Synthesis and properties of mRNA cap analogs containing imidodiphosphate moiety—fairly mimicking natural cap structure, yet resistant to enzymatic hydrolysis

Rydzik, Anna M.; Kulis, Marta; Łukaszewicz, Maciej; Kowalska, Joanna; Zuberek, Joanna; Darżynkiewicz, Zbigniew; Darżynkiewicz, Edward; Jemielity, Jacek

doi:10.1016/j.bmc.2012.01.013

Cited by 52 publications

(65 citation statements)

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“…Our data suggest that 12b competes for the active site of Dcp2 and may act as a tightly bound mimic of the 5 ′ cap, paving the way for future structural studies and the development of potent, selective inhibitors of Dcp2. Observations made during our initial screening of the synthetic nucleotide library for Dcp2 inhibition are consistent with earlier reports concerning the influences of structural alterations of nucleotide phosphate chains on cap-protein interactions (Kowalska et al 2008(Kowalska et al , 2014Rydzik et al 2012). We find that the introduction of charge-retaining nonbridging modifications (S − , BH 3 − ) into cap analogs seemed to generally have higher impact on Dcp2 decapping activity than the bridging (CH 2 and NH) modifications.…”

Section: Discussionsupporting

confidence: 90%

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Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex

Ziemniak

Mugridge

Kowalska

et al. 2016

RNA

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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 Gp S ppp S m 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 Gp S ppp S m 7 G is a mixed inhibitor that competes for the Dcp2 active site with micromolar affinity. m 7 Gp S ppp S m 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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Section: Discussionsupporting

confidence: 90%

“…1) were synthesized as previously described: compound 2 (Kalek et al 2005), compound 3 (Rydzik et al 2012), compounds 4a, 4b (Strenkowska et al 2012), compound 5 (Baranowski et al 2015), compounds 9-11, 12-15 (Ziemniak et al 2015, compounds 1, 6, 16, 17 (Jemielity et al 2003).…”

Section: Compound Librarymentioning

confidence: 99%

Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex

Ziemniak

Mugridge

Kowalska

et al. 2016

RNA

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“…Such an approach provides a relatively simple way to obtain a wide scope of chemically modified oligophosphate mono-and diesters (Fig. 7), including phosphorothioates [79][80][81], seleno- [82], borano- [83], and fluorophosphates [84], as well as phosphoramidates [85], C-phosphonates [86], and bisphosphonates [87]. P-imidazolides were shown to react readily with other inorganic nucleophiles such as fluorides [84] and sulfates [88] to yield fluorophosphates and phosphosulfates, respectively.…”

Section: Synthesis Of Rna Caps: P-imidazolides and MCL 2 -Mediated Comentioning

confidence: 99%

Applications of Phosphate Modification and Labeling to Study (m)RNA Caps

Warmiński

Sikorski

Kowalska

et al. 2017

Phosphate Labeling and Sensing in Chemical Biology

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The cap is a natural modification present at the 5 0 ends of eukaryotic messenger RNA (mRNA), which because of its unique structural features, mediates essential biological functions during the process of gene expression. The core structural feature of the mRNA cap is an N7-methylguanosine moiety linked by a 5 0 -5 0 triphosphate chain to the first transcribed nucleotide. Interestingly, other RNA 5 0 end modifications structurally and functionally resembling the m 7 G cap have been discovered in different RNA types and in different organisms. All these structures contain the 'inverted' 5 0 -5 0 oligophosphate bridge, which is necessary for interaction with specific proteins and also serves as a cleavage site for phosphohydrolases regulating RNA turnover. Therefore, cap analogs containing oligophosphate chain modifications or carrying spectroscopic labels attached to phosphate moieties serve as attractive molecular tools for studies on RNA metabolism and modification of natural RNA properties. Here, we review chemical, enzymatic, and chemoenzymatic approaches that enable preparation of modified cap structures and RNAs carrying such structures, with emphasis on phosphate-modified mRNA cap analogs and their potential applications.M. Warminski and P. J. Sikorski have contributed equally to this work.

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“…5, 6 We have recently shown that some chemical modifications of the oligophosphate chain within the cap structure can increase the affinity to eIF4E and confer resistance towards DcpS. 1,[7][8][9] For instance, replacement of one of the c-oxygens in m 7 Gp c p b p a G or a-oxygens in m 7 GTP with either BH 3 or S generally stabilises the complex with eIF4E 10,11 and significantly decreases susceptibility to hydrolysis by DcpS. Inhibition studies in RRL (Rabbit Reticulocyte Lysate) have shown that a combination of these two features results in compounds that are potent and stable inhibitors of cap-dependent translation.…”

Section: Introductionmentioning

confidence: 99%

“…15 One example could be m 2 7,2 0 -O Gpp S pG, which provides considerable improvement in both stability and translational yield of mRNA; hence, it has been applied in gene therapy against cancer. 16 Although previously synthesised compounds have been shown to be resistant to cap-specific degradation, 1,7,[9][10][11]17,18 field for improvement, for example, by protection against chemical degradation or unspecific enzymatic degradation by cellular or extracellular pyrophosphatases. To verify whether the biological properties of cap analogues can be further modulated, here, we synthesised and characterised a set of cap analogues 1-9 based on m 7 GTP and m 7 Gppppm 7 G structures, which were extensively modified within the oligophosphate bridge (Fig.…”

Section: Introductionmentioning

confidence: 99%

Phosphate-modified analogues of m 7 GTP and m 7 Gppppm 7 G—Synthesis and biochemical properties

Ziemniak

Kowalska

Łukaszewicz

et al. 2015

Bioorganic & Medicinal Chemistry

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Synthesis and properties of mRNA cap analogs containing imidodiphosphate moiety—fairly mimicking natural cap structure, yet resistant to enzymatic hydrolysis

Cited by 52 publications

References 50 publications

Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex

Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex

Applications of Phosphate Modification and Labeling to Study (m)RNA Caps

Phosphate-modified analogues of m 7 GTP and m 7 Gppppm 7 G—Synthesis and biochemical properties

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