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Lago-Santomé H, Meana-Pañeda R, Alonso R. A Convergent Approach to the Dioxaadamantane Core of (±)-Tetrodotoxin. J Org Chem 2014; 79:4300-5. [DOI: 10.1021/jo500056w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo Lago-Santomé
- Departments of Organic Chemistry
and Physical Chemistry, University of Santiago de Compostela, Campus
Vida s/n, 15782 Santiago de Compostela, A Coruña, Spain
| | - Rubén Meana-Pañeda
- Departments of Organic Chemistry
and Physical Chemistry, University of Santiago de Compostela, Campus
Vida s/n, 15782 Santiago de Compostela, A Coruña, Spain
| | - Ricardo Alonso
- Departments of Organic Chemistry
and Physical Chemistry, University of Santiago de Compostela, Campus
Vida s/n, 15782 Santiago de Compostela, A Coruña, Spain
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2
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Šimák O, Pachl P, Fábry M, Buděšínský M, Jandušík T, Hnízda A, Skleničková R, Petrová M, Veverka V, Řezáčová P, Brynda J, Rosenberg I. Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-nucleotidases. Org Biomol Chem 2014; 12:7971-82. [DOI: 10.1039/c4ob01332h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-deoxynucleotidases.
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Affiliation(s)
- Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
- 14220 Prague 4, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Department of Chemistry of Natural Compounds
- Institute of Chemical Technology
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Radka Skleničková
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
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Králíková S, Buděšínský M, Barvík I, Masojídková M, Točík Z, Rosenberg I. Synthesis and properties of ApA analogues with shortened phosphonate internucleotide linkage. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:524-43. [PMID: 21888544 DOI: 10.1080/15257770.2011.581259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A complete series of the 2 '-5 ' and 3 '-5 ' regioisomeric types of r(ApA) and 2 '-d(ApA) analogues with the α-hydroxy-phosphonate C3 '-O-P-CH(OH)-C4 ″ internucleotide linkage, isopolar but non-isosteric with the phosphodiester one, were synthesized and their hybridization properties with polyU studied. Due to the chirality on the 5 '-carbon atom of the modified internucleotide linkage bearing phosphorus and hydroxy moieties, each regioisomeric type of ApA dimer is split into epimeric pairs. To examine the role of the 5 '-hydroxyl of the α-hydroxy-phosphonate moiety during hybridization, the appropriate r(ApA) analogues with 3 '(2 ')-O-P-CH(2)-C4 ″ linkage lacking the 5 '-hydroxyl were synthesized. Nuclear magnetic resonance (NMR) spectroscopy study on the conformation of the modified sugar-phosphate backbone, along with the hybridization measurements, revealed remarkable differences in the stability of complexes with polyU, depending on the 5 '-carbon atom configuration. Potential usefulness of the α-hydroxy-phosphonate linkage in modified oligoribonucleotides is discussed.
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Affiliation(s)
- Sárka Králíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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4
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Páv O, Panova N, Snášel J, Zborníková E, Rosenberg I. Activation of human RNase L by 2'- and 5'-O-methylphosphonate-modified oligoadenylates. Bioorg Med Chem Lett 2011; 22:181-5. [PMID: 22169265 DOI: 10.1016/j.bmcl.2011.11.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/08/2011] [Accepted: 11/10/2011] [Indexed: 10/15/2022]
Abstract
To determine the influence of internucleotide linkage and sugar ring conformation, and the role of 5'-terminal phosphate, on the activation of human RNase L, a series of 2'- and 5'-O-methylphosphonate-modified tetramers were synthesized from appropriate monomeric units and evaluated for their ability to activate human RNase L. Tetramers pAAAp(c)X modified by ribo, arabino or xylo 5'-phosphonate unit p(c)X activated RNase L with efficiency comparable to that of natural activator. Moreover, incorporation of phosphonate linkages ensured the stability against cleavage by nucleases. The substitution of 5'-terminal phosphate for 5'-terminal phosphonate in tetramer p(c)XAAA afforded tetramers with excellent activation efficiency and with complete stability against cleavage by phosphomonoesterases.
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Affiliation(s)
- Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
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Petrová M, Buděšínský M, Klepetářová B, Rosenberg I. 5′-Epimeric 3′-deoxy-3′,4′-didehydronucleoside-5′-C-phosphonates: synthesis and structural assignment by NMR and X-ray analyses. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.04.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Poláková I, Buděšínský M, Točík Z, Rosenberg I. Tetrofuranose nucleoside phosphonic acids: Synthesis and properties. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
New isoelectronic, non-isosteric phosphonate analogues of nucleoside 5′-phosphates featuring the phosphorus moiety directly attached on the sugar ring in the C4′ position are described. The analogues were synthesised by a nucleosidation reaction from tetrofuranosyl phosphonate synthons and silylated nucleobases. The pyrimidine compounds with erythro and threo configuration in both D- and L-series were prepared, and the structures were assigned by NMR spectroscopy. The results of NMR conformational studies show that all calculated conformers have a maximum pucker in the range typical for nucleosides. In all compounds, the S-type conformer is preferred and is more significant in α-D-threo-compounds. Studies on inhibition of thymidine phosphorylase revealed that one of the prepared phosphonic acids was a competitive inhibitor of the enzyme (Ki = 4 μM).
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Pressová M, Budesínský M, Kosiová I, Kopecký V, Cvacka J, Kasicka V, Simák O, Tocík Z, Rosenberg I. Oligomerization of adenosin-5'-O-ylmethylphosphonate, an isopolar AMP analogue: evaluation of the route to short oligoadenylates. Biopolymers 2010; 93:277-89. [PMID: 19844977 DOI: 10.1002/bip.21329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In an attempt to prepare a library of short oligoadenylate analogues featuring both the enzyme-stable internucleotide linkage and the 5'-O-methylphosphonate moiety and thus obtain a pool of potential RNase L agonists/antagonists, we studied the spontaneous polycondensation of the adenosin-5'-O-ylmethylphosphonic acid (p(c)A), an isopolar AMP analogue, and its imidazolide derivatives employing N,N'-dicyclohexylcarbodiimide under nonaqueous conditions and uranyl ions under aqueous conditions, respectively. The RP LC-MS analyses of the reaction mixtures per se, and those obtained after the periodate treatment, along with analyses and separations by capillary zone electrophoresis, allowed us to characterize major linear and cyclic oligoadenylates obtained. The structure of selected compounds was supported, after their isolation, by NMR spectroscopy. Ab initio calculation of the model structures simulating the AMP-imidazolide and p(c)A-imidazolide offered the explanation why the latter compound exerted, in contrast to AMP-imidazolide, a very low stability in aqueous solutions.
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Affiliation(s)
- Martina Pressová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, v. v. i., Flemingovo 2, 16610 Prague 6, Czech Republic
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8
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Structural diversity of nucleoside phosphonic acids as a key factor in the discovery of potent inhibitors of rat T-cell lymphoma thymidine phosphorylase. Bioorg Med Chem Lett 2010; 20:862-5. [DOI: 10.1016/j.bmcl.2009.12.081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 12/18/2009] [Accepted: 12/21/2009] [Indexed: 11/20/2022]
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9
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Páv O, Barvík I, Buděšínský M, Masojídková M, Rosenberg I. Ring Enlargement of Cyclic Acetals and Ketals: A Way to Seven-Membered Nucleoside Phostones. Org Lett 2007; 9:5469-72. [DOI: 10.1021/ol7023899] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Ivan Barvík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Milena Masojídková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
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Electrophile-promoted addition of hydroxymethylphosphonate to 4′,5′-didehydronucleosides: a way to novel isosteric analogues of 5′-nucleotides. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.03.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Králíková Š, Buděšínský M, Tomečková I, Rosenberg I. Oxidative cleavage of ribofuranose 5-(α-hydroxyphosphonates): a route to erythrofuranose-based nucleoside phosphonic acids. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.07.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Rinaldo-Matthis A, Rampazzo C, Balzarini J, Reichard P, Bianchi V, Nordlund P. Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors. Mol Pharmacol 2004; 65:860-7. [PMID: 15044615 DOI: 10.1124/mol.65.4.860] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Monophosphate nucleotidases are enzymes that dephosphorylate nucleotides to their corresponding nucleosides. They play potentially important roles in controlling the activation of nucleotide-based drugs targeted against viral infections or cancer cells. The human mitochondrial deoxyribonucleotidase (dNT-2) dephosphorylates thymidine and deoxyuridine monophosphates. We describe the high resolution structures of the dNT-2 enzyme in complex with two potent nucleoside phosphonate inhibitors, (S)-1-[2'-deoxy-3',5'-O-(1-phosphono) benzylidene-beta-d-threo-pentofuranosyl]thymine (DPB-T) at 1.6-A resolution and (+/-)-1-trans-(2-phosphonomethoxycyclopentyl)uracil (PMcP-U) at 1.4-A resolution. The mixed competitive inhibitor DPB-T and the competitive inhibitor PMcP-U both bind in the active site of dNT-2 but in distinctly different binding modes, explaining their different kinetics of inhibition. The pyrimidine part of the inhibitors binds with very similar hydrogen bond interactions to the protein but with their phosphonate moieties in different binding sites compared with each other and to the previously determined position of phosphate bound to dNT-2. Together, these phosphate/phosphonate binding sites describe what might constitute a functionally relevant phosphate entrance tunnel to the active site. The structures of the inhibitors in complex with dNT-2, being the first such complexes of any nucleotidase, might provide important information for the design of more specific inhibitors to control the activation of nucleotide-based drugs.
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Páv O, Budesínský M, Rosenberg I. Ribo-, xylo-, and arabino-configured adenine-based nucleoside phosphonates: synthesis of monomers for solid-phase oligonucleotide assembly. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1053-6. [PMID: 14565342 DOI: 10.1081/ncn-120022734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Adenine-based, regioisomeric nucleoside phosphonates with ribo, xylo and arabino configuration were synthesized in the protected form suitable for the phosphotriester-like, solid-phase synthesis of oligonucleotides. Phosphonate moiety was protected by 4-methoxy-1-oxido-2-picolyl group and the furanose hydroxyl by the dimethoxytrityl group.
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Affiliation(s)
- Ondrej Páv
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
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15
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Mazzon C, Rampazzo C, Scaini MC, Gallinaro L, Karlsson A, Meier C, Balzarini J, Reichard P, Bianchi V. Cytosolic and mitochondrial deoxyribonucleotidases: activity with substrate analogs, inhibitors and implications for therapy. Biochem Pharmacol 2003; 66:471-9. [PMID: 12907246 DOI: 10.1016/s0006-2952(03)00290-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nucleoside analogs act as prodrugs that must be converted to 5'-phosphates by intracellular kinases to become active in the treatment of viral and oncological diseases. Activation may be reversed by dephosphorylation if the 5'-phosphates are substrates for 5'-nucleotidases. Dephosphorylation by cytosolic enzymes decreases the efficacy of the analogs, whereas dephosphorylation by mitochondrial enzymes may decrease mitochondrial toxicity. Both effects may influence the outcome of therapy. We investigated the dephosphorylation of the 5'-phosphates of commonly used nucleoside analogs by two cytosolic (cN-II and dNT-1) and one mitochondrial (dNT-2) nucleotidase. Most uracil/thymine nucleotide analogs were dephosphorylated by all three human enzymes but cytosine-containing nucleotide analogs were inactive. Only cN-II showed some activity with the monophosphates of the two purine analogs 2-chloro-2'-deoxyadenosine and 9-beta-D-arabinosylguanine. We conclude that overproduction of any of the three 5'-nucleotidases cannot explain development of resistance against cytosine analogs but that overproduction of cN-II could lead to resistance against purine analogs. Of the tested analogs, only (E)-5-(2-bromovinyl)-2'-deoxyuridine was preferentially dephosphorylated by mitochondrial dNT-2. We propose that in future developments of analogs this aspect be considered in order to reduce mitochondrial toxicity. We tested inhibition of dNT-1 and dNT-2 by a large variety of synthetic metabolically stable nucleoside phosphonate analogs and found one (PMcP-U) that inhibited dNT-1 and dNT-2 competitively and a second (DPB-T) that inhibited dNT-2 by mixed inhibition. Both inhibitors are useful for specific 5'-nucleotidase assays and structural studies and may open up possibilities for therapy.
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Affiliation(s)
- Cristina Mazzon
- Department of Biology, University of Padova, 35131 Padova, Italy
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Králíková S, Masojídková M, Budĕsínský M, Rosenberg I. Study on reactivity and protection of the alpha-hydroxyphosphonate moiety in 5'-nucleotide analogues: formation of the 3'-O-P-C(OH)-C4' internucleotide linkage. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:329-47. [PMID: 12816391 DOI: 10.1081/ncn-120021432] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The recently described epimeric nucleosidyl-5'-C-phosphonates (alpha-hydroxyphosphonates) represent novel nucleotide analogues that can be incorporated into chimeric oligonucleotides by the phosphotriester condensation method. In order to prepare suitable protected monomer(s) we have studied condensation reaction between protected 2'-deoxythymidine and 2'-deoxythymidinyl-5'-C-phosphonate, both as model compounds, in dependence on the nature of the 5'-hydroxyl protecting group. We have found that the O-acetyl group is unstable in the presence of TPSCl or MSNT used as condensing agents for activation of the phosphorus moiety. This instability negatively influences the scope of the condensation process. On the other hand, introduction of the O-methoxycarbonyl group gave excellent results. The O-methoxycarbonyl group does not participate in the condensation process, and its quantitative introduction into the nucleotide analo gues is accomplished using a novel acylating agent, methoxycarbonyl tetrazole.
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Affiliation(s)
- Sárka Králíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
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Gallinaro L, Crovatto K, Rampazzo C, Pontarin G, Ferraro P, Milanesi E, Reichard P, Bianchi V. Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects. J Biol Chem 2002; 277:35080-7. [PMID: 12124385 DOI: 10.1074/jbc.m203755200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deoxynucleoside triphosphates (dNTPs) used for mitochondrial DNA replication are mainly formed by phosphorylation of deoxynucleosides imported into mitochondria from the cytosol. We earlier obtained evidence for a mitochondrial 5'-nucleotidase (dNT2) with a pronounced specificity for dUMP and dTMP and suggested that the enzyme protects mitochondrial DNA replication from excess dTTP. In humans, accumulation of dTTP causes a mitochondrial genetic disease. We now establish that dNT2 in vivo indeed is located in mitochondria. The native enzyme shows the same substrate specificity and affinity for inhibitors as the recombinant dNT2. We constructed ponasterone-inducible cell lines overproducing dNT2 with and without the green fluorescent protein (GFP) linked to its C terminus. The fusion protein occurred in mitochondria mostly in an inactive truncated form, with only a short C-terminal fragment of dNT2 linked to GFP. No truncation occurred when dNT2 and GFP were not linked. The cell mitochondria then contained a large excess of active dNT2 with or without the mitochondrial presequence. After removal of ponasterone overproduced dNT2 disappeared only slowly from the cells, whereas dNT2-mRNA was lost rapidly. Overproduction of dNT2 did not lead to an increased excretion of pyrimidine deoxyribonucleosides, in contrast to overproduction of the corresponding cytosolic deoxynucleotidase, suggesting that the mitochondrial enzyme does not affect overall cellular deoxynucleotide turnover.
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Affiliation(s)
- Lisa Gallinaro
- Department of Biology, University of Padova, I-35131 Padova, Italy
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Generation of dialkyl phosphonodithioyl radicals and their addition onto alkenes. Synthesis of 3-phosphonodithiomethyl-3-deoxofuranosides. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01830-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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