we screened a small library of synthetic m(7)G nucleotides (cap analogs) bearing modifications in the oligophosphate chain. One of the most potent cap analogs, m(7)GpSpppSm(7)G, inhibited Dcp1/2 20 times more efficiently than m(7)GpppN or m(7)GDP. NMR experiments revealed that the compound interacts with specific surfaces of both regulatory and catalytic domains of Dcp2 with submillimolar affinities. Kinetics analysis revealed that m(7)GpSpppSm(7)G is a mixed inhibitor that competes for the Dcp2 active site with micromolar affinity. m(7)GpSpppSm(7)G-capped RNA undergoes rapid decapping, suggesting that the compound may act as a tightly bound cap mimic. Our identification of the first small molecule inhibitor of Dcp2 should be instrumental in future studies aimed at understanding the structural basis of RNA decapping and may provide insight toward the development of novel therapeutically relevant decapping inhibitors.
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Affiliation(s)
- Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Robert E Rhoads
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130-3932, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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15
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Alguacil J, Reyes D, Aubin Y, Roy B, Périgaud C, Champagne E, Peyrottes S. Exploring synthetic pathways for nucleosidic derivatives of potent phosphoantigens. NEW J CHEM 2016. [DOI: 10.1039/c5nj03614c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Bhattarai S, Freundlieb M, Pippel J, Meyer A, Abdelrahman A, Fiene A, Lee SY, Zimmermann H, Yegutkin GG, Sträter N, El-Tayeb A, Müller CE. α,β-Methylene-ADP (AOPCP) Derivatives and Analogues: Development of Potent and Selective ecto-5'-Nucleotidase (CD73) Inhibitors. J Med Chem 2015; 58:6248-63. [PMID: 26147331 DOI: 10.1021/acs.jmedchem.5b00802] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
ecto-5'-Nucleotidase (eN, CD73) catalyzes the hydrolysis of extracellular AMP to adenosine. eN inhibitors have potential for use as cancer therapeutics. The eN inhibitor α,β-methylene-ADP (AOPCP, adenosine-5'-O-[(phosphonomethyl)phosphonic acid]) was used as a lead structure, and derivatives modified in various positions were prepared. Products were tested at rat recombinant eN. 6-(Ar)alkylamino substitution led to the largest improvement in potency. N(6)-Monosubstitution was superior to symmetrical N(6),N(6)-disubstitution. The most potent inhibitors were N(6)-(4-chlorobenzyl)- (10l, PSB-12441, Ki 7.23 nM), N(6)-phenylethyl- (10h, PSB-12425, Ki 8.04 nM), and N(6)-benzyl-adenosine-5'-O-[(phosphonomethyl)phosphonic acid] (10g, PSB-12379, Ki 9.03 nM). Replacement of the 6-NH group in 10g by O (10q, PSB-12431) or S (10r, PSB-12553) yielded equally potent inhibitors (10q, 9.20 nM; 10r, 9.50 nM). Selected compounds investigated at the human enzyme did not show species differences; they displayed high selectivity versus other ecto-nucleotidases and ADP-activated P2Y receptors. Moreover, high metabolic stability was observed. These compounds represent the most potent eN inhibitors described to date.
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Affiliation(s)
- Sanjay Bhattarai
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Marianne Freundlieb
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jan Pippel
- ‡Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, D-04103 Leipzig, Germany
| | - Anne Meyer
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Aliaa Abdelrahman
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Amelie Fiene
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Sang-Yong Lee
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Herbert Zimmermann
- §Institute of Cell Biology and Neuroscience, Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Gennady G Yegutkin
- ∥MediCity Research Laboratory, University of Turku, 20520 Turku, Finland
| | - Norbert Sträter
- ‡Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, D-04103 Leipzig, Germany
| | - Ali El-Tayeb
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Christa E Müller
- †PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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17
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Warminski M, Warminska Z, Kowalska J, Jemielity J. mRNA Cap Modification through Carbamate Chemistry: Synthesis of Amino- and Carboxy-Functionalised Cap Analogues Suitable for Labelling and Bioconjugation. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Baranowski MR, Nowicka A, Rydzik AM, Warminski M, Kasprzyk R, Wojtczak BA, Wojcik J, Claridge TDW, Kowalska J, Jemielity J. Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for ¹⁹F NMR studies. J Org Chem 2015; 80:3982-97. [PMID: 25816092 DOI: 10.1021/acs.joc.5b00337] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To broaden the scope of existing methods based on (19)F nucleotide labeling, we developed a new method for the synthesis of fluorophosphate (oligo)nucleotide analogues containing an O to F substitution at the terminal position of the (oligo)phosphate moiety and evaluated them as tools for (19)F NMR studies. Using three efficient and comprehensive synthetic approaches based on phosphorimidazolide chemistry and tetra-n-butylammonium fluoride, fluoromonophosphate, or fluorophosphate imidazolide as fluorine sources, we prepared over 30 fluorophosphate-containing nucleotides, varying in nucleobase type (A, G, C, U, m(7)G), phosphate chain length (from mono to tetra), and presence of additional phosphate modifications (thio, borano, imido, methylene). Using fluorophosphate imidazolide as fluorophosphorylating reagent for 5'-phosphorylated oligos we also synthesized oligonucleotide 5'-(2-fluorodiphosphates), which are potentially useful as (19)F NMR hybridization probes. The compounds were characterized by (19)F NMR and evaluated as (19)F NMR molecular probes. We found that fluorophosphate nucleotide analogues can be used to monitor activity of enzymes with various specificities and metal ion requirements, including human DcpS enzyme, a therapeutic target for spinal muscular atrophy. The compounds can also serve as reporter ligands for protein binding studies, as exemplified by studying interaction of fluorophosphate mRNA cap analogues with eukaryotic translation initiation factor (eIF4E).
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Affiliation(s)
- Marek R Baranowski
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Anna Nowicka
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,§Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Anna M Rydzik
- ‡Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Marcin Warminski
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Renata Kasprzyk
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Blazej A Wojtczak
- §Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Jacek Wojcik
- ∥Laboratory of Biological NMR, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Timothy D W Claridge
- ‡Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Joanna Kowalska
- †Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- §Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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19
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Thillier Y, Sallamand C, Baraguey C, Vasseur JJ, Debart F. Solid-Phase Synthesis of Oligonucleotide 5′-(α-P-Thio)triphosphates and 5′-(α-P-Thio)(β,γ-methylene)triphosphates. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Honcharenko M, Zytek M, Bestas B, Moreno P, Jemielity J, Darzynkiewicz E, Smith CIE, Strömberg R. Synthesis and evaluation of stability of m3G-CAP analogues in serum-supplemented medium and cytosolic extract. Bioorg Med Chem 2013; 21:7921-8. [PMID: 24184216 DOI: 10.1016/j.bmc.2013.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 02/02/2023]
Abstract
Increased efficiency in splice-correction (splice-switching) has been shown by use of a synthetic RNA 5'-end nuclear localization signal composed of an m3G-CAP. Use of the m3G-CAP as an NLS signal for therapeutic compounds in vivo is likely to require additional stability towards enzymatic degradation. For this reason introduction of stabilizing modifications into the triphosphate bridge may be beneficial. Here we report on synthesis of three m3G-CAP derivatives with a 'native' (m3GpppAOMe) as well as with a methylenephosphonate stabilized triphosphate bridge (m3GpCH2ppAOMe, m3GppCH2pAOMe) and the investigation of the enzymatic stability of these compounds in 10% (v/v) fetal bovine serum (FBS) and cytosolic extract from HeLa cells, thus mimicking in vivo conditions. Our results indicate that introduction of methylene group between the β and γ phosphates in m3GpCH2ppAOMe improves to some extent stability of this analogue in 10% serum but does not prolong life of this compound in the cytosolic extract. In contrast the stabilization introduced between α and β phosphates in m3GppCH2pAOMe offers threefold longer life in 10% serum and almost complete protection in cytosolic extract.
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Affiliation(s)
- Malgorzata Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-14183 Huddinge, Sweden.
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21
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Ziemniak M, Szabelski M, Lukaszewicz M, Nowicka A, Darzynkiewicz E, Rhoads RE, Wieczorek Z, Jemielity J. Synthesis and evaluation of fluorescent cap analogues for mRNA labelling. RSC Adv 2013; 3. [PMID: 24273643 DOI: 10.1039/c3ra42769b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We describe the synthesis and properties of five dinucleotide fluorescent cap analogues labelled at the ribose of the 7-methylguanosine moiety with either anthraniloyl (Ant) or N-methylanthraniloyl (Mant), which have been designed for the preparation of fluorescent mRNAs via transcription in vitro. Two of the analogues bear a methylene modification in the triphosphate bridge, providing resistance against either the Dcp2 or DcpS decapping enzymes. All these compounds were prepared by ZnCl2-mediated coupling of a nucleotide P-imidazolide with a fluorescently labelled mononucleotide. To evaluate the utility of these compounds for studying interactions with cap-binding proteins and cap-related cellular processes, both biological and spectroscopic features of those compounds were determined. The results indicate acceptable quantum yields of fluorescence, pH independence, environmental sensitivity, and photostability. The cap analogues are incorporated by RNA polymerase into mRNA transcripts that are efficiently translated in vitro. Transcripts containing fluorescent caps but unmodified in the triphosphate chain are hydrolysed by Dcp2 whereas those containing a α-β methylene modification are resistant. Model studies exploiting sensitivity of Mant to changes of local environment demonstrated utility of the synthesized compounds for studying cap-related proteins.
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Affiliation(s)
- Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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22
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Szczepaniak SA, Zuberek J, Darzynkiewicz E, Kufel J, Jemielity J. Affinity resins containing enzymatically resistant mRNA cap analogs--a new tool for the analysis of cap-binding proteins. RNA (NEW YORK, N.Y.) 2012; 18:1421-32. [PMID: 22589334 PMCID: PMC3383972 DOI: 10.1261/rna.032078.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/12/2012] [Indexed: 05/21/2023]
Abstract
Cap-binding proteins have been routinely isolated using m⁷GTP-Sepharose; however, this resin is inefficient for proteins such as DcpS (scavenger decapping enzyme), which interacts not only with the 7-methylguanosine, but also with the second cap base. In addition, DcpS purification may be hindered by the reduced resin capacity due to the ability of DcpS to hydrolyze m⁷GTP. Here, we report the synthesis of new affinity resins, m⁷GpCH₂pp- and m⁷GpCH₂ppA-Sepharoses, with attached cap analogs resistant to hydrolysis by DcpS. Biochemical tests showed that these matrices, as well as a hydrolyzable m⁷GpppA-Sepharose, bind recombinant mouse eIF4E²⁸⁻²¹⁷ specifically and at high capacity. In addition, purification of cap-binding proteins from yeast extracts confirmed the presence of all expected cap-binding proteins, including DcpS in the case of m⁷GpCH₂pp- and m⁷GpCH₂ppA-Sepharoses. In contrast, binding studies in vitro demonstrated that recombinant human DcpS efficiently bound only m⁷GpCH₂ppA-Sepharose. Our data prove the applicability of these novel resins, especially m⁷GpCH₂ppA-Sepharose, in biochemical studies such as the isolation and identification of cap-binding proteins from different organisms.
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Affiliation(s)
- Sylwia Anna Szczepaniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Corresponding authorsE-mail E-mail
| | - Jacek Jemielity
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Corresponding authorsE-mail E-mail
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23
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Rydzik AM, Kulis M, Lukaszewicz M, Kowalska J, Zuberek J, Darzynkiewicz ZM, Darzynkiewicz E, Jemielity J. Synthesis and properties of mRNA cap analogs containing imidodiphosphate moiety--fairly mimicking natural cap structure, yet resistant to enzymatic hydrolysis. Bioorg Med Chem 2012; 20:1699-710. [PMID: 22316555 DOI: 10.1016/j.bmc.2012.01.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 11/19/2022]
Abstract
We describe synthesis and properties of eight dinucleotide mRNA 5' cap analogs containing imidodiphosphate moiety within 5',5'-tri- or tetraphosphate bridge (NH-analogs). The compounds were obtained by coupling an appropriate nucleoside 5'-imidodiphosphate with nucleotide P-imidazolide mediated by divalent metal chloride in anhydrous DMF. To evaluate the novel compounds as tools for studying cap-dependent processes, we determined their binding affinities for eukaryotic translation initiation factor 4E, susceptibilities to decapping pyrophosphatase DcpS and, for non-hydrolysable analogs, binding affinities to this enzyme. The results indicate that the O to NH substitution in selected positions of oligophosphate bridge ensures resistance to enzymatic decapping and suggest that interactions of NH-analogs with cap binding proteins fairly mimic interactions of unmodified parent compounds. Finally, we identified NH-analogs as potent inhibitors of cap-dependent translation in cell free system, and evaluated their utility as reagents for obtaining 5' capped mRNAs in vitro to be rather moderate.
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Affiliation(s)
- Anna M Rydzik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, Warsaw, Poland
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24
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N⁴-[Alkyl-(hydroxyphosphono)phosphonate]-cytidine-new drugs covalently linking antimetabolites (5-FdU, araU or AZT) with bone-targeting bisphosphonates (alendronate or pamidronate). Bioorg Med Chem 2011; 19:3520-6. [PMID: 21536448 DOI: 10.1016/j.bmc.2011.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/09/2011] [Indexed: 11/23/2022]
Abstract
Amino-bisphosphonates (alendronate, pamidronate) were covalently linked in a three step synthesis, with protected and triazolylated derivatives of therapeutically used nucleoside analogs (5-FdU, araC, AZT) by substitution of their triazolyl residue. From the deprotected and chromatographically purified reaction mixtures N⁴-[alkyl-(hydroxyphosphono) phosphonate]-cytidine combining two differently cytotoxic functions were obtained. This new family of bisphosphonates (BPs) contains as novelty an alkyl side chain with a cytotoxic nucleoside. The BPs moiety allows for a high binding to hydroxyapatite which is a prerequisite for bone targeting of the drugs. In vitro binding of 5-FdU-alendronate (5-FdU-ale) to hydroxyapatite showed a sixfold increased binding of these BPs as compared to 5-FdU. Exploratory cytotoxic properties of 5-FdU-ale were tested on a panel of human tumor cell lines resulting in growth inhibition ranging between 5% and 38%. The determination of IC₅₀-concentrations of the conjugate in Lewis lung carcinoma and murine macrophages showed an incubation time dependent growth inhibition with higher sensitivity towards the tumor cells. We assume that the antimetabolite-BPs can be cleaved into different active metabolites that may exert cytotoxic and other therapeutic effects. However, the underlying mechanisms of these promising new antimetabolite-BPs conjugates remain to be evaluated in future experiments.
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25
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Jemielity J, Kowalska J, Rydzik AM, Darzynkiewicz E. Synthetic mRNA cap analogs with a modified triphosphate bridge – synthesis, applications and prospects. NEW J CHEM 2010. [DOI: 10.1039/c0nj00041h] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Rydzik AM, Lukaszewicz M, Zuberek J, Kowalska J, Darzynkiewicz ZM, Darzynkiewicz E, Jemielity J. Synthetic dinucleotide mRNA cap analogs with tetraphosphate 5',5' bridge containing methylenebis(phosphonate) modification. Org Biomol Chem 2009; 7:4763-76. [PMID: 19865714 DOI: 10.1039/b911347a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An effective and facile synthesis of six novel tetraphosphate cap analogs modified with a methylenebis(phosphonate) moiety (1-6) is presented. Analogs have been rationally designed to bind tightly to the eukaryotic initiation factor 4E (eIF4E) responsible for cap binding during the initiation of translation, and have increased stability owing to resistance to enzymatic degradation. Final compounds turned out to have significantly higher association constant values (K(AS)) for binding to eIF4E (5-9 fold higher than standard). Four of the analogs were resistant towards enzymatic degradation by human Decapping Scavenger enzyme (DcpS). Binding studies of non-hydrolyzable analogs with DcpS revealed a broad range of K(AS) values for different analogs. All of the analogs were potent inhibitors of translation in a rabbit reticulocyte lysate system (RRL) and those resistant to DcpS turned out to be stable under an elongated time of preincubation while the inhibitory potency of standard was diminished in these conditions. For Anti Reverse Cap Analog (ARCA) dinucleotides (4-6), we have shown that they are effectively incorporated into mRNA and transcripts capped with these analogs undergo translation in vitro.
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Affiliation(s)
- Anna Maria Rydzik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
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27
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Upton TG, Kashemirov BA, McKenna CE, Goodman MF, Prakash GKS, Kultyshev R, Batra VK, Shock DD, Pedersen LC, Beard WA, Wilson SH. Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Org Lett 2009; 11:1883-6. [PMID: 19351147 PMCID: PMC2722935 DOI: 10.1021/ol701755k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.
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Affiliation(s)
- Thomas G. Upton
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, California 90089
| | - Boris A. Kashemirov
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, California 90089
| | - Charles E. McKenna
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, California 90089
| | - Myron F. Goodman
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, California 90089
| | - G. K. Surya Prakash
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, California 90089
| | - Roman Kultyshev
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, California 90089
| | - Vinod K. Batra
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - David D. Shock
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - William A. Beard
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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Pankiewicz KW, Gao G, Patterson SE. Synthesis of methylenebis(phosphonate) analogs of dinucleotide pyrophosphates. ACTA ACUST UNITED AC 2008; Chapter 13:Unit 13.5. [PMID: 18428948 DOI: 10.1002/0471142700.nc1305s24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A facile method is described for preparation of nonsymmetrical P1,P2-methylenebis(phosphonate) diesters based on the 31P-NMR-controlled reaction of methylenebis(phosphonate) monoesters with diisopropylcarbodiimide, resulting in the formation of the intermediate P1,P4-disubstituted bicyclic trisanhydride. This intermediate, after treatment with an another nucleoside, carbohydrate, or alcohol followed by hydrolysis, is converted into the corresponding methylenebis(phosphonate) diester. An analog of a natural dinucleotide pyrophosphate can be obtained when a nucleoside 5'-methylenebis(phosphonate) is coupled with another nucleoside. This method is suitable for preparation of metabolically stable (resistant to phosphodiesterase cleavage) analogs of NAD, FAD, and related natural pyrophosphates. The resulting compounds are useful for mechanistic studies of enzymes that use the natural pyrophosphates as cofactors or substrates, and in development of inhibitors that have potential applications as therapeutic agents.
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29
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Ko H, Carter RL, Cosyn L, Petrelli R, de Castro S, Besada P, Zhou Y, Cappellacci L, Franchetti P, Grifantini M, Van Calenbergh S, Harden TK, Jacobson KA. Synthesis and potency of novel uracil nucleotides and derivatives as P2Y2 and P2Y6 receptor agonists. Bioorg Med Chem 2008; 16:6319-32. [PMID: 18514530 PMCID: PMC2483329 DOI: 10.1016/j.bmc.2008.05.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/02/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
Abstract
The phosphate, uracil, and ribose moieties of uracil nucleotides were varied structurally for evaluation of agonist activity at the human P2Y(2), P2Y(4), and P2Y(6) receptors. The 2-thio modification, found previously to enhance P2Y(2) receptor potency, could be combined with other favorable modifications to produce novel molecules that exhibit high potencies and receptor selectivities. Phosphonomethylene bridges introduced for stability in analogues of UDP, UTP, and uracil dinucleotides markedly reduced potency. Truncation of dinucleotide agonists of the P2Y(2) receptor, in the form of Up(4)-sugars, indicated that a terminal uracil ring is not essential for moderate potency at this receptor and that specific SAR patterns are observed at this distal end of the molecule. Key compounds reported in this study include 9, alpha,beta-methylene-UDP, a P2Y(6) receptor agonist; 30, Up(4)-phenyl ester and 34, Up(4)-[1]glucose, selective P2Y(2) receptor agonists; dihalomethylene phosphonate analogues 16 and 41, selective P2Y(2) receptor agonists; 43, the 2-thio analogue of INS37217 (P(1)-(uridine-5')-P(4)-(2'-deoxycytidine-5')tetraphosphate), a potent and selective P2Y(2) receptor agonist.
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Affiliation(s)
- Hyojin Ko
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA
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30
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Niedzwiecka A, Stepinski J, Antosiewicz JM, Darzynkiewicz E, Stolarski R. Biophysical approach to studies of cap-eIF4E interaction by synthetic cap analogs. Methods Enzymol 2008; 430:209-45. [PMID: 17913640 DOI: 10.1016/s0076-6879(07)30009-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Specific recognition of mRNA 5' cap by eukaryotic initiation factor eIF4E is a rate-limiting step in the translation initiation. Structural determination of the eIF4E-cap complexes, as well as complexes of eIF4E with other proteins regulating its activity, requires complementary experiments that allow for energetic and dynamic aspects of formation and stability of the complexes. Such a combined approach provides information on the binding mechanisms and, hence, may lead to mechanistic models of eIF4E functioning and regulation on the molecular level. This chapter summarizes in detail the method of experiments used to probe the cap-binding center of eIF4E, steady state and stopped-flow fluorescence, and microcalorimetry. The studies were performed with a wide class of synthetic, structurally modified cap analogs that resembles in some respect an application of site directed mutagenesis of the protein. The chapter presents a general recipe as to how to investigate protein-ligand interactions if the protein has no enzymatic activity and both the protein and the ligand absorb and emit UV/VIS radiation in the same spectral ranges.
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Affiliation(s)
- Anna Niedzwiecka
- Division of Biophysics, Institute of Experimental Physics, Warsaw University, Warszawa, Poland
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31
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Guranowski A, Starzyńska E, Pietrowska-Borek M, Jemielity J, Kowalska J, Darzynkiewicz E, Thompson MJ, Blackburn GM. Methylene analogues of adenosine 5'-tetraphosphate. Their chemical synthesis and recognition by human and plant mononucleoside tetraphosphatases and dinucleoside tetraphosphatases. FEBS J 2006; 273:829-38. [PMID: 16441668 DOI: 10.1111/j.1742-4658.2006.05115.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosine 5'-polyphosphates have been identified in vitro, as products of certain enzymatic reactions, and in vivo. Although the biological role of these compounds is not known, there exist highly specific hydrolases that degrade nucleoside 5'-polyphosphates into the corresponding nucleoside 5'-triphosphates. One approach to understanding the mechanism and function of these enzymes is through the use of specifically designed phosphonate analogues. We synthesized novel nucleotides: alpha,beta-methylene-adenosine 5'-tetraphosphate (pppCH2pA), beta,gamma-methylene-adenosine 5'-tetraphosphate (ppCH2ppA), gamma,delta-methylene-adenosine 5'-tetraphosphate (pCH2pppA), alphabeta,gammadelta-bismethylene-adenosine 5'-tetraphosphate (pCH2ppCH2pA), alphabeta, betagamma-bismethylene-adenosine 5'-tetraphosphate (ppCH2pCH2pA) and betagamma, gammadelta-bis(dichloro)methylene-adenosine 5'-tetraphosphate (pCCl2pCCl2ppA), and tested them as potential substrates and/or inhibitors of three specific nucleoside tetraphosphatases. In addition, we employed these p4A analogues with two asymmetrically and one symmetrically acting dinucleoside tetraphosphatases. Of the six analogues, only pppCH2pA is a substrate of the two nucleoside tetraphosphatases (EC 3.6.1.14), from yellow lupin seeds and human placenta, and also of the yeast exopolyphosphatase (EC 3.6.1.11). Surprisingly, none of the six analogues inhibited these p4A-hydrolysing enzymes. By contrast, the analogues strongly inhibit the (asymmetrical) dinucleoside tetraphosphatases (EC 3.6.1.17) from human and the narrow-leafed lupin. ppCH2ppA and pCH2pppA, inhibited the human enzyme with Ki values of 1.6 and 2.3 nm, respectively, and the lupin enzyme with Ki values of 30 and 34 nm, respectively. They are thereby identified as being the strongest inhibitors ever reported for the (asymmetrical) dinucleoside tetraphosphatases. The three analogues having two halo/methylene bridges are much less potent inhibitors for these enzymes. These novel nucleotides should prove valuable tools for further studies on the cellular functions of mono- and dinucleoside polyphosphates and on the enzymes involved in their metabolism.
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Affiliation(s)
- Andrzej Guranowski
- Department of Biochemistry and Biotechnology, Agricultural University, Poznań, Poland.
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32
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Kalek M, Jemielity J, Darzynkiewicz ZM, Bojarska E, Stepinski J, Stolarski R, Davis RE, Darzynkiewicz E. Enzymatically stable 5' mRNA cap analogs: synthesis and binding studies with human DcpS decapping enzyme. Bioorg Med Chem 2006; 14:3223-30. [PMID: 16431118 DOI: 10.1016/j.bmc.2005.12.045] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 12/14/2005] [Accepted: 12/20/2005] [Indexed: 11/17/2022]
Abstract
Four novel 5' mRNA cap analogs have been synthesized with one of the pyrophosphate bridge oxygen atoms of the triphosphate linkage replaced with a methylene group. The analogs were prepared via reaction of nucleoside phosphor/phosphon-1-imidazolidates with nucleoside phosphate/phosphonate in the presence of ZnCl2. Three of the new cap analogs are completely resistant to degradation by human DcpS, the enzyme responsible for hydrolysis of free cap resulting from 3' to 5' cellular mRNA decay. One of the new analogs has very high affinity for binding to human DcpS. Two of these analogs are Anti Reverse Cap Analogs which ensures that they are incorporated into mRNA chains exclusively in the correct orientation. These new cap analogs should be useful in a variety of biochemical studies, in the analysis of the cellular function of decapping enzymes, and as a basis for further development of modified cap analogs as potential anti-cancer and anti-parasite drugs.
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Affiliation(s)
- Marcin Kalek
- Department of Biophysics, Experimental Physics Institute, Warsaw University, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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