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Poznanski J, Bretner M, Kulikowski T, Balzarini J, Van Aerschot A, De Clercq E. Synthesis, Solution Conformation and Anti-HIV Activity of Novel 3-Substituted-2′,3′-Dideoxy-5-Hydroxymethyl-Uridines and Their 4,5-Substituted Analogues. ACTA ACUST UNITED AC 2016; 14:127-38. [PMID: 14521329 DOI: 10.1177/095632020301400302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To decrease the toxicity of potent anti-HIV nucleosides 3-azido-2′,3′-dideoxythymidine (AZT) and 2,3′-dideoxy-3′-fluorothymidine (3-FddThd, FLT), their new analogues, 3-azido-2′,3′-dideoxy-5-hydroxymethyluridine (3-Az5HmddUrd) and 2,3′-dideoxy-3′-fluoro-5-hydroxymethyluridine (3′-F5HmddUrd), were synthesized. The reaction of 3′-azido-2′,3′-dideoxyuridine (3′-AzddUrd) and 2,3′-dideoxy-3′-fluorouridine (3′-FddUrd) with formaldehyde, under strongly alkaline conditions and at elevated temperature, proceeded after 4 days to completion to afford the corresponding 5-hydroxymethyl derivatives 3′-Az5HmddUrd and 3′-F5HmddUrd in good yield. These compounds were also prepared by oxidation of AZT and FLT with the use of K2S2O8. 1H NMR analyses were subjected to the series of 3′,4 and 5-substituted pyrimidine 2′-deoxy- and 2′,3′-dideoxynucleosides involving 3′-Az5HmddUrd and 3′-F5HmddUrd. Analysis of the sugar furanose ring puckering demonstrated that all 3′-fluorine derivatives exhibited strong domination of the S conformation (∼100%) while 3-substitution by electron-donating groups, such as NH2, increased population of the N conformation. Experimentally observed substituent effect on the furanose ring puckering equilibrium was reconstructed in the 100 ps molecular dynamic trajectories obtained for AZT, FLT, dThd, 2′,3′-ddThd and 3′-amino-2′,3′-ddThd. It may be concluded that anti-HIV activity is linked to a direct interaction of the 3′-sub-stituent with reverse transcriptase (RT) binding site. Anti-HIV activities of 3′-Az5HmddUrd and 3′-F5HmddUrd are lower than activity of AZT and FLT; however, 3′-Az5HmddUrd and 3′-F5HmddUrd are less toxic than AZT and FLT.
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Affiliation(s)
- Jaroslaw Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Cadet J, Decarroz C, Wang SY, Midden WR. Mechanisms and Products of Photosensitized Degradation of Nucleic Acids and Related Model Compounds. Isr J Chem 2013. [DOI: 10.1002/ijch.198300061] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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3
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a-Anilinoketones, Esters and Amides: A Chemical Study. Pharmaceuticals (Basel) 2012; 5:591-612. [PMID: 24281663 PMCID: PMC3763659 DOI: 10.3390/ph5060591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/17/2022] Open
Abstract
A group of α-anilinoketones, 2-aminoalcohols, α-anilinoesters and α-anilinoamides were successfully synthesized and characterized by NMR spectroscopy and mass spectrometry. The yields were, in general, moderate to good (up to 75.4%), except for the α-anilinoesters (16.9–35.6%). The α-halocarbonyl starting materials showed different chemical reactivities. α-Haloketones and α-chloroacetates afforded monoalkylation, while small α-chloroamides afforded dialkylation. Finally, NMR spectroscopy revealed interesting structural features about the 2-aminoalcohols and diphenylamides.
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Crean C, Geacintov NE, Shafirovich V. Intrastrand G-U cross-links generated by the oxidation of guanine in 5'-d(GCU) and 5'-r(GCU). Free Radic Biol Med 2008; 45:1125-34. [PMID: 18692567 PMCID: PMC2577587 DOI: 10.1016/j.freeradbiomed.2008.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 07/10/2008] [Accepted: 07/10/2008] [Indexed: 12/18/2022]
Abstract
It has been suggested that carbonate radical anions are biologically important because they may be produced during the inflammatory response. The carbonate radicals can selectively oxidize guanine in DNA and RNA by one-electron transfer mechanisms and the guanine radicals thus formed decay by diverse competing pathways with other free radicals or nucleophiles. Using a photochemical method to generate CO(3)(-) radicals in vitro, we compare the distributions of products initiated by the one-electron oxidation of guanine in the trinucleotides 5'-r(GpCpU) and 5'-d(GpCpU) in aqueous buffer solutions (pH 7.5). Similar distributions of stable end products identified by LC-MS/MS methods were found in both cases. The guanine oxidation products include the diastereomeric pair of spiroiminodihydantoin (Sp) and 2,5-diamino-4H-imidazolone (Iz). In addition, intrastrand cross-linked products involving covalent bonds between the G and the U bases (GCU) were also found, although with different relative yields in the 2'-deoxy- and the ribotrinucleotides. The positive-ion MS/MS spectra of the 5'-r(GpCpU) and 5'-d(GpCpU) products clearly indicate the presence of covalently linked G-U products that have a mass smaller by 2 Da than the sum of the G and U bases in both types of trinucleotides. The 5'-d(GCU) cross-linked product was further characterized by 1D and 2D NMR methods that confirm its cyclic structure in which the guanine C8 atom is covalently linked to the uracil N3 atom.
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Affiliation(s)
| | | | - Vladimir Shafirovich
- Corresponding author. Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA. Tel: + 1 212 998 8456; Fax: + 1 212 998 8421, E-mail address: (V. Shafirovich)
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Buchko GW, Cadet J. Identification of the alpha and beta anomers of 1-(2-deoxy-D-erythro-pentofuranosyl)-oxaluric acid at the site of riboflavin-mediated photooxidation of guanine in 2'-deoxyguanosine and thymidylyl-(3'-5')-2'-deoxyguanosine. Photochem Photobiol 2006; 82:191-9. [PMID: 16489851 DOI: 10.1562/2005-06-01-ra-562] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Products of riboflavin-mediated photosensitization of 2'-deoxyguanosine (dG) and thymidylyl-(3'-5')-2'-deoxyguanosine (TpdG) by 350-nm light in oxygen-saturated aqueous solution have been isolated and identified as 1-(2-deoxy-beta-D-erythro-pentofuranosyl) oxaluric acid (beta-dOx) and thymidylyl-(3'-5')-1-(2-deoxy-beta-D-erythro-pentofuranosyl) oxaluric acid (Tpbeta-dOx), respectively. In aqueous solution the modified beta-deoxyribonucleoside is slowly converted to the alpha-anomer, generating alpha-dOx and Tpalpha-dOx. These modified nucleosides and dinucleoside monophosphates have been isolated by HPLC and characterized by proton and carbon NMR spectroscopy, fast atom bombardment mass spectrometry, and enzymatic analyses. Both alpha-dOx and Tpalpha-dOx slowly convert back into the modified beta-deoxyribonucleoside, indicating that the furanosidic anomers are in dynamic equilibrium. Relative to TpdG, the rate of hydrolysis of Tpbeta-dOx and Tpalpha-dOx by spleen phosphodiesterase is greatly reduced. Hot piperidine (1.0 M, 90 degrees C, 30 min) destroys Tpbeta-dOx and Tpalpha-dOx. Riboflavin-mediated photosensitization of TpdG in D2O instead of H2O has no detectable effect on the yield of Tpbeta-dOx, suggesting that oxaluric acid is generated through a Type-I reaction mechanism, likely through the intermediary on initially generated 8-oxo-7,8-dihydro-2'-deoxyguanosine.
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Affiliation(s)
- Garry W Buchko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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Gimisis T, Cismaş C. Isolation, Characterization, and Independent Synthesis of Guanine Oxidation Products. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500581] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thanasis Gimisis
- Department of Chemistry, University of Athens, Panepistimiopolis, 15771 Athens, Greece
| | - Crina Cismaş
- Department of Chemistry, University of Athens, Panepistimiopolis, 15771 Athens, Greece
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Rivière J, Klarskov K, Wagner JR. Oxidation of 5-hydroxypyrimidine nucleosides to 5-hydroxyhydantoin and its alpha-hydroxy-ketone isomer. Chem Res Toxicol 2005; 18:1332-8. [PMID: 16097807 DOI: 10.1021/tx050121i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of hydroxyl radicals with 2'-deoxycytidine (dCyd), as well as the decomposition of dCyd radical cations, leads to a complex mixture of oxidation products in aqueous aerated solutions. The oxidation of dCyd gives products with a relatively low oxidation potential that are highly susceptible to further oxidation, including 5-hydroxy-2'-deoxycytidine (5-oh-dCyd) and 5-hydroxy-2'-deoxyuridine (5-oh-dUrd). Previously, we showed that the oxidation of 2'-deoxyuridine (dUrd) involves the formation of dialuric acid and isodialuric acid intermediates, followed by ring contraction to N1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-hydroxyhydantoin (5-oh-dHyd). In this work, we have examined the oxidation of 5-oh-dCyd and 5-oh-dUrd in greater detail. The oxidation of these substrates by Br2 led to a similar profile of intermediate and stable products indicating that the dialuric and isodialuric acid derivatives of dCyd largely undergo deamination before they transform into 5-oh-dHyd. Analysis of the final mixture of oxidation products by HPLC revealed the formation of two novel products. On the basis of NMR and MS, these products were identified as the diastereomers of N1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-hydroxyimidazolidine-2,5-dione (iso-4-oh-dHyd). These products arise from alpha-hydroxy-ketone isomerization of 5-oh-dHyd. The isomerization of 5-oh-dHyd to iso-4-oh-dHyd was reversible, and each diastereomer produced a specific diastereomer of the other structural isomer. The rate of isomerization was accelerated in going from pH 5 to pH 9, whereas all isomers decomposed at higher pH. In contrast, interconversion between each pair of diastereomers was minor. Thus, we conclude that the oxidation of 5-oh-dCyd or 5-oh-dUrd gives a mixture of four isomers of 5-oh-dHyd and iso-4-oh-dHyd as final products. The biological consequences of dCyd oxidation may ultimately depend on the effects of these products.
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Affiliation(s)
- Johann Rivière
- Group in the Radiation Sciences and Mass Spectrometry Laboratory, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Douki T, Vadesne-Bauer G, Cadet J. Formation of a methide derivative upon photolysis of thymidine bromohydrins. J Org Chem 2003; 68:478-82. [PMID: 12530874 DOI: 10.1021/jo026606i] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reaction of bromine with thymidine in aqueous solution produces, in high yield, the corresponding 5-bromo-6-hydroxy-5,6-dihydroderivative (thymidine bromohydrins). UVC photolysis of thymidine bromohydrins gives rise to a reactive intermediate that is converted into 5-(hydroxymethyl)-2'-deoxyuridine upon incubation in water. When the former compound is left in methanol, ethanol, or propanol, the corresponding 5-alkoxymethyl derivatives are produced. The proposed structure for the primary photolysis product of thymidine bromohydrins is a methide derivative of the thymine ring. This compound could be an interesting intermediate in the synthesis of methyl-substituted thymidine.
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Affiliation(s)
- Thierry Douki
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR 5046, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, France.
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Poznański J, Felczak K, Bretner M, Kulikowski T, Remin M. 1H NMR Conformational Study of a Variety of α-Anomers of C5-Substituted 2′-Deoxyuridines: Comparison to Their Antiherpetic β Counterparts. Biochem Biophys Res Commun 2001; 283:1142-9. [PMID: 11355892 DOI: 10.1006/bbrc.2001.4921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although alpha-nucleosides are not found in nucleic acid, they do occur as constituents of smaller molecules in living cells, e.g., in vitamin B(12). There are now several examples of alpha-nucleosides exerting a biological activity in some instances equal to, or even exceeding, that of the corresponding beta-anomer. Examples include growth inhibitory properties against mouse leukemia cells and antitumor activity. From stereochemical point of view, alpha-anomers serve as references for studying of interaction of the base with the sugar moiety in beta-anomers and may help in better understanding of structure-activity relationships. One important problem preventing conformational analysis of alpha nucleosides is uncertainty in the determination of vicinal coupling constants from simulation of overlapping sugar proton resonances of strongly coupled spin systems. A successful resolution of near-isochronous H3' and H4' resonances made possible a full conformational analysis for a series of alpha-anomers C5-substituted 2'-deoxyuridines, including methyl, ethyl, isopropyl, fluor, vinyl, and bromovinyl, in comparison to their beta counterparts. Conformation of the sugar ring is determined from proton-proton coupling constants and described in terms of pseudorotation between two main puckering domains C2'endo (S) and C3'endo (N). A thorough analysis of chemical shifts as well as conformation of the sugar ring and C4'-C5' rotamers made possible determination of conformational preferences in equilibrium about the glycosidic bond between two regions, anti and syn. This work provides insights into the role of anomeric configuration of the base in conformational behavior of the sugar moiety, a link in the backbone of nucleic acids.
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Affiliation(s)
- J Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, Warsaw, 02-106, Poland
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Poznański J, Felczak K, Kulikowski T, Remin M. 1H NMR conformational study of antiherpetic C5-substituted 2'-deoxyuridines: insight into the nature of structure-activity relationships. Biochem Biophys Res Commun 2000; 272:64-74. [PMID: 10872804 DOI: 10.1006/bbrc.2000.2725] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
1H NMR study and conformational analysis of a broad series of biologically important C5-substituted 2'-deoxyuridines, including alkyl, halogen, vinyl, hydroxymethyl, and hydroxy derivatives as well as nitro, formyl, trifluoromethyl, and dimethylamino substituents, is presented. A thorough analysis of chemical shifts in correlation with C5-substituent electronegativity as well as calculations by SCF semi-empirical method of the formal charge localized on C6 carbon is discussed in terms of charge distribution for electron attracting and electron donating groups. Conformation of the sugar ring is determined from proton-proton coupling constants and described in terms of pseudorotation between two main puckering domains C2'endo (S) and C3'endo (N). Generally, electron donating groups destabilise the N conformation, simultaneously decreasing the mean pseudorotation amplitude. Absolute assignments of the H5' and H5'' methylene protons in 1H NMR spectra permitted the unequivocal determination of molar fractions of the three classical exocyclic C4'-C5' rotamers gauche+, trans, and gauche-, and correlation of them with the sugar ring puckering domains. Conformation about the glycosidic bond is described in terms of equilibrium between two conformational regions, anti and syn. Finally, the role of the C5-substituent in the creation of cytotoxic activity is considered on the basis of a simplified model assuming that compound activity is a function of substituent polar surface, its molecular volume, and its molecule polarity defined at the relative partition of the polar atoms.
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Affiliation(s)
- J Poznański
- Department of Physics, University of Warsaw, Poland
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Voituriez L, Cadet J. Isolation and Characterization of Two Furan-side Photoadducts of 7-Methylpyrido[3,4-c] Psoralen to the Sugar Moiety of 2-Deoxyadenosine. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb07983.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Gasparutto D, Da Cruz S, Bourdat AG, Jaquinod M, Cadet J. Synthesis and biochemical properties of cyanuric acid nucleoside-containing DNA oligomers. Chem Res Toxicol 1999; 12:630-8. [PMID: 10409403 DOI: 10.1021/tx980255e] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)cyanuric acid (cyanuric acid nucleoside, dY) (1) has been shown to be formed upon exposure of DNA components to ionizing radiation and excited photosensitizers. To investigate the biological and structural significance of dY residue in DNA, the latter modified 2'-deoxynucleoside was chemically prepared and then site-specifically incorporated into oligodeoxyribonucleotides (ODNs). This was achieved in good yields using the phosphoramidite approach. For this purpose, a convenient glycosylation method involving 3,5-protected 2-deoxyribofuranoside chloride and cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine) was devised. The anomeric mixture of modified 2'-deoxyribonucleosides (1/2 alpha/beta) was resolved by silica gel purification of the 5'-O-dimethoxytritylated derivatives, and then, phosphitylation afforded the desired beta-phosphoramidite monomer (5). After solid-phase condensation and final deprotection, the purity and the integrity of the modified synthetic DNA fragments were checked using different complementary techniques such as HPLC and polyacrylamide gel electrophoresis, together with electrospray ionization and MALDI-TOF mass spectrometry. The presence of cyanuric acid nucleoside in a 14-mer was found to have destabilizing effects on the double-stranded DNA fragment as inferred from melting temperature measurements. The piperidine test applied to dY-containing ODNs supported the high stability of cyanuric acid nucleoside inserted into the oligonucleotide chain. Several enzymatic experiments aimed at determining the biological features of such a DNA lesion were carried out. Thus, processing of dY by nuclease P(1), snake venom phosphodiesterase (SVPDE), calf spleen phosphodiesterase (CSPDE), and repair enzymes, including Escherichia coli endonuclease III (endo III) and Fapy glycosylase (Fpg), was investigated. Finally, a 22-mer ODN bearing a cyanuric acid residue was used as a template to study the in vitro nucleotide incorporation opposite the damage by the Klenow fragment of E. coli polymerase I.
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Affiliation(s)
- D Gasparutto
- Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, F-38054 Grenoble Cedex 9, France
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13
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Wagner JR, Decarroz C, Berger M, Cadet J. Hydroxyl-Radical-Induced Decomposition of 2‘-Deoxycytidine in Aerated Aqueous Solutions. J Am Chem Soc 1999. [DOI: 10.1021/ja982461e] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. Richard Wagner
- Contribution from the Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4, and Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA/Grenoble, F-38054 Grenoble, Cedex 9, France
| | - Chantal Decarroz
- Contribution from the Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4, and Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA/Grenoble, F-38054 Grenoble, Cedex 9, France
| | - Maurice Berger
- Contribution from the Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4, and Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA/Grenoble, F-38054 Grenoble, Cedex 9, France
| | - Jean Cadet
- Contribution from the Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4, and Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA/Grenoble, F-38054 Grenoble, Cedex 9, France
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Photochemical reactions of 5-fluorouracil and 5-fluoro-2′-deoxyuridine with Nα-acetyl-L-tryptophan N-ethylamide in aqueous solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1998. [DOI: 10.1016/s1011-1344(98)00090-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Boal JH, Wilk A, Scremin CL, Gray GN, Phillips LR, Beaucage SL. Synthesis of (2-Deoxy-α- and -β-d-erythro-pentofuranosyl)(thymin-1-yl)alkanes and Their Incorporation into Oligodeoxyribonucleotides. Effect of Nucleobase−Sugar Linker Flexibility on the Formation of DNA−DNA and DNA−RNA Hybrids. J Org Chem 1996. [DOI: 10.1021/jo961548k] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jila H. Boal
- Division of Hematologic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, and Laboratory of Drug Discovery Research and Development, Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21701
| | - Andrzej Wilk
- Division of Hematologic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, and Laboratory of Drug Discovery Research and Development, Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21701
| | - Carlo L. Scremin
- Division of Hematologic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, and Laboratory of Drug Discovery Research and Development, Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21701
| | - Glenn N. Gray
- Division of Hematologic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, and Laboratory of Drug Discovery Research and Development, Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21701
| | - Lawrence R. Phillips
- Division of Hematologic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, and Laboratory of Drug Discovery Research and Development, Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21701
| | - Serge L. Beaucage
- Division of Hematologic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, and Laboratory of Drug Discovery Research and Development, Developmental Therapeutics Program, National Cancer Institute, Frederick, Maryland 21701
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Bienvenu C, Wagner JR, Cadet J. Photosensitized Oxidation of 5-Methyl-2‘-deoxycytidine by 2-Methyl-1,4-naphthoquinone: Characterization of 5-(Hydroperoxymethyl)-2‘-deoxycytidine and Stable Methyl Group Oxidation Products. J Am Chem Soc 1996. [DOI: 10.1021/ja962073h] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carine Bienvenu
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA-Grenoble, 17 avenue des Martyrs, F-38054 Grenoble Cedex 9, France, and Département de Médecine Nucléaire et Radiobiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - J. Richard Wagner
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA-Grenoble, 17 avenue des Martyrs, F-38054 Grenoble Cedex 9, France, and Département de Médecine Nucléaire et Radiobiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Jean Cadet
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB/LAN, CEA-Grenoble, 17 avenue des Martyrs, F-38054 Grenoble Cedex 9, France, and Département de Médecine Nucléaire et Radiobiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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Raoul S, Cadet J. Photosensitized Reaction of 8-Oxo-7,8-dihydro-2‘-deoxyguanosine: Identification of 1-(2-Deoxy-β-d-erythro-pentofuranosyl)cyanuric Acid as the Major Singlet Oxygen Oxidation Product. J Am Chem Soc 1996. [DOI: 10.1021/ja952347l] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Celewicz L. Photochemical reactions of 5-bromocytosine and its N-1-substituted derivatives with in aqueous solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1995. [DOI: 10.1016/1011-1344(95)07176-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Anselmino C, Cadet J. Photoreaction of 5-methoxypsoralen with thymidine. Isolation and characterization of a pyrone-side monoadduct involving the pyrimidine methyl group. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1995; 27:167-75. [PMID: 7714676 DOI: 10.1016/1011-1344(94)07072-v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The UVA-mediated photoreaction of 5-methoxypsoralen (5-MOP) with thymidine has been investigated in the dry state. Under these conditions, the main products are 5-MOP pyrone-side monoadducts to thymidine. We report the isolation and characterization of an unusual 5-MOP-thymidine photoproduct. The assignment of the photoadduct was achieved on the basis of extensive spectroscopic measurements (UV, mass spectrometry (MS), 1H and 13C nuclear magnetic resonance (NMR), nuclear Overhauser effect (NOE) experiments). The formation of the photoadduct, which is rationalized in terms of a radical mechanism, appears to involve, in a covalent bond, the C-4 pyrone moiety of 5-MOP and the methyl group of thymidine.
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Affiliation(s)
- C Anselmino
- CEA/Département de Recherche Fondamentale sur la Matière Condensée, SESAM/LAN, Grenoble, France
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21
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Connick TJ, Reilly RT, Dunlap RB, Ellis PD. Phosphorus-31 nuclear magnetic resonance studies of complexes of thymidylate synthase. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1208:118-26. [PMID: 8086425 DOI: 10.1016/0167-4838(94)90168-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The interactions of thymidylate synthase (TS) with deoxyuridylate (dUMP), deoxythymidylate (dTMP) and 5-fluorodeoxyuridylate (FdUMP) were examined by 31P-NMR. Single 31P resonances appeared at 3.3 ppm, 3.2 ppm and 3.0 ppm from the standard, 85% phosphoric acid, for unbound dUMP, dTMP, and FdUMP, respectively. Incubation of the enzyme with either dUMP or dTMP, alone, resulted in new resonances at 3.9 and 3.6 ppm, respectively, which were assigned to noncovalent complexes with the enzyme. The same experiment employing FdUMP as the ligand gave two new resonances appearing at 3.6 and 4.6 ppm, which were attributed to noncovalent and covalent binary complexes, respectively. When the cofactor, CH2H4 folate, was present in the solution with enzyme and FdUMP, a new resonance appeared at 5.1 ppm, corresponding to the covalent inhibitory ternary complex. The ternary complex comprised of the enzyme, dUMP and the quinazoline folate CB 3731 produced a resonance at 5.0 ppm at the expense of the resonance due to the enzyme-dUMP binary complex at 3.9 ppm. Similarly, the ternary complex consisting of TS with dTMP and CB 3731 showed a deshielding of the resonance at 3.6 ppm by 0.8 ppm. A maximum binding of 1.5 nucleotides per enzyme dimer was found for dUMP and dTMP in both the presence and the absence of the quinazoline folate. The deshielding observed was attributed to changes in the interaction of the phosphate group with the nearby residues of the active site of the enzyme.
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Affiliation(s)
- T J Connick
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia 29208
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22
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Latha YS, Yathindra N. Stereochemical studies on nucleic acid analogues. I. Conformations of alpha-nucleosides and alpha-nucleotides: interconversion of sugar puckers via O4'-exo. Biopolymers 1992; 32:249-69. [PMID: 1581546 DOI: 10.1002/bip.360320306] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The preferred conformations of ribo and deoxyribo alpha-nucleosides and alpha-nucleotides, the stereoisomers of the naturally occurring beta-isomers, are worked out by minimizing the conformational energy as a function of all the major parameters including the sugar ring conformations along the pseudorotation path. The results of the studies bring out certain distinct conformational features that are at variance with their beta counterparts. The range of glycosyl conformations are found to be not only quite restricted here but favor predominantly the anti conformation. The syn glycosyl conformation for the entire region of P values are found to be energetically less favorable, with the barrier to anti in equilibrium with syn interconversion being higher especially in alpha-ribonucleosides. The energetically preferred range of pseudorotation phase angles (P) is also considerably restricted and P values corresponding to the C1'-exo range of sugars are highly unfavorable for alpha-nucleosides, in sharp contrast to the broad range of sugar ring conformations favored by beta-isomers. While both trans congruent to 180 degrees and skew congruent to 270 degrees conformations around the C3'-O3' (phi') bond are favored for alpha-3'-nucleotides with deoxyribose sugars, ribose sugars seem to favor only the skew values of phi'. Most interestingly and in sharp contrast to beta-stereoisomers, an energy barrier is encountered at P values corresponding to O4'-endo sugars. This suggests that the possible sugar pucker interconversion between C2'-endo/C3'-exo and C3'-endo/C2'-exo in alpha-anomers could take place only through the O4'-exo region. Likewise the possible path of anti in equilibrium with syn interconversion in alpha-nucleosides is not via high anti, in sharp contrast to beta-nucleosides. These observations should be borne in mind while assigning the sugar ring conformers in alpha-nucleosides and those containing them from nmr investigations. Comparison of the results with beta-anomers seem to suggest on the whole a lack of conformational variability or the restricted nature of alpha-stereoisomers. This could be one of the reasons for its nonselection in the naturally occurring nucleic acids.
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Affiliation(s)
- Y S Latha
- Department of Crystallography and Biophysics, University of Madras, India
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23
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Shetlar MD, Rose RB, Hom K, Shaw AA. Ring opening photoreactions of 5-bromouracil and 5-bromo-2'-deoxyuridine with selected alkylamines. Photochem Photobiol 1991; 53:595-609. [PMID: 1881960 DOI: 10.1111/j.1751-1097.1991.tb08486.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several studies in the literature indicate that histones (lysine rich proteins found associated with DNA in eukaryotic chromatin), as well as poly-L-lysine, can be photocross-linked by ultraviolet (UV) light to DNA in which 5-bromo-2'-deoxyuridine has been substituted for thymidine. To gain some insight into the possible nature of this cross-linking, we have studied the photoreactions occurring in deoxygenated aqueous solutions containing 5-bromouracil (I) (BrUra) or 5-bromo-2'-deoxyuridine (III) (BrdUrd) and ethylamine, a lysine side chain analog. In the case of I this reaction produced the ring opened compound N-(N'-ethylcarbamoyl)-3-amino-2-bromoacrylamide (Ia). A small amount of N-(N'-ethylcarbamoyl)-3-ethylamino-2-bromoacrylamide (Ic) was also isolated. It was found that purified Ia, standing in the presence of ethylamine, was gradually converted to Ic in a dark reaction. The beta and alpha anomers of N-(N'-ethylcarbamoyl)-3-(2'deoxyribofuranos-1'-yl) amino-2-bromoacrylamide (IIIa and IIIb respectively) were isolated as products in the photoreaction of III with ethylamine; the alpha anomer was produced in a dark reaction from the beta anomer. The identity of these anomers was established by comparison of their proton NMR spectra with those of the four corresponding alpha and beta furanosyl and pyranosyl isomeric nucleosides of thymine, which are presented in the Appendix. A study was also made of the reaction of I with methylamine; a ring opened product analogous to Ia, viz. N-(N'-methylcarbamoyl)-3-amino-2-bromoacrylamide (IIa) was formed. A similar study with 5-bromo-1-methyluracil produced N-(N'-methylcarbamoyl)-3-methylamino-2-bromoacrylamide (IIc) as a product. Likewise, the reaction of 5-chlorouracil with ethylamine was studied and N-(N'-ethylcarbamoyl)-3-amino-2-chloroacrylamide (Ie), which is analogous in structure to Ia, was found to be produced. Structural identifications were made through use of UV spectroscopy, high resolution 1H-NMR spectroscopy, mass spectrometry and, in the case of Ia and IIa, 13C-NMR spectroscopy. In the BrUra and BrdUrd reaction systems, described above, dehalogenation reactions accounted for a major portion of the products. The yields of ring opened products, determined at pH 10, ranged from a high of 10.3% in the BrUra-ethylamine system to a low of 1.7% in the MeBrUra-methylamine system.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- M D Shetlar
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143
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Tourigny G, Stuart AL, Ekiel I, Aduma PJ, Gupta SV. Conformation and Antiherpes Activity of 3′- and 5′-Azido and Amino Analogs of 5-Methoxymethyl-2′-Deoxyuridine. ACTA ACUST UNITED AC 1989. [DOI: 10.1080/07328318908054326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cadet J, Voituriez L, Nardin R, Viari A, Vigny P. A new class of psoralen photoadducts to DNA components: isolation and characterization of 8-MOP adducts to the osidic moiety of 2'-deoxyadenosine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1988; 2:321-39. [PMID: 3148697 DOI: 10.1016/1011-1344(88)85052-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The near-UV-induced photoreaction of the bifunctional 8-methoxypsoralen (8-MOP) with 2'-deoxyadenosine (dAdo) was investigated in the dry state. Four main monoadducts of 8-MOP to 2'-deoxyadenosine were separated by high performance liquid chromatography and subsequently characterized by soft ionization mass spectrometry (fast atom bombardment and plasma desorption mass spectrometries) and extensive 1H NMR analysis including nuclear Overhauser effect (NOE) measurements. These new types of furocoumarin-nucleic acid component which appear to be specific to 2'-deoxyadenosine were shown to result from recombination of the 3,4-dihydropyron-4-yl radical of 8-MOP with 2'-deoxyadenosyl radical either at the 1' or the 5' position.
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Affiliation(s)
- J Cadet
- Département de Recherche Fondamentale, Centre d'Etudes Nucleáires de Grenoble, France
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Remin M. The nature of conformational correlations in alpha- and beta-anomers of nucleic acid components in aqueous solution by nuclear magnetic resonance. J Biomol Struct Dyn 1988; 6:367-82. [PMID: 2856037 DOI: 10.1080/07391102.1988.10507719] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The solution distribution of combinations of the sugar ring puckering domains, C2'endo(S), C3'endo(N), and C4'-C5' rotamers, +sc(g+), ap(t), -sc(g-), in alpha and beta-anomers in ribo- and deoxyribo- pyrimidine nucleic acid components can be determined from vicinal coupling constants (M. Remin, J. Biomol. Str. Dyn. 2, 211 (1984). A general correlation pattern with a conformational constant lambda reflecting an intrinsic physical property of the sugar-side chain ensemble, is developed and expressed in terms of four principles: I) The +sc rotamer contributes to the C3'endo population to a higher extent (1-Yt) than to C2'endo, (1-Yt-Yg-/Xs). II) The ap rotamer contributes to both C2'endo and C3'endo populations to the same extent (Yt). III) The -sc rotamer contributes only to the C2'endo population, (Yg-/Xs). IV) The molar fractions Xs, Yt and Yg- of conformations C2'endo, ap and -sc, respectively, are strongly correlated, lambda = (Yg-/Xs)/Yt approximately 0.5, and therefore Yt is a basic variable parameter which determines all others in the correlation pattern. In alpha-anomers, regardless of the type and conformation of the sugar ring and base, the molar fraction Yt = 0.37 +/- 0.02. This finding means that different alpha-anomers show one correlation pattern free of the influence of the base. In beta-anomers, structure and conformation of the base are important factors which modulate (through Yt) the correlation pattern, conserving its fundamental features. Yt is considerably increased by a syn-oriented pyrimidine base, but decreases when the base is anti. The transition from anti to syn orientation of the base is followed by destabilization of (C2'endo, +sc) in favor of (C3'endo, ap). The principles of conformational correlations rationalize a variety of correlations observed in the past.
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Affiliation(s)
- M Remin
- University of Warsaw, Department of Biophysics, Poland
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Remin M. Determination of the complete correlation between the sugar ring puckers and 5'-exocyclic group rotamers in conformationally-flexible nucleic acid components from NMR study. J Biomol Struct Dyn 1984; 2:211-20. [PMID: 6400930 DOI: 10.1080/07391102.1984.10507558] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inspection of stereochemical models suggests a possible correlation between the proportion (Yg-/Yt) of the g- and t rotamers and the S pucker populations irrespective of the anti-syn conformational composition of the base. Interpretation of the NMR vicinal coupling constants in terms of conformational populations shows a decline of Yg-/Yt with XS approaching zero, consistent with high unfavorability of the Ng- conformational combination in solution, a result supported by a X-ray crystallographic data survey. Hence, the underlying assumption introduced into the present study is that the g- rotamer and the N pucker do not coexist together in solution. Therefore, the limiting value of Yg-/Yt corresponding to the S pucker could be determined for each compound individually. Finally, populations and relative free energies of all conformational combinations of Ng+, Nt, Sg+, St and Sg- (except Ng- which is not important) have been estimated. Results of the present study suggest several interesting regularities concerning the syn-anti effect on populations and energies of the conformational combinations in ribo- and deoxyribo-nucleosides. (a) In the anti-type nucleosides, the Ng+ conformation is about 2 kJ/mol more stable than Nt, but in the syn-type, the Ng+ and Nt have comparable energy. (b) No important changes are observed in the Ng+ population comparing the anti-type and syn-type of ribo- and deoxyribo-nucleosides separately. (c) The Nt is considerable stabilized and simultaneously the Sg+ is strongly destabilized in the syn-type nucleosides relative to the anti-type. (d) Irrespective of the syn-anti composition the St is always more stable (1-2 kJ/mol) than the Sg- conformational combination.
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Affiliation(s)
- M Remin
- Department of Biophysics, University of Warsaw, Poland
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Cadet J, Voituriez L, Gaboriau F, Vigny P, Della Negra S. Characterization of photocycloaddition products from reaction between thymidine and the monofunctional 3-carbethoxypsoralen. Photochem Photobiol 1983; 37:363-71. [PMID: 6856687 DOI: 10.1111/j.1751-1097.1983.tb04487.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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29
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Niemczura WP, Hruska FE, Sadana KL, Loewen PC. Proton magnetic resonance study of nucleosides, nucleotides, and dideoxynucleoside monophosphates containing asyn pyrimidine base. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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