Oligonucleotides Incorporating N7-(2′-Deoxy-β-d-erythro-pentofuranosyl)isoguanine

Abstract

The H-phosphonate and the phosphoramidite of N⁷-2′-deoxyisoguanosine (2) were prepared and incorporated into oligonucleotide duplexes. Their base pairing properties were investigated and compared with those of the parent purine nucleosides.     

Reactions of [PtCl(dien)]Cl with glutathione,oxidized glutathione and S-methyl glutathione. Formation of an S-bridged dinuclear unit

The reaction of the monofunctional platinum compound [PtCl(dien)]Cl with the tripeptide glutathione (GSH), oxidized glutathione (GSSG) and S-methyl glutathione (GS-Me) has been investigated by ¹H, ¹³C and ¹⁹⁵Pt magnetic resonance spectroscopy and by potentiometric titrations. It appears that platinum binds with a high degree of specificity to the GSH sulfhydryl group. The reaction of platinum with GSH proceeds in two steps. In the first step only one platinum binds to the sulfur atom and, in the second step, another [Pt(dien)]²⁺ unit binds to [Pt(dien)GS]⁺ forming an S-bridged dinuclear unit [{Pt(dien)}₂GS]³⁺. The rate of the first binding step is pH-dependent, whereas the rate of the second step is not. At pH < 7 the rate of the first binding step is slow compared to the rate of the second binding step. At pH > 10, on the other hand, the rate of the first binding step is faster than the rate of the second binding step. Consequently, at pH < 7 one can only isolate the [{Pt(dien)}₂GS]³⁺ complex. In the presence of free GSH, at pH > 7, one [Pt(dien)]²⁺ unit of [{Pt(dien)}₂GS]³⁺ dissociates forming [Pt(dien)GS]⁺. The mechanism of the pH-dependent rate of the first platinum binding step and the ligand-exchange reaction are discussed. GSSG reacts with [Pt(dien)]²⁺, also forming the S-bridged dinuclear unit [{Pt(dien)}₂GS]³⁺, probably through a redox disproportionation reaction with a catalytic function of [PtCl(dien)]Cl. GS-Me reacts with [Pt(dien)]²⁺ forming the S-coordinated [Pt(dien)GS-Me]²⁺. [Pt(dien)GS-Me]²⁺ exists as a pair of diastereomers due to different configurations about sulfur. The rate of the inversion of configuration at the coordinated sulfur atom is slow on the NMR time-scale.     

Novel bis(diethylenetriamine)thallium(III) complex. Synthesis and characterization in pyridine solution and in solid

A new complex of thallium(III) with the nitrogen donor ligand diethylenetriamine (dien) has been prepared and characterized by multinuclear NMR (¹H, ¹³C, ²⁰⁵Tl), infrared and Raman spectroscopy, and X-ray diffraction. In solution, the symmetric s-facial isomer of [Tl(dien)₂]³⁺ is formed. This is a fluxional molecule even at low temperature (235 K); therefore, the different rotamers cannot be observed separately. A complete characterization of the complex is given from its non-trivial NMR spectra. The crystal structure of [Tl(dien)₂](ClO₄)₃·H₂O shows u-facial geometry, where the coordination environment around thallium can be described as a distorted trigonal prism.     

Manganese(II), iron(II) and nickel(II) chloride complexes with monodeprotonated anionic guanine

Upon refluxing 2:1 mixtures of guanine (guH) and MnCl₂, FeCl₂ or NiCl₂ in a 7:3 (v/v) mixture of ethanol and triethyl orthoformate for 1–2 weeks, partial substitution of gu^? for Cl^? groups occurs, and solid complexes of the M(gu)Cl·2ROH (R = C₂H₅ for M = Mn; R = H for M = Fe, Ni) type are obtained. The new complexes are pentacoordinated and appear to be linear chainlike polymeric species, involving a single-bridged

_n backbone. Coordination number five is attained by the presence of one terminal chloro and two terminal ROH ligands per metal ion. Most probable binding sites of bidentate bridging gu^? are the N(7) and N(9) imidazole ring nitrogens. IR evidence rules out the possibility of coordination of gu^? through any of the exocyclic potential ligand sites (O(6) oxygen or N(2) nitrogen) [1].     

Benzimidazole 2′-Isonucleosides: Design,Synthesis, and Antiviral Activity of 2-Substituted-5,6-Dichlorobenzimidazole 2′-Isonucleosides

Abstract

2,5,6-Trihalogenated benzimidazole-β-D-ribofuranosyl nucleosides and 2-substituted amino-5,6-dichlorobenzimidazole-β-L-ribofuranosyl nucleosides are potent and selective inhibitors of human cytomegalovirus (HCMV). The D-ribofuranosyl analogs are metabolized rapidly in vivo rendering them unsuitable as drug candidates. The primary source of instability is thought to be the anomeric bond. The synthesis of a series of chemically stable benzimidazole-2′-isonucleosides is presented. The synthetic schemes employed are based on nucleophilic displacements of a 2′-tosylate from carbohydrate intermediates with 2-bromo-5,6-dichlorobenzidazole. 2-Bromo and 2-isopropyl amino analogs with 3′- and 5′-oxo and deoxy substitutions were prepared. The benzimidazole-2′-isonucleosides presented here demonstrated reduced activity against HCMV when compared to other D-ribofuranosyl benzimidazole analogs. In addition, they were not found to be inhibitors of HIV.     

Kinetic and thermodynamic investigation of the (dien)Pd(II)-polycytidylic acid system

The reaction between (dien)PdCl+ and polycytidylic acid was studied using spectroscopic and stopped-flow methods. In neutral solution, the palladium complex binds at the N3 site of the cytosine base and causes a noncooperative disruption of the ordered helical structure of poly(C). Interaction at the phosphate group of the polynucleotide was also demonstrated by using the dye acridine orange as an indicator. The results of this study show that the mechanism previously proposed for cytidine and CMP can be applied to poly(C), taking into account particular features of the polymer (polyelectrolytic nature, structure, etc.). In particular, electrostatic effects seem to play a major role in the interaction with metal ion complexes like (dien)Pd(II).     

Some Examples of the Use of Trifluoromethane Sulfonic Anhydride in Nucleic Acid Chemistry

Abstract

Trifluoromethane sulfonic anhydride has been used for the inversion of configuration at the 3′-position of 2′-deoxypurine nucleosides, for the modification of the base moiety of purine and pyrimidine nucleosides, for nucleophilic substitution in the sugar moiety, for the synthesis of O²,3′-cyclothymidine and for sugar-base condensation reactions. Reaction can be carried out under very mild conditions. The conditions for these reactions are quite different so that a good selectivity can be obtained when different reactive groups are present.     

Oxidation of copper(II)-coordinated diethylenetriamine by hexacyanoferrate(III) ion. A kinetic investigation

The stoichiometry and kinetics of the reaction between [Cu(dien)(OH)]⁺ and [Fe(CN)₆]³⁻ in aqueous alkaline medium are described. The rate equation − (d[Fe(III)]/dt = {k₁[OH⁻]²[[Cu(dien)(OH)]⁺] + k₂[OH⁻] × [[Cu(dien)(OH)]⁺]²}([Fe(III)]/[Fe(II)]) (Fe(III) = [Fe(CN)₆]³⁻; Fe(II) = [Fe(CN)₆]⁴⁻, the 4:4:1 OH⁻/Fe(III)/[Cu(dien)(OH)]⁺ stoichiometric ratio and the nature of the ultimate products identified in the reaction solution suggest the fast formation of a doubly deprotonated Cu(III)-diamido complex which slowly undergoes an internal redox process where the ligand is oxidised to the Schiff base H₂NCH₂CH₂NCHCHNH.The [[Cu(dien)(OH)]⁺]² term in the rate equation is explained with the formation of a transient μ-hydroxo mixed-valence Cu dimer. A two-electron internal reduction of the Cu(III) complex yielding a Cu(I) intermediate is suggested to account for the presence of monovalent copper in a precipitate which forms at relatively high reactant concentrations and in the absence of dioxygen.     

A bulky platinum triamine complex that reacts faster with guanosine 5′-monophosphate than with N-acetylmethionine

A bulky platinum triamine complex, [Pt(Me₅dien)(NO₃)]NO₃ (Me₅dien = N,N,N′,N′,N′′-pentamethyldiethylenetriamine) has been prepared and reacted in D₂O with N-acetylmethionine (N-AcMet) and guanosine 5′-monophosphate (5′-GMP); the reactions have been studied using ¹H NMR spectroscopy. Reaction with 5′-GMP leads to two rotamers of [Pt(Me₅dien)(5′-GMP-N7)]⁺. Reaction with N-AcMet leads to formation of [Pt(Me₅dien)(N-AcMet-S)]⁺. When a sample with equimolar mixtures of [Pt(Me₅dien)(D₂O)]²⁺, 5′-GMP, and N-AcMet was prepared, [Pt(Me₅dien)(5′-GMP-N7)]⁺ was the dominant product observed throughout the reaction. This selectivity is the opposite of that observed for a similar reaction of [Pt(dien)(D₂O)]²⁺ with 5′-GMP and N-AcMet. To our knowledge, this is the first report of a platinum(II) triamine complex that reacts substantially faster with 5′-GMP than with N-AcMet; the effect is most likely due to steric clashes between the methyl groups of the Me₅dien ligand and the N-AcMet.     

(Dien)M(II) (M=Pd, Pt) and (NH3)3Pt(II) complexes of 1-methylcytosine: Linkage and rotational isomerism, metal-promoted deamination, and pathways to dinuclear species

Despite their structural similarity, [Pt(dien)(1-MeC-N3)](2+) (1), [Pd(dien)(1-MeC-N3)](2+) (2), and [Pt(NH(3))(3)(1-MeC-N3)](2+) (3) (with dien=diethylenetriamine and 1-MeC=neutral 1-methylcytosine) behave in part markedly different at strongly alkaline pH (12-13) and at room temperature. While 1 and 2, yet not 3 show linkage isomerization from N3 to N4, deamination of the cytosine nucleobase to 1-methyluracilate occurs with 1 and 3, yet not with 2. Pathways leading to N3,N4-diplatinated 1-MeC(-) complexes (1-MeC(-)=1-methylcytosine, deprotonated at exocyclic amino group N4) have been studied at high pH by starting from 1 and 3, respectively, and adding (dien)Pt(II). It appears that initial migration of the metal entity from N3 to N4, followed by binding of the second metal to the available N3 site, is favored over sequential coordination to N3 and then N4. X-ray crystal data of 1-3 density functional theory (DFT) calculations, and NMR ((1)H, (195)Pt) data are presented.     

Fluorescence Properties and Base Pair Stability of Oligonucleotides Containing 8-Aza-7-deaza-2′-deoxyisoinosine or 2′-Deoxyisoinosine

Abstract

The fluorescence and the base pairing properties of 8-aza-7-deaza-2′-deoxyisoinosine (1) are described and compared with those of 2′-deoxyisoinosine (2). The corresponding phosphoramidites (11,12) are synthesized using the diphenyl-carbamoyl (DPC) residue for the 2-oxo group protection. The nucleosides 1 and 2 base pair with 2′-deoxy-5-methylisocytidine in DNA duplexes with antiparallel chain orientation and with 2′-deoxycytidine in a parallel DNA. These base pairs are less stable than the canonical dA-dT pair and that of 2′-deoxyinosine (4) with 2′-deoxycytidine. The fluorescence of the nucleosides 1 and 2 is quenched (～95%) in duplex DNA. The residual fluorescence is used to determine the T_m-values, which are found to be the same as determined UV-spectrophotometrically.     

Crystal and molecular structure of [Cu(5'-inosine monophosphate) (dipyridylamine) (H2O)]2.4H2O.

The ternary complex [Cu(5′-IMP)(dpa)(H₂O)]₂ has been prepared and its structure analyzed by x-ray diffraction. It has a dimeric structure in which the 5′-IMP ligands coordinate solely through their phosphate groups. This geometry is in marked contrast to that of another $\text{Cu}\text{5′-}\text{IMP}$ ternary complex, [Cu(5′-IMPH)(bipy)(H₂O)₂]⁺, which shows metal binding through the purine base rather than the phosphate group.     

Mechanistic flexibility in the reduction of copper(II) complexes of aliphatic polyamines by mercapto amino acids

The reactions of copper(II)-ahphatic polyamine complexes with cysteine, cysteine methyl ester, penicillamine. and glutathione have been investigated, with the goal of understanding the relationship between RS^?-Cu(II) adduct structure and preferred redox decay pathway. Considerable mechanistic flexibility exists within this class of mercapto ammo acid oxidations, as changes in the rate law could be induced by modest variations in reductant concentration (at fixed [Cu(II)]_o), pH, and the structure of the redox partners. With excess cysteine present at 25°C, pH 5 0, I = 0 2 M (NaOAc), decay of 1:1 cys-S^?-Cu(II) transient adducts was found to be first order in both cys-SH and transient. Second-order rate constants characteristic of Cu(dien)²⁺ (6 1 × 10³M^?1sec^?1), Cu(Me₅dien)²⁺ (2.7 × 10³M^?1 sec^?1), Cu(en)₂²⁺ (2.1 × 10³M^?1 sec^?1), and Cu(dien)₂²⁺ (4.7 × 10³ M^?1 sec ^?1) are remarkably similar, considering substantial differences in the composition and geometry of the oxidant first coordination sphere. A mechanism involving attack of cysteine on the coordinated sulfur atom of the transient, giving a disulfide anion radical intermediate, is proposed to account for these results Moderate reactivity decreases in the cysteine-Cu(dien)²⁺, Cu(Me₅dien)²⁺ reactions with increasing [H⁺] (pH 4–6) reflect partial protonation of the polyamine ligands. A very different rate law, second order in the RS^?-Cu(II) transient and approximately zeroth order in mercaptan, applies in the pH 5.0 oxidations of cysteine methyl ester, penicillamine, and glutathione by Cu(dien)²⁺ and Cu(Me₅dien)²⁺. This behavior suggests the mtermediacy of di-μ-mercapto-bridged binuclear Cu(II) species, in which a concerted two-electron change yields the disulfide and Cu(I) products. Similar hydroxo-bridged intermediates are proposed to account for the transition from first- to second-order transient dependence in cysteine oxidations by Cu(dien)²⁺ and Cu(Me₅dien)²⁺ as the pH is increased from 5 to 7. Yet another rate law, second order in transient and first order in cysteine, applies in the pH 5.0 oxidation of cysteine by Cu(Me₆tren)²⁺ (k(25°C) 7.5 × 10⁷ M^?2 sec^?1, I = 0.2 M). Steric rigidity of this trigonal bipyramidal oxidant evidently protects the coordinated sulfur atom from attack in a RSSR^?-forming pathway. Formation of a coordinated disulfide in the rate-determining step is purposed, coupled with attack of a noncoordinated cysteine molecule on a vacated coordination position to stabilize the (Me₆(tren)Cu(I) product.     

Binding of cis- and trans-diamminedichloroplatinum(II) to deoxyribonucleic acid exposes nucleosides as measured immunochemically with anti-nucleoside antibodies

We report the use of anti-nucleoside antibodies to probe for local denaturation of calf thymus DNA upon binding of the antitumor drug cis-diamminedichloroplatinum(II), cis-DDP, and the biologically inactive analogues trans-diamminedichloroplatinum(II), trans-DDP, and chloro(diethylenetriamine)platinum(II) chloride, [Pt(dien)Cl]Cl. These antibodies specifically recognize each of the four DNA nucleosides. They bind well to denatured DNA, but not to native DNA in which the bases are less accessible owing to Watson-Crick duplex structure. At relatively high levels of modification (D/N approximately 0.1), cis-DDP causes significant disruption of DNA base pairing as reflected by the increased binding of anti-cytidine, anti-adenosine, and anti-thymidine antibodies. At lower levels of platinum adduct formation, however, all four anti-nucleoside antibodies bind more to DNA modified with trans-DDP. This result indicates that adducts formed by trans-DDP disrupt the DNA structure to a greater extent than those formed by cis-DDP at low D/N ratios. Modification of DNA by the monofunctional complex [Pt(dien)Cl]Cl does not affect its recognition by anti-nucleoside antibodies, demonstrating that base pair disruption is a consequence of bifunctional binding. The relative anti-nucleoside antibody recognition of cis-DDP-modified DNA is anti-cytosine greater than anti-adenosine approximately anti-thymidine much greater than anti-guanosine, consistent with the major adduct being an intrastrand d(GpG) cross-link. These results reveal that base pair disruption in a naturally occurring DNA modified by either cis-DDP or trans-DDP is sufficient to be detected by protein (antibody) binding. The relevance of these findings to current ideas about the molecular mechanism of action of cis-DDP is discussed.     

NMR and FT-IR conformational studies of 8-substituted guanine nucleosides and nucleotides and their metal adducts and cancer

NMR and FT-IR Studies of the conformational changes of guanosine and guanosine-5′-monophosphate upon substitution of the H8 of guanine by a heavy, large atom, such as bromine, are presented. The conformational forms, syn, anti, C2′-endo and C3′-endo and gg, gt and tg rotamers of the above molecules are compared to those of their metal (Mg²⁺ and P^t2+) adducts, where the metal is fixed to the N7 nitrogen atom of guanine. The antitumor activity of cisplatin is discussed with relation to the conformational form and the effect of cisplatin is compared to the effects of the Mg²⁺ ion and carcinogens.     

Guanine complexes with dysprosium(III), thorium(IV) and uranium(IV) chlorides

By refluxing mixtures of guanine (guH) and DyCl₃, ThCl₄ or UCl₄ in ethanol-triethyl orthoformate, solid complexes of the Dy(guH)₂(gu)Cl₂ and M(gu)₂Cl₂ (M = Th, U) types were isolated. The insolubility of the new complexes in organic media, combined with the coordination number six suggested by the spectral evidence, favors polymeric configurations. Most likely structures involve a linear, chainlike, single-bridged polymeric backbone

The Dy³⁺ complex is probably a linear polymer, also containing terminal unidentate guanine ligands, whilst for M = Th⁴⁺, U⁴⁺ highly polymeric structures arising from cross-linking between linear polymeric

units seems most likely. IR evidence rules out participation of the O(6) oxygen of guanine in coordination, despite the hard acid character of the metal ions under study. Guanine apparently coordinates exclusively through ring nitrogens in the new metal complexes; N(9) and N(7). N(9) are, respectively, the most likely binding sites of terminal unidentate and bridging bidentate guanine. The chloro ligands present in the complexes seem to be exclusively terminal.     

Synthesis of new compartmental amino-phenolic ligands. Basicity, coordination properties towards Cu(II) and Zn(II) ions. A fluorescent chemosensor for H and Zn(II)

The syntheses of three new compartmental ligands are reported. Each ligand shows two 1,4,7-triazaheptane (dien) moieties separated by different rigid aromatic groups. The dien unit is linked to the spacer through its central N-atom, while each aromatic moiety contains two hydroxyl-phenolic functions. The synthetic aspects involved in attaching two dien subunits to an aromatic group containing two hydroxyl functions were explored. Each ligand synthesized can coordinate two metal ions positioned far from each other; the single dinuclear units will be useful as building blocks in new supramolecular aggregates. The basicity and binding properties of one of the synthesized ligands (3,3′-bis[N,N-bis(2-aminoethyl)aminomethyl]-4,4′-dihydroxybiphenyl (L2)) were potentiometrically studied in aqueous solution. L2 was found to behave as a diprotic acid and as a pentaprotic base under the experimental conditions used. L2 forms stable mononuclear and dinuclear complexes with Cu(II) and Zn(II) ions; the mononuclear species show a tendency to dimerize, while the dinuclear ones are predominant in the presence of two equivalents of M(II) ions in solution.Both protonation and the presence of Zn(II) strongly affect the fluorescence emission properties of L2, which can be used as a new chemosensor for H⁺ and Zn(II) ions. L2 exhibits pH-dependent fluorescence and the emission due to the different protonation of L2 and can be ascribed, above all, to the degree of protonation of the 4,4′-biphenol unit; thus, L2 is more emitting at acidic pH values where the aromatic unit is fully protonated. On the contrary, the Zn-dinuclear species are more emitting from neutral to alkaline pH values exhibiting a CHEF effect which reaches its maximum values (seven times those of the free ligand) at pH 9 with the [Zn₂H₋₂L2]²⁺ species, thus highlighting the sensing properties of this new chemosensor towards Zn(II).     

Studies on Metabolic Pathway of NAD in Yeast

Quantitative studies on yeast 5′-nucIeotidase are presented.

K_m values for purine 5′-nucleotides were generally smaller than those for pyrimidine 5′-nucleotides and, among purine series, K_m value for 5′-AMP was the smallest, while their V values were almost same.

The enzyme activity was inhibited in the competitive type by bases, nucleosides, 3′- or 2′-nucleotides, and NMN and in the mixed type by NAD and NADP.

Base-, ribose-, 3′- or 5′-phosphate moiety of nucleoside and nucleotide had some effects on binding with enzyme; especially the structure of base moiety characterizes the K_m or K_i value.

The enzyme activity was accelerated by Ni⁺⁺ or Co⁺⁺, which increases V value but never affects K_m value.

The relationship between the structure of substrate and its affinity towards enzyme is discussed.     

Dicarbonylrhodium(I) complexes of 8-azaadenine bases with N1 or N3 as metal binding sites

Reaction of [Rh(CO)₂Cl]₂ with the bases 8-aza-9-methyladenine (MAAd) and 8-aza-9-benzyladenine (BAAd) yields the complexes [RhCl(CO)₂(MAAd)] (1) and [RhCl(CO)₂(BAAd)] (2), which were characterized by their IR and ¹H NMR spectra and by X-ray structural analyses. Whereas N1 of the pyrimidine ring is coordinated by rhodium in 1, N3 is the chosen position for 2 (purine numbering scheme). This finding is in accordance with MNDO calculations which indicate that N1 and N3 of the pyrimidine ring should complete as metal binding sites in N9-substituted 8-azaadenines. The rhodium(I) coordination plane is twisted with respect to the base ring system to dihedral angles of respectively 62.6° and 68.4° in 1 and 2. The relevance of the present findings for the biological properties of 8-azaadenine nucleosides is discussed.     

Interaction of some Pd(II) complexes with Na+ / K+-ATPase: inhibition, kinetics, prevention and recovery

The aim of this work was to investigate the influence of [PdCl4]2-, [PdCl(dien)]+ and [PdCl(Me4dien)]+ complexes on Na+ / K+-ATPase activity. The dose-dependent inhibition curves were obtained in all cases. IC50 values determined by Hill analysis were 2.25 x 10(-5) M, 1.21 x 10(-4) M and 2.36 x 10(-4) M, respectively. Na+ / K+-ATPase exhibited typical Michelis-Menten kinetics in the presence of Pd(II) complexes. Kinetic parameters (Vmax, Km) derived using Eadie-Hofstee transformation indicated a noncompetitive type of Na+ / K+-ATPase inhibition. The inhibitor constants (Ki) were determined from Dixon plots. The order of complex affinity for binding with Na+ / K+-ATPase, deducted from Ki values, was [PdCl4]2- > [PdCl(dien)]+ > [PdCl(Me4dien)]+. The results indicated that the potency of Pd(II) complexes to inhibit Na+/ K +-ATPase activity depended strongly on ligands of the related compound. Furthermore, the ability of SH-donor ligands, L-cysteine and glutathione, to prevent and recover the Pd(II) complexes-induced inhibition of Na+ / K+-ATPase was examined. The addition of 1 mM L-cysteine or glutathione to the reaction mixture before exposure to Pd(II) complexes prevented the inhibition by increasing the IC50 values by one order of magnitude. Moreover, the inhibited enzymatic activity was recovered by addition of SH-donor ligands in a concentration-dependent manner.