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Kopina BJ, Missoury S, Collinet B, Fulton MG, Cirio C, van Tilbeurgh H, Lauhon CT. Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli. Nucleic Acids Res 2021; 49:2141-2160. [PMID: 33524148 PMCID: PMC7913687 DOI: 10.1093/nar/gkab026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/14/2022] Open
Abstract
The tRNA modification N6-threonylcarbamoyladenosine (t6A) is universally conserved in all organisms. In bacteria, the biosynthesis of t6A requires four proteins (TsaBCDE) that catalyze the formation of t6A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP). While the formation and stability of this intermediate has been studied in detail, the mechanism of its transfer to A37 in tRNA is poorly understood. To investigate this step, the structure of the TsaBD heterodimer from Escherichia coli has been solved bound to a stable phosphonate isosteric mimic of TC-AMP. The phosphonate inhibits t6A synthesis in vitro with an IC50 value of 1.3 μM in the presence of millimolar ATP and L-threonine. The inhibitor binds to TsaBD by coordination to the active site Zn atom via an oxygen atom from both the phosphonate and the carboxylate moieties. The bound conformation of the inhibitor suggests that the catalysis exploits a putative oxyanion hole created by a conserved active site loop of TsaD and that the metal essentially serves as a binding scaffold for the intermediate. The phosphonate bound crystal structure should be useful for the rational design of potent, drug-like small molecule inhibitors as mechanistic probes or potentially novel antibiotics.
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Affiliation(s)
- Brett J Kopina
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Sophia Missoury
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Bruno Collinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne-Université, UMR7590 CNRS, MNHN, Paris, France
| | - Mark G Fulton
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Charles Cirio
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Charles T Lauhon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
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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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Pierrat P, Laverny G, Creusat G, Wehrung P, Strub JM, VanDorsselaer A, Pons F, Zuber G, Lebeau L. Phospholipid-Detergent Conjugates as Novel Tools for siRNA Delivery. Chemistry 2013; 19:2344-55. [DOI: 10.1002/chem.201203071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Indexed: 12/23/2022]
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Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA. Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc Natl Acad Sci U S A 2010; 107:15693-8. [PMID: 20724659 PMCID: PMC2936638 DOI: 10.1073/pnas.1007430107] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is difficult to overestimate the importance of nucleoside triphosphates in cellular chemistry: They are the building blocks for DNA and RNA and important sources of energy. Modifications of biologically important organic molecules with fluorine are of great interest to chemists and biologists because the size and electronegativity of the fluorine atom can be used to make defined structural alterations to biologically important molecules. Although the concept of nonhydrolyzable nucleotides has been around for some time, the progress in the area of modified triphosphates was limited by the lack of synthetic methods allowing to access bisCF(2)-substituted nucleotide analogs-one of the most interesting classes of nonhydrolyzable nucleotides. These compounds have "correct" polarity and the smallest possible steric perturbation compared to natural nucleotides. No other known nucleotides have these advantages, making bisCF(2)-substituted analogs unique. Herein, we report a concise route for the preparation of hitherto unknown highly acidic and polybasic bis(difluoromethylene)triphosphoric acid 1 using a phosphorous(III)/phosphorous(V) interconversion approach. The analog 1 compared to triphosphoric acid is enzymatically nonhydrolyzable due to substitution of two bridging oxygen atoms with CF(2) groups, maintaining minimal perturbations in steric bulkiness and overall polarity of the triphosphate polyanion. The fluorinated triphosphoric acid 1 was used for the preparation of the corresponding fluorinated deoxynucleotides (dNTPs). One of these dNTP analogs (dT) was demonstrated to fit into DNA polymerase beta (DNA pol beta) binding pocket by obtaining a 2.5 A resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate/Mg(2+) interaction over Watson-Crick hydrogen bonding was found and discussed.
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Affiliation(s)
- G. K. Surya Prakash
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Mikhail Zibinsky
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Thomas G. Upton
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Boris A. Kashemirov
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Charles E. McKenna
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Keriann Oertell
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Myron F. Goodman
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Vinod K. Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - David D. Shock
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - George A. Olah
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
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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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Johnson DC, Widlanski TS. Overview of the synthesis of nucleoside phosphates and polyphosphates. ACTA ACUST UNITED AC 2008; Chapter 13:Unit 13.1. [PMID: 18428921 DOI: 10.1002/0471142700.nc1301s15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This overview summarizes methodology used for the synthesis of nucleoside mono-, di-, and triphosphates. Selected techniques such as the Mitsunobu reaction, displacement reactions involving nucleoside 5'-tosylates, "anion-exchange" techniques, and phosphoramidite and phosphoramidate methodologies are highlighted. The chemistry of phosphorylation is detailed with respect to advantages and limitations under various conditions. Applicability of the methods toward the synthesis of analogs such as imidophosphates, phosphorothioates, and radiolabeled nucleotides is also addressed.
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Taylor SD, Mirzaei F, Bearne SL. Bismethylene triphosphate nucleotides of uridine 4-phosphate analogues: a new class of anionic pyrimidine nucleotide analogues. J Org Chem 2008; 73:1403-12. [PMID: 18215061 DOI: 10.1021/jo702249j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytidine-5'-triphosphate synthase (CTPS) catalyzes the formation of cytidine triphosphate (CTP) from glutamine, uridine 5'-triphosphate (UTP), and adenosine 5'-triphosphate (ATP). This reaction proceeds via formation of the high-energy intermediate UTP-4-phosphate (UTP-4-P). Stable analogues of UTP-4-P may be potent inhibitors of CTPS and useful as lead structures for the development of anticancer and antiviral agents. Several bismethylene triphosphate (BMT) nucleotides of uridine 4-phosphate (U-4-P) analogues have been prepared. A key step was the selective methanolysis, with the aid of a tin catalyst, of the 5' ester moiety of 2',3',5'-tri-O-acetyl or tri-O-benzoyl U-4-P analogues. We believe this represents the first general approach to the selective cleavage of 5' benzoyl esters in benzoylated nucleosides. Mitsunobu coupling of these 5'-deprotected U-4-P analogues to an unsymmetrical, protected BMT bearing a free phosphonic acid moiety at one of the terminal positions gave fully protected BMT-U-4-P analogues. Global deprotection of these species was achieved using TMSBr followed by treatment with NH4OH-MeOH or NH4OH-pyridine. The resulting BMT nucleotides represent a new class of anionic pyrimidine nucleotide analogues.
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Affiliation(s)
- Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada.
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Khaled A, Piotrowska O, Dominiak K, Augé C. Exploring specificity of glycosyltransferases: synthesis of new sugar nucleotide related molecules as putative donor substrates. Carbohydr Res 2007; 343:167-78. [PMID: 18048019 DOI: 10.1016/j.carres.2007.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 10/23/2007] [Accepted: 11/07/2007] [Indexed: 11/26/2022]
Abstract
We investigated the specificity of glycosyltransferases toward donor substrates in two complementary directions. First we prepared simple N-acetyl-alpha-D-glucosamine 1-diphosphates: methyl-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-diphosphate, benzyl-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-diphosphate, 4-phenylbutyl-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-diphosphate, by the coupling of the corresponding activated alkyl phosphates with N-acetyl-alpha-D-glucosamine 1-phosphate. These diphosphates as well as 2-acetamido-2-deoxy-alpha-D-glucopyranose 1-diphosphate, tested as donors of N-acetylglucosamine in a reaction catalyzed by Neisseria meningitidis N-acetylglucosaminyltransferase (LgtA), proved to be devoid of activity. Evaluated as inhibitors, only 2-acetamido-2-deoxy-alpha-D-glucopyranose 1-diphosphate showed some inhibitory activity with an IC50 value of 7 mM. In the second approach, we prepared sugar nucleotide mimics having the diphosphate bridge replaced by the oxycarbonylaminosulfonyl linker. The surrogate of GDP-Fuc was synthesized as a 9:1 alpha/beta anomeric mixture, in 40% yield, starting from chlorosulfonyl isocyanate, perbenzylated l-fucopyranose, and a guanosine derivative, protected on the exocyclic amine and secondary hydroxyl functions of ribose. Then two deprotection steps, hydrogenolysis and enzymatic hydrolysis catalyzed by penicillin G amidase afforded the target molecule to be tested as fucose donor with recombinant human alpha-(1-->3/4)-fucosyltransferase (FucT-III). Tested as a 4:1 alpha/beta anomeric mixture, both in the absence and in the presence of cationic cofactors, this new guanosine fucose conjugate proved to be ineffective. Its inhibitory activity toward FucT-III evaluated through a competition fluorescence assay was very poor (IC50 value of 20 mM). The surrogate of UDP-GlcNAc that was already known as its protected acetylated derivative, tested as N-acetylglucosamine donor with LgtA in the presence of Mn(2+) turned out not to be active either.
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Affiliation(s)
- Amira Khaled
- Glycochimie Moléculaire et Macromoléculaire, Laboratoire de Chimie Organique Multifonctionnelle, UMR 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Bâtiment 420, Univ Paris-Sud, F-91405 Orsay, France
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10
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Taylor SD, Mirzaei F, Bearne SL. An unsymmetrical approach to the synthesis of bismethylene triphosphate analogues. Org Lett 2007; 8:4243-6. [PMID: 16956197 DOI: 10.1021/ol0615432] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A protected, unsymmetrical bismethylene triphosphate analogue was prepared by sequential Michaelis-Arbuzov reactions on ethyl bis(halomethyl)phosphinates. This species was monodeprotected at one of the terminal phosphonate groups in high yield. The resulting monodeprotected compound was used to achieve the first syntheses of the bismethylene triphosphate analogues of UTP and CTP.
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Affiliation(s)
- Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1.
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Ashton TD, Scammells PJ. An expedient synthesis of N6-substituted-5′-modified adenosines. Bioorg Med Chem Lett 2006; 16:4564-6. [PMID: 16793263 DOI: 10.1016/j.bmcl.2006.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 05/18/2006] [Accepted: 06/06/2006] [Indexed: 11/15/2022]
Abstract
Herein we report a short and efficient synthesis of N(6)-substituted 5'-modified adenosines, which was achieved in four steps from 2',3',5'-tris-O-(tert-butyldimethylsilyl)inosine.
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Affiliation(s)
- T D Ashton
- Department of Medicinal Chemistry, Victorian College of Pharmacy, Monash University, Parkville, Vic., Australia
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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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