Uracil Ring Research Articles

Resonance Raman characterization of the binary and ternary complexes of thymidylate synthase with 5-nitrodeoxyuridylate

Resonance Raman (RR) spectra are reported for the binary complex of Escherichia coli thymidylate synthase (TS) with the substrate analog inhibitor 5-nitrodeoxyuridylate (NDU). The TS/NDU binary complex RR spectrum shows many similarities to the RR spectra of thiol adducts of NDU or of 5-nitro-1-methyluracil formed in solution, providing strong evidence in support of the formation of a covalent link between Cys146 of TS and C6 of NDU. Spectral differences between the model compounds and the binary complex reflect the consequences of fixing the conformations of the uracil and ribose rings at the enzyme active site. The RR spectra of the ternary complexes of TS/NDU with either tetrahydrofolate (H4-folate) or the cofactor 5,10-methylenetetrahydrofolate (CH2H4-folate) show that a covalent link is not formed between C11 of CH2H4-folate and C5 of NDU. Neither does the methylene bridge of CH2H4-folate remain intact in the ternary complex; either CH2H4-folate is present as the N5 iminium cation species or the methylene group is lost as formaldehyde. A shift in the NO2 symmetric stretching frequency in the ternary complex indicates expulsion of water molecules from the region of the NO2 group by the cofactor.

Photochemical reaction of ( η5-cyclopentadienyl) dicarbonyliron iodide with 1-substituted uracils in the presence of diisopropylamine: crystal structure of the ( η5-C 5H 5Fe(CO) 2 complex of deprotonated 5-fluoro-1-(tetrahydro-2-furyl) uracil (Ftorafur)

Irradiation with visible light of a mixture of Fe(Cp)(CO) 2I (Cp = η 5-cyclopentadienyl) with 1-methyyluracil ( 1a), 5-fluoro-1-(tetrahydro-2-furyl)uracil (Ftorafur) ( 1b) or 6-azauridine-2′3′5′-triacetate ( 1c) in the presence of diisopropylamine affords complexes in which the Fe(Cp)(CO) 2 moiety is bound to the deprotonated N(3) atom of the uracil moiety. The crystal structure of 2b, made from 1b, was determined and is compared with the known structures of the α A, α B and β forms of Ftorafur and that of its η 1-Au complex. Complex 2b shows the shortest intramoleculaar CH …O hydrogen bond between the tetrahydrofuran and uracil rings. The stereochemistry of this complex is also discussed.

A heterodinuclear anti oximate-bridged copper(II)-nickel(II) complex: crystal structure and magnetic properties

The crystal structure of [Cu(ClO 4)(μ-L)Ni(CTH)](ClO 4)·H 2O (where H 2L is α,ω-bis(1,3-dimethyl-5-nitrosouracil-6-yl-amine)propane and CTH is d, l-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane) has been determined by X-ray methods. The complex crystallizes in the monoclinic space group C2/ c with a=41.848(16), b=12.738(3), c=20.005(7) A ̊ , β=114.92(2)° . The structure consists of discrete dimetallic cations [Cu(ClO 4)(μ-L)Ni(CTH)] +, one perchlorate anion and one non-bonded disordered molecule of water. Within the dinuclear cation, copper(II) and nickel(II) are bibridged by an exocyclic oxygen atom of the uracil ring and an anti nitroso-oximato group, resulting in a Cu···Ni distance of 4.972(2) Å. The copper(II) ion occupying the inside site of the double deprotonated ligand L 2− exhibits a N 4O distorted square-pyramidal coordination environment, whereas the nickel(II) ion is in a distorted octahedral geometry. Magnetic susceptibility measurements in the temperature range 300-2 K revealed the occurrence of a strong antiferromagnetic exchange interaction between copper(II) and nickel(II) ions with a J value of −136.4 cm −1. Magnetic and structural parameters of this and other related complexes are compared in order to know how the type of NO bridging conformation affects the magnetic properties.

Electron‐impact induced decomposition of some 3‐alkyl‐5‐substituted‐6‐methyl uracils

AbstractMass spectrometry was used to study the main fragmentation routes of some 3‐alkyl‐5‐substituted‐6‐methyl uracils. Differences in fragmentation were caused by changes in the structure of the alkyl group in position 3 of the uracil ring, with the same substituent in position 5, and by differences in the substituent in position 5.

6-Amino-5-hydroxyiminomethyl-1,3-dimethyluracil

The structure of the title compound [6-amino-5-hydroxyiminomethyl-1,3-dimethyl-2,4(1H,3H)-pyrimidinedione, C 7 H 10 N 4 O 3 ] shows that there is extensive electronic delocalization in the uracil ring, as found in analogous uracil derivatives

Structural studies of some 5-(perfluoroalkenyl) uracils

Abstract Structures of the most stable conformers of derivatives of 5-vinyluracil and fluorinated analogues have been determined using MM and semiempirical MNDO calculations. It has been found that the most stable conformers of 5-trifluorovinyl and 5- E / Z -pentafluoropropenyl groups are almost perpendicular to the plane of the uracil ring. These findings are in good agreement with X-ray data obtained for 1,3,6-trimethyl-5-trifluorovinyluracil. The calculated energy barrier for rotation of exocylic 5-substituents depends on the structure of the fluorinated fragments as well as on the nature of the substituent at the 6-position of uracil. A methyl group at the 6-position causes steric hindrance and significantly disturbs the rotation of fluorinated groups.

Synthetic Nucleosides and Nucleotides. XXXI.1Inhibitory Effects of 2′-Deoxy-5-styryluridine 5′-Triphosphate Analogues on Retroviral Reverse Transcriptases and Higher Eukaryotic DNA Polymerases

Abstract Some new 5′-triphosphate derivatives of 2′,3′-dideoxy-5-styryluridine analogues have been synthesized and examined for their inhibitory effects on retroviral reverse transcriptases and eukaryotic DNA polymerases. We describe here the mode of inhibition and the influence of the substituent at the 5-position of uracil ring of 2′,3′-dideoxyUTP analogues.

Willardiines differentiate agonist binding sites for kainate- versus AMPA-preferring glutamate receptors in DRG and hippocampal neurons

Concentration jump responses to 5-substituted (S)-willardiines were recorded from dorsal root ganglion (DRG) and hippocampal neurons under voltage clamp. After block of desensitization by concanavalin-A, dose-response analysis for activation of kainate-preferring receptors in DRG neurons gave the potency sequence trifluoromethyl > iodo > bromo approximately chloro > nitro approximately cyano > kainate > methyl > fluoro > (R,S)-AMPA >> willardiine; EC50 values for the most and least potent willardiine derivatives, 5-trifluoromethyl (70 nM) and 5-fluoro (69 microM), differed 1000-fold. The potency sequence for equilibrium responses at AMPA-preferring receptors in hippocampal neurons was strikingly different from that obtained in DRG neurons: fluoro > cyano approximately trifluoromethyl approximately nitro > chloro approximately bromo > (R,S)-AMPA > iodo > willardiine > kainate > methyl. In hippocampal neurons EC50 values for the most and least potent willardiine derivatives, 5-fluoro (1.5 microM) and 5-methyl (251 microM), differed only 170-fold. Consistent with equilibrium potency measurements, in DRG neurons the kinetics of deactivation for willardiines, recorded following a return to agonist-free solution, were rapid for 5-fluoro (tau off = 43 msec) but slow for 5-iodo (tau off = 4.2 sec), while the opposite sequence was observed for hippocampal neurons, slow for 5-fluoro (tau off = 2.1 sec) and rapid for 5-iodo (tau off = 188 msec). The kinetics of recovery from desensitization showed comparable agonist- and cell-dependent differences. Structure-activity analysis for agonist responses recorded from DRG and hippocampal neurons suggests that for both kainate-preferring and AMPA-preferring receptors the binding of willardiines involves interactions with polar groups such that potency is related to ionization of the uracil ring, and hence the electron-withdrawing ability of the 5-position substituent. However, kainate-preferring receptors differ from AMPA-preferring receptors in possessing a lipophilic pocket that further enhances agonist potency by hydrophobic bonding of the 5-substituent. In contrast, AMPA-preferring receptors lack such a lipophilic site, and for 5-position substituents of the same electron-withdrawing ability, potency decreases with increase in size.

Design and Synthesis of Regioisomeric Analogues of a Specific Anti-HIV-1 Agent 1-[(2-Hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT)

Abstract Regioisomeric analogues of the anti-HIV-1 lead 1-[(2-hydroxy-ethoxy)methyl]-6-(phenylthio)thymine (1: HEPT) have been synthesized. These compounds, having an ethoxymethyl side chain at C-5 and an ethyl group at the N-1 position of the uracil ring, also possess activity against HIV-1.

Platinum complex [(en)Pt(uracilate)]44+: a metal analog of calix[4]arene. Similarities and differences with classical calix[4]arenes

The preparation, X-ray crystal structure, and the solution behavior of a cyclic, tetranuclear nucleobase complex of (en)Pt II , [(en)Pt(UH-N1,N3)] 4 (NO 3 ) 4 (2) (with en=1.2-diaminoethane, UH=uracil monoanion, N1,N3=platination sites) is described. The tetranuclear cation of 2 displays close similarities with calix[4]arenes as far as overall geometry and conformational behavior is concerned. The affinity of the metal analogue 2 for metal cations appears to be more pronounced as compared to typical calix[4]arenes, however. In the solid state, 2 adopts a 1,3-alternate conformation of the four uracil rings, but in solution and after deprotonation to [(en)Pt(U-N1,N2)] 4 a second major species (cone conformer) occurs in solution

New and convenient protection system for pseudouridine, highly suitable for solid-phase oligoribonucleotide synthesis

The pivaloyloxymethyl (Pom) group has been used simultaneously to protect both nitrogens in the uracil ring system of pseudouridine. This enabled the synthesis of a 2′-O-[1-(2-fluorophenyl)-4-methoxypiperidin-4-yl]-protected (Fpmp protected) pseudouridine building block suitable for solidphase oligoribonucleotide synthesis by the phosphoramidite method as well as a useful 2′-O-methylpseudouridine building block. Both compounds were incorporated in high yield into synthetic oligonucleotides, the Pom groups being cleaved during an extended deblock with ammonia.

Synthesis of brain-targeted 1-(2-deoxy-2-fluoro-β- D-ribofuranosyl)-( E)-5-(2-iodovinyl)uracil coupled to a dihydropyridine ⇋ pyridinium salt redox chemical-delivery system

1-(2-Deoxy-2-fluoro-β- d-ribofuranosyl-( E)-5-(2-iodovinyl)uracil (IVFRU) was coupled to a dihydropyridine ⇋ pyridinium salt redox chemical-delivery system (CDS) via a cleavable sugar-ester linkage as a site-directed approach to increase diffusion of the parent nucleoside into the central nervous system. Treatment of 1-(2-deoxy-2-fluoro-β- d-ribofuranosyl)uracil with Bu tMe 2SiCl in the presence of imidazole in DMF yielded the protected 5- O- tert-butyldimethylsilyl derivative. Subsequent reaction with nicotinoyl chloride hydrochloride in pyridine afforded 1-[5- O-tert-butyldimethylsilyl-2-deoxy-2-fluoro-3- O-(3-pyridylcarbonyl)-β- d- ribofuranosyl]uracil. Reaction with iodine monochloride in methanol simultaneously cleaved the silyl ether moiety and iodinated the uracil ring at the 5-position. Coupling with ( E)-Bu 3Sn-CHCH-SiMe 3 in the presence of (Ph 3P) 2Pd 2(II)Cl 2 in THF gave 1-[2-deoxy-2-fluoro-3- O- (3-pyridylcarbonyl)-β- d-ribofuranosyl]-( E)-5-(2-trimethylsilylvinyl)uracil. Quaternization with iodomethane in acetone yielded the N-methylpyridinium iodide salt. Iodination of the reactive ( E)-trimethylsilylvinyl moiety with iodine monchloride in acetonitrile and reduction of the quaternary pyridinium iodide salt with sodium dithionite in the presence of sodium bydrogen carbonate was carried out as a one-pot procedure to afford 1-[2-deoxy-2-fluoro-3- O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-β- d- ribofuransyl]-( E)-5-(2-iodovinyl)uracil (IVFRU-CDS). This synthetic strategy is readily amenable to the high specfi-activity radioiodination of IVFRU.

Intramolecular photocyclisation of molecules containing both 3-phenylcyclopentenone and uracil rings

Photolysis of both 3-phenyl-(5- and 6-uracilylmethyl)cyclopentenones gove single products which have been identified as 5,7-diaza-10-phenyl[7.2.1.05,9]tetracyclodecane-2,5,7-trione, respectively.

PH effect on structural character of uracil in aqueous solution studied by single-shot CARS

A preliminary study is reported on the structure of uracil, a base residue of nucleic acid, in aqueous solutions of different pH values by coherent anti-Stokes Raman scattering (CARS). The results obtained reveal that Raman lines associated with the stretching and bending vibration modes of the uracil ring around 1000 and 1240 cm −1 are sensitive to the pH of the solutions. All thes findings, however, are difficult to observe by laser resonance Raman spectroscopy, which is used widely in practice at present. In addition, we conclude that CARS measurement seems to be a powerful tool capable of offering structural specificity associated with molecular vibrational frequencies of base residues of nucleic acids and their interactions with the surrounding media.

Chemical, biochemical and genetic endeavours characterizing the interaction of sparsomycin with the ribosome

Sparsomycin interaction with the ribosome and characteristics of the drug binding site in the particle were studied using chemical modification of the drug, affinity labeling methods and isolation of drug resistant mutants. The structure-function relationship studies, performed with a large number of drug derivatives, indicate that the drug interacts with the ribosome by its western and eastern moieties. The uracil ring, in the western end of the drug molecule, probably forms hydrogen bonds with the rRNA, while the apolar CH 3SCH 3 group in the eastern end interacts with a hydrophobic ribosomal domain that affinity labeling results seem to indicate is formed by protein. An increase in lipophilicity in this part of the antibiotic results in a dramatic increase in the inhibitory activity of the drug. The sparsomycin binding site is not accessible in free ribosomes, but the presence of an N-blocked amino acyl-tRNA at the P-site turns the particles capable of reversible interaction with the drug. After failure using Escherichia coli, a sparsomycin-resistant mutant was obtained by direct mutagenesis on Halobacterium halobium, a species with a unique copy of rRNA genes, stressing the role of rRNA on the drug interaction site.

Enthalpies of solvation of alkylated uracils in water, nonaqueous and mixed solvents

The enthalpies of solution of uracil and its alkylated derivatives in water, methanol, N,N-dimethylformamide (DMF) and water+DMF mixtures were measured at 25°C. The enthalpies of solvation were determined. The enthalpies of cavity formation, corresponding to the enthalpies of solvent-solvent interactions were calculated and the enthalpies of solute-solvent interactions were obtained. The presence of the alkyl groups was found to have different effects on the enthalpy of interaction depending on the position and size of the substitution. The effect of alkylation at the nonpolar side of the uracil ring was found to arise mostly from the enhancement of the van der Waals interactions. The alkyl substitutions at the polar side resulted also in the removal of the solvent molecules interacting specifically with the polar groups of uracil. The enthalpy of those specific interactions was determined and found to be stronger in methanol and DMF than in water. Enthalpies of solvation in the binary water+DMF solvent were found to depend in a nonlinear way on the solvent composition. The nonlinearities in the water-rich region were found to arise from the decay of the hydrophobic hydration of the solutes with the increasing DMF content. The substitution of two methyl groups caused the uracil molecule to bahave as a predominantly hydrophobic solute. The nonlinearities in the DMF-rich region were found only for those solutes which can form hydrogen bonds with DMF.

FT-IR spectroscopic study of uracil derivatives and their hydrogen bonded complexes with proton donors: Part III. Hydrogen bonding of uracils with H 2O in argon matrices

The hydrogen bond interaction of uracils (uracil, 1-CH 3-uracil, 3-CH 3-uracil, 5-CH 3-uracil, 1,3-diCH 3-uracil) and thiouracils (2-thiouracil, 4-thiouracil, 1-CH 3-2-thiouracil, 1-CH 3-5-Br-2-thiouracil) with water is investigated using matrix-isolation FT-IR spectroscopy. It is demonstrated that H 2O forms both CO⋯HO and NH⋯OH complexes in low temperature Ar matrices. No experimental evidence is obtained for the existence of a closed CO⋯HO⋯HN heterodimer which has been predicted from ab initio calculations. Different amounts of C 2O and C 4O, and of N 1H and N 3H complexes are formed in the matrix depending on the substitution (methyl, thio, halogen) on the uracil ring. The monomer assignments in earlier reports are supported by the shifts observed on H-bonding with H 2O.

Orotate complexes. Synthesis and crystal structure of lithium orotate(—I) monohydrate and magnesium bis[ orotate(—I)] octahydrate

AbstractNeutralization of orotic acid (OrH2) by lithium or magnesium hydroxide in aqueous medium yields the crystalline metal orotate hydrates Li(OrH). H2O (1) and Mg(OrH)2. (H2O)6 (2). By single‐crystal X‐ray diffraction studies it has been shown that 1 (space group P1) forms a layer structure, with lithium in a tetrahedral environment of oxygen atoms from three different orotate( ‐ I) anions (one carboxylate and two uracil oxygen atoms) and the water molecule. 2 (space group P21/c) has been shown to feature a hexaquo complex of magnesium, the Mg(H2O)26 cations being associated with two hydrated OrH⊖ ions only through hydrogen bonds. The anions are also engaged in “base‐pairing” hydrogen bonds between the planar uracil ring systems of different units. The results are relevant for applications of magnesium orotates in magnesium therapy.

De novo synthesis of uracil nucleotides in mouse liver and intestine studied using [15N]alanine

The amount of newly synthesized uracil nucleotides in mouse liver and intestine was determined by analysis of 15N incorporation into the uracil nucleotide pool of these tissues after intraperitoneal infusion of 15N-labelled amino acids. The appearance of newly synthesized uracil nucleotides was linear with time, and essentially independent of the rate of infusion of L-[15N]alanine. Varying the amino acid used in the infusion could affect the enrichment in the uracil ring nitrogens, but had no significant effect on the calculated amount of de novo synthesis. These results demonstrate the utility of this method in measuring de novo uracil nucleotide synthesis in mouse liver and intestine in vivo. The method should be a valuable tool in the effort to understand the regulation and pharmacological manipulation of de novo uracil nucleotide synthesis.

13C N.M.R. spectra of some 5-substituted-3-isopropyl-6-methyl uracils

13C n.m.r. spectra of some 5-substituted-3-isopropyl-6-methyl uracils were determined in deuterated dimethyl sulfoxide (d 6 - DMSO). The substituents are : H, Cl, Br, J, NO 2, NH 2, N(CH 3) 2, C 6H 5, C 6H 4-NO 2-p and C 6H 4-NH 2-p. It has been shown that 13C chemical shifts of C-5 of some of the examined compounds correlated linearly with the 13C chemical shifts of C-5 in the 5-substituted uracils as well as with the 13C chemical shifts of the substituted carbon in an analogues series of monosubstituted benzenes. The 13C chemical shifts of C-6 in some of the above compounds depend on the steric effects of the substituent in position 5 of the uracil ring.