Nucleosides and nucleotides as potential therapeutic agents

The present article summarizes recent progress in the study of nucleoside derivatives as antiviral and immunosuppressive agents. A number of 5′-substituted 5′-deoxy nucleosides have been found to be permeable and nonincorporable antimetabolites of 5′-nucleotides. N⁶-isopentenyladenosine and analogs show certain promising immunosuppressive activities. Encouraged by the antibody-stimulating effect of oligonucleotides, we have developed a convenient synthesis of oligonucleotides using fully protected phosphorylated intermediates. A group of tetradeoxyribonucleotides, dApdApdApdX, was prepared for biological and physical evaluations. Nucleotide derivatives may prove valuable in the treatment of several immunological disorders.     

Nucleotides. Part LXXVIII

Several N(‐hydroxyalkyl)‐2,4‐dinitroanilines were transformed into their phosphoramidites (see 5 and 6 in Scheme 1) in view of their use as fluorescence quenchers, and modified 2‐aminobenzamides (see 9, 10, 18 , and 19 in Scheme 1) were applied in model reactions as fluorophors to determine the relative fluorescence quantum yields of the 3′‐Aba and 5′‐Dnp‐3′‐Aba conjugates (Aba=aminobenzamide, Dnp=dinitroaniline). Thymidine was alkylated with N‐(2‐chloroethyl)‐2,4‐dinitroaniline ( 24 ) to give 25 which was further modified to the building blocks 27 and 28 (Scheme 3). The 2‐amino group in 29 was transformed by diazotation into the 2‐fluoroinosine derivative 30 used as starting material for several reactions at the pyrimidine nucleus (→ 31, 33 , and 35 ; Scheme 4). The 3′,5′‐di‐O‐acetyl‐2′‐deoxy‐N²‐[(dimethylamino)methylene]guanosine ( 37 ) was alkylated with methyl and ethyl iodide preferentially at N(1) to 43 and 44 , and similarly reacted N‐(2‐chloroethyl)‐2,4‐dinitroaniline ( 24 ) to 38 and the N‐(2‐iodoethyl)‐N‐methyl analog 50 to 53 (Scheme 5). The 2′‐deoxyguanosine derivative 53 was transformed into 3′,5′‐di‐O‐acetyl‐2‐fluoro‐1‐{2‐[(2,4‐dinitrophenyl)methylamino]ethyl}inosine ( 54 ; Scheme 5) which reacted with 2,2′‐[ethane‐1,2‐diylbis(oxy)]bis[ethanamine] to modify the 2‐position with an amino spacer resulting in 56 (Scheme 6). Attachment of the fluorescein moiety 55 at 56 via a urea linkage led to the doubly labeled 2′‐deoxyguanosine derivative 57 (Scheme 6). Dimethoxytritylation to 58 and further reaction to the 3′‐succinate 59 and 3′‐phosphoramidite 60 afforded the common building blocks for the oligonucleotide synthesis (Scheme 6). Similarly, 30 reacted with N‐(2‐aminoethyl)‐2,4‐dinitroaniline ( 61 ) thus attaching the quencher at the 2‐position to yield 62 (Scheme 7). The amino spacer was again attached at the same site via a urea bridge to form 64 . The labeling of 64 with the fluorescein derivative 55 was straigthforward giving 65 . and dimethoxytritylation to 66 and further phosphitylation to 67 followed known procedures (Scheme 7). Several oligo‐2′‐deoxynucleotides containing the doubly labeled 2′‐deoxyguanosines at various positions of the chain were formed in a DNA synthesizer, and their fluorescence properties and the T_ms in comparison to their parent duplexes were measured (Tables 1–5).     

Fluorescent oligonucleotide incorporating 5-(1-ethynylpyrenyl)-2-deoxyuridine: sequence-specific fluorescence changes upon duplex formation

We describe the design and properties of a pyrene-labeled deoxyuridine that can be inserted efficiently into oligodeoxynucleotides using phosphoramidite chemistry. An oligonucleotide incorporating the pyrene-labeled deoxyuridine is a sensitive fluorescence probe that can discriminate between perfect and single-base-mismatched pairing by changes in its fluorescence intensity.     

Nucleotides. Part LXXVI

A series of new fluorescing 8‐(6‐hydroxyhexyl)isoalloxazine (=8‐(6‐hydroxyhexyl)benzo[g]pteridine‐2,4(1H,3H)‐dione) derivatives 4 – 13 were synthesized from 6‐[(6‐hydroxyhexyl)amino]uracil ( 2 ) with 1‐chloro‐4‐nitrosobenzene via 8‐chloro‐10‐(6‐hydroxyhexyl)isoalloxazine ( 3 ) and subsequent substitution of the Cl‐atom of 3 by various amines (Scheme). Analogously, 8‐substituted 10‐{3‐[(2,2‐dimethyl‐1,3‐dioxolan‐4‐yl)methoxy]propyl}isoalloxazines 19, 20 , and 23 – 25 were prepared which yielded on deprotection the corresponding 10‐[3‐(2,3‐dihydroxypropoxy)propyl]alloxazines 21, 22 , and 26 – 28 . Their conversion into the 3″‐O‐(4,4′‐dimethoxytrityl) derivatives 29 – 33 and subsequent transformation into the corresponding 2″‐(2‐cyanoethyl N,N‐diisopropylphosphoramidites) 34 – 38 led to new building blocks for oligonucleotide synthesis. A series of 21‐mer oligodeoxyribonucleotides carrying the fluorescing isoalloxazine 37 in various positions of the chain were assembled in a DNA synthesizer. Combination with the complementary sequence yielded the stable duplexes 40 – 54 showing by the melting temperatures T_m that the fluorophor ( F ) does not harm the stability of the unmodified duplex 39 (Table).     

A direct method for the synthesis of nucleoside 5′-methylenebis(phosphonate)s from nucleosides

An efficient method for the preparation of nucleoside 5′-methylenebis(phosphonate)s has been developed. Unprotected nucleosides are phosphonylated directly with methylenebis(phosphonic dichloride). Reaction conditions were optimized to prevent side product formation.     

In-water reactivity of nucleosides and nucleotides: one-step preparation and biological evaluation of novel ferrocenyl-derivatives

The reactivity in water of a series of nucleosides and nucleotides towards ferrocenemethanol was investigated. Several adducts incorporating the ferrocenemethyl moiety into the heterocyclic base were isolated and their activity was tested against HIV-1, HBV, YFV, BVDV and several bacteria. However, none of the new compounds showed significant antiviral activity nor cytotoxicity. The reaction with ferrocenemethanol of the model dinucleotide ^5′dCpdG^3′, for a direct comparison of the behaviour of purine versus pyrimidine bases, is also discussed.     

胶束电动力学毛细管色谱法测定尿中核苷

用胶束电动力学毛细管色谱法测定尿中核苷.通过苯基硼酸亲和色谱柱对尿中核苷进行纯化,以十二烷基磺酸钠(SDS)-十水合四硼酸钠-磷酸二氢钠为缓冲液(pH=6.96),在未涂层石英毛细管上,于7kV恒压,29℃下进行电泳分离,检测波长为254nm.此方法用于28个正常人尿中14种核苷的测定,确定了正常成年人(汉族)尿中核苷的排放范围.     

Cleavage of Nucleotides by Lanthanide Metal Complexes*

ＩｎｔｒｏｄｕｃｔｉｏｎＳｙｎｔｈｅｔｉｃｎｕｃｌｅａｓｅｓｗｈｉｃｈｅｆｉｃｉｅｎｔｌｙａｎｄｓｅｌｅｃｔｉｖｅｌｙｍａｋｅｎｕｃｌｅｉｃａｃｉｄｓｃｌｅａｖｅｄｕｎｄｅｒｍｉｌｄｃｏｎｄｉｔｉｏｎｓｈａｖｅｍａｎｙｉｍｐｏｒｔａｎｔｐｏｔｅｎｔｉ...     

Nucleotides. Part LXXIX

Two series of new ribonucleoside 3′‐phosphoramidites (see 36 – 42 ) carrying the photolabile [2‐(2‐nitrophenyl)propoxy]carbonyl group at the 5′‐O‐position were synthesized and characterized as monomeric building blocks for photolithographic syntheses of RNA chips. Base protection was achieved in the well‐known manner by the 2‐(4‐nitrophenyl)ethyl (npe) and the [2‐(4‐nitrophenyl)ethoxy]carbonyl (npeoc) group. The carbohydrate moiety carried in addition the 2′‐O‐(tetrahydro‐4‐methoxy‐2H‐pyran‐4‐yl) group for blocking the 2′‐OH function.     

Rapid Chromatographic Analysis of Nucleosides and N-Bases in Physiologic Fluids

Abstract

A high-resolution anion-exchange system has been developed to analyze specifically for the nucleosides and bases present in physiologic fluids. This sytem employs a unique coupled-column operation that allows rapid column stripping and regeneration on completion of each run. Results obtained in the analysis of urine for nucleosides and bases are presented.     

Nucleotides. Part LXXV

The reactivity of the 2′‐deoxy‐N⁴‐(phenoxycarbonyl)cytidine derivatives 3 and 4 with aromatic amines was studied to form new types of urea derivatives (see 5 – 10 ). On the same basis, labeling of 3 and 4 with 5‐aminofluorescein ( 14 ) was achieved to give the conjugates 15 and 17 , respectively (Scheme 1). Treatment of 17 with 2‐(4‐nitrophenyl)ethanol in a Mitsunobu reaction led to double protection of the fluorescein moiety (→ 18 ) and desilylation yielded 19 . Dimethoxytritylation (→ 20 ) and subsequent phosphitylations afforded the new building blocks 21 and 22 . Synthesis of the fully protected trimer 28 was achieved by condensation of 21 with 23 to 26 which after detritylation (→ 27 ) was coupled with 25 to give 28 (Scheme 2). Deprotection of all blocking groups was performed with 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) in one step to give 29 . The synthesis of the decamer 5′‐d(C^FluCCG GCC CGC)‐3′ ( 33 ) started from 30 which was attached to the solid support and then elongated with 31, 32 , and 22 at the 5′‐terminal end (C^Flu=deprotected phosphate derivative of 22 ). Hybridization with the complementary oligomer 5′‐d(G GGC CGG GCG)‐3′ ( 34 ) showed the influence of the fluorescein label on the stability of the duplex.     

Interactions of cadmium(II) ions with adenosine as well as adenosine-5′-monophosphate and diamine or triamines in the ternary systems

The mode of coordination in complexes formed in the systems Cd(II)/Ado/di- or triamine and Cd(II)/AMP/di- or triamine has been established on the basis of the equilibrium and spectral investigation. The overall stability constants (log?β) and equilibrium constants of formation (log?K _e) of the complexes formed in the above systems have been determined. In the species, the main interaction centres are the nitrogen atoms N(1) or N(7) of the purine ring of Ado and AMP, while in the nucleotide also the oxygen atoms of the phosphate group and donor nitrogen atoms of the polyamine (PA) molecule. The effect of polyamine on the coordination dichotomy has been ascertained. For example, the presence of polyamine in the ternary system is responsible for involvement of only N(7) of the nucleoside in the metallation in Cd(Ado)H(Put), while in the binary system Cd(II)/Ado, the N(1)/N(7) dichotomy occurs in the whole pH range studied. Polyamine can also affect the character of the phosphate group of the nucleotide. The phosphate group, inactive in the binary system Cd(II)/AMP, after introduction of the polyamine becomes engaged in the interactions, e.g. in the complex Cd(AMP)H(dien). In Cd(AMP)H(en) and Cd(AMP)H(Put) no participation of the oxygen atom of the phosphate group has been found. This group is involved in weak interactions with a protonated amine group PA located in the outer coordination sphere. On the other hand, in the Cd(AMP)H(3,3-tri) complex the phosphate group is the only site of Cd(II) bonding. In this species the donor nitrogen atoms N(1) and N(7) of the nucleotide are outside the inner coordination sphere and involved in noncovalent interactions with protonated amine group from 3,3-tri.     

Nucleotides and nucleolipids derivatives interaction effects during multi-lamellar vesicles formation

In this paper a micellar interface, constituted by the cationic surfactant CTAB, in presence of 1,2-epoxydodecane and nucleotides was used for catanionic multi-lamellar vesicles (MLVs) formation. The micellar solution of CTAB is able to disperse the 1,2 epoxydodecane in the micellar core promoting the reaction of this reagent with the nucleotide attracted by the positive surface charge of the micellar aggregates. The alkylation of AMP and UMP nucleotides leads to the synthesis of nucleolipids. The behaviour of the supramolecular structures formed depends on the starting reagents (AMP, UMP and AMP+UMP) and on the assembly capabilities of the products. In particular nucleotides and nucleotides derivatives interaction effects are evaluated during the multi-lamellar vesicles formation. NMR spectroscopy and UV-vis measurements performed on MLVs showed strong aryl interactions. Interestingly, NMR spectra revealed prevailing stacking interactions between complementary nucleolipids. The assembly of complementary nucleotides affects the course of the reaction during the MLVs formation. Moreover the MLVs supramolecular stability has been tested by means of turbidity and UV-vis measurements. In particular, an enhanced stability has been found in systems prepared with complementary nucleotides confirming that in these systems the self-assembly process is influenced by nucleolipids interactions. Furthermore by following the hypocromic effect during the micellar catalysis, we showed that even in the earlier stages of the reaction significant differences are detectable.     

High-Performance Liquid Chromatography of some Bases and Nucleosides on Alkylphosphonate-Modified Magnesia-Zirconia Column

ABSTRACT

The high-performance liquid chromatographic behavior of some bases and nucleosides was studied on a new reversed-phase stationary phase, alkylphosphonate-modified magnesia-zirconia. The effect of mobile phase variable such as methanol content, ionic strength and pH on their behavior was investigated. It was found that the retention behavior of the bases and nucleosides on the new stationary phase is similar to that on ODS stationary phase. The retention mechanism on the new stationary phase was also discussed. The separation of some bases and nucleosides was accomplished on the new stationary phase.     

Interference of Copper(II) ions with Non-covalent Interactions in Uridine or Uridine 5′-Monophosphate Systems with Adenosine,Cytidine, Thymidine and their Monophosphates in Aqueous Solution

Coordination reactions of copper(II) ions and their effect on non-covalent interactions in uridine (Urd) or uridine 5′-monophosphate (UMP) systems with nucleosides (Ado, Cyd, Thd) and nucleotides (AMP and CMP) in aqueous solutions have been studied. At high pH the effective coordination centers are deprotonated N(3) atoms from Urd and Thd, whereas at low pH, the N(3) atoms of pyrimidine nucleosides are blocked for coordination and the metallation sites are endocyclic nitrogen atoms from Ado, Cyd, AMP and CMP. Moreover, at low pH, the main reaction center in nucleotide solutions is the phosphate group. The NMR study has proven the occurrence of non-covalent ion-dipole interactions and stacking interactions in the systems considered. Introduction of a copper ion in the majority of systems causes the disappearance of weak interactions between ligands. The structures of the complexes in solution have been inferred from the equilibrium study: an analysis of the pH range of their occurrence with respect to the pH range of deprotonation of particular groups in the compounds studied, using Vis, EPR and ¹³C as well as ³¹P NMR spectral analysis.     

Synthesis of Functionalized Lipids,and Their Use for a Tunable Hydrophobization of Nucleosides and Nucleic Acids

Two series of functionalized single and double side‐chained lipid molecules (Schemes 1 and 2) were prepared. The compounds carry either terminal COOH, OH, or halogen substituents. Moreover, the double side‐chained lipid 18 carries an internal alkyne functionality. The latter compound was used to hydrophobize thymidine at N(3) by base‐catalyzed alkylation. Additionally, fully protected thymidine, 32 , was N(3)‐alkylated with the double side‐chained alcohol 9 applying Mitsunobu reaction conditions.     

高效毛细管电泳-安培检测研究核苷酸水解反应

核酸是重要的生命物质,近些年来,对核酸水解作用的研究已成为人们关注的焦点,寻找一种在温和的生理条件下能够迅速催化水解核酸的人工酶,对于进一步探索核酸的结构及其在生命活动中的作用,阐明细胞间信息传递的机理,以及对于抗癌药物的研制等具有重要意义.有关稀土金属离子及其配合物对核酸的催化作用已有报道[1～3],这种选择性的水解作用断裂点单一,无碎片产生,克服了以往通过氧化作用断裂核酸带来的弊端[4～5],但其作用的机理、水解体系的优化尚需进一步的探讨.以往对核酸水解作用的研究,主要是通过高效液相色谱(HPLC)[1,6]、化学滴定和…