Emissive RNA alphabet

A fluorescent ribonucleoside alphabet consisting of highly emissive purine ((th)A, (th)G) and pyrimidine ((th)U, (th)C) analogues, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, is described. Structural and biophysical analyses demonstrated that the emissive analogues are faithful isomorphic nucleoside surrogates. Photophysical analysis established that the nucleosides offer highly desirable qualities, including visible emission, high quantum yield, and responsiveness to environmental perturbations, traits entirely lacking in their native counterparts.     

Probing the reactivity of nebularine N1-oxide. A novel approach to C-6 C-substituted purine nucleosides

A novel approach to the synthesis of purine nucleoside analogues, featuring the reaction of the C6-N1-O⁻ aldonitrone moiety of 9-ribosyl-purine (nebularine) N1-oxide with some representative dipolarophiles, as well as Grignard reagents, is reported. Addition of Grignard reagents to the electrophilic C-6 carbon of the substrate allows a facile access to C-6 C-substituted purine nucleosides without using metal catalysts. 1,3-Dipolar cycloaddition processes lead to novel nucleoside analogues via opening, degradation or ring-enlargement of the pyrimidine ring of the base system of the first-formed isoxazoline or isoxazolidine cycloadduct.     

Nucleoside-boron cluster conjugates - Beyond pyrimidine nucleosides and carboranes

General methods for the synthesis of new purine and pyrimidine nucleosides modified with borane clusters and metallacarborane complexes are presented. They include: (1) attachment of carborane modification at 2′ position of nucleoside via formacetal linkage formation, (2) tethering of the metallacarborane group at nucleobase part of the nucleoside via dioxane ring opening in oxonium metallacarborane, carborane or dodecaborate derivatives, and (3) ‘‘click” chemistry approach based on Huisgen 1,3-dipolar cycloaddition. Proposed methodologies extend the range of nucleoside-boron cluster conjugates available and open new areas for their applications.     

Selectivity between N-1 and N-7 nucleosides: regioselective synthesis of BMK-Y101, a potent cdk7 and 9 inhibitor

BMK-Y101 is a new pyrrolo[2,3-d]pyrimidine-based potent cdk7 and 9 inhibitor, which is characterized by an intriguing structural feature of N-1 nucleoside, departing from previously reported N-7 nucleoside Cdk inhibitor, xylocydine. Though N-1 nucleosides have appeared in the literature, they have often been considered as kinetic products and thus intermediates of N-7 glycosylation. In the course of the synthetic studies of xylocydine derivatives, we have developed a highly regioselective method to obtain the N-1 nucleoside. The origin of the selectivity is apparently based on the reactivity of the silylated nucleobase and the stability of the resulting N-1 nucleoside. The choice of BSA as a silylating agent was critical in securing the N-1 nucleoside, BMK-Y101. On the other hand, proper selection of reaction conditions promoting transglycosylation provides an efficient route to N-7 nucleosides.     

Synthesis and Reactions of Some Novel Triazolo‐, Azolo‐, Tetrazolo‐Pyridopyrimidine and Their Nucleoside Derivatives

Pyridopyrimidine reacted with aromatic aldehydes afforded the arylhydrazone 2a,b which could be cyclized into the pyrido[2,3‐d][1,2,4]triazolo[4,3‐a]pyrimidine 3a,b , with formic acid, and carbon disulphide to give pyrido[2,3‐d][1,2,4]traizolo[4,3‐a]pyrimidine 4, 5. Reaction of 1 with nitrous acid afforded tetrazolo[1,5‐a]pyrido[2,3‐d]pyrimidine 6 , which was reduced by zinc dust to give 2‐amino‐pyrido‐[2,3‐d]pyrimidine 7. Finally the reaction of 2‐hydrazino 1 with D‐xylose or D‐glucose afforded the acyclic N‐nucleoside 8, 11 which were converted into tetra/penta O‐acetate acyclic C‐nucleoside 9, 12 in acetic anhydride/pyridine. De‐acetylation of compounds 9, 12 afforded C‐nucleosides 10, 13.     

New nucleoside analogues and their 5′-triphosphates: Synthesis and biological properties

Bicyclic furano-and pyrrolo[2,3-d]pyrimidine nucleosides and purine nucleosides modified at the N¹ atom and/or the 6-position have been synthesized. Among the tested nontoxic bicyclic nucleosides and N⁶-carboxyalkyladenosines, only furo[2,3-d]pyrimidine with the C₁₀H₂₁ substituent and N⁶-carboxymethyladenosine exhibit moderate anti-HCV activity in the virus replicon system and N¹-hydroxyinosine exhibits high anti-HCV activity and significant cytotoxicity. The corresponding 5′-triphosphates have been synthesized and studied as substrates/inhibitors of HCV enzymes: NS5B protein (RNA-dependent RNA polymerase) and NS3 protein (NTP-dependent RNA helicase).     

Preparation of 8‐Aza‐7‐deazaaristeromycin and ‐neplanocin A and Their 5′‐Homologs

The synthesis of new members of the aristeromycin and neplaoncin A families of carbocyclic nucleosides possessing the 1H‐pyrazolo[3,4‐d]pyrimidine ring is reported. For this purpose, an adapted route to 4‐amino‐1H‐pyrazolo[3,4‐d]pyrimidine is described.     

Synthesis of some acyclonucleosides with the alkylating chain of acyclovir

The synthesis of some acyclic 1-[1,2,3-triazol-(4 and 5)-ylmethyl]-1H-pyrazolo[3,4-d]pyrimidine nucleosides, via 1,3-dipolar cycloaddition reaction, from 4-substituted N₁-propargyl-1H-pyrazolo[3,4-d]pyrimidines 7a,b and azido derivative 8 is described. Compounds 7a,b and all deprotected acyclic nucleosides 11a,b, 12a,b and 13–22 were evaluated against: HIV-1, HIV-2 and a series of tumour cell-lines. No marked activity was found. Their anti-tuberculosis evaluation showed that compound 7b had marked activity.     

Efficient synthesis of 5′-O(N)-carbamyl and -polycarbamyl nucleosides

A simple and efficient method for the preparation of 5′-O(N)-carbamyl and 5′-O(N)-polycarbamyl nucleoside derivatives is reported. The method consisted of treatment of 2′,3′-O-protected purine (Ado, Ino) or pyrimidine nucleosides (Thd, Urd) with trichloroacetylisocyanate, followed by cleavage of the trichloroacetyl moiety by silica-gel promoted methanolysis during column chromatography. Iterative application of this method gave mono, di, and tricarbamyl derivatives in good to excellent yields (ave = 80%).     

9-Deazapurine nucleosides. The synthesis of certain N-5-β-d-ribofuranosylpyrrolo[3,2-d]pyrimidines

Several N-5 ribofuranosyl-2,4-disubstituted pyrrolo[3,2-d]pyrimidine (9-deazapurine) nucleosides were prepared by the single phase sodium salt glycosylation of 2,4-dichloro-5H-pyrrolo[3,2-d]pyrimidine ( 3 ) using 1-chloro-2,3-O-isopropylidene-5-O-(t-butyl)dirnethylsilyl-α-D-ribofuranose ( 2 ). Use of 2 for the glycosylation avoided the formation of “orthoamide” products 1 and provided an excellent yield of the β nucleoside, 2,4-dichloro-5-[2,3-O-isopropylidene-5-O-(t-butyl)dimethylsilyl-β-D-ribofuranosyl]-5H-pyrrolo[3,2-d]pyrimidine ( 4 ), along with a small amount of the corresponding α anomer, 5 . Compound 4 served as the versatile intermediate from which the N-7 ribofuranosyl analogs of the naturally-occurring purine nucleosides adenosine, inosine and guanosine were synthesized. Thus, controlled amination of 4 followed by sugar deprotection and dehalogenation yielded the adenosine analog, 4-amino-5-β-D-ribofuranosyl-5H-pyrrolo[3,2-d]pyrimidine ( 8 ) as the hydrochloride salt. Base hydrolysis of 4 followed by deprotection gave the 2-chloroinosine analog, 10 , and subsequent dehalogenation provided the inosine analog, 5-β-D-ribofuranosyl-5H-pyrrolo[3,2-d]-pyrimidin-4(3H)-one ( 11 ). Amination of 10 furnished the guanosine analog, 2-amino-5-β-D-ribofuranosyl-5H-pyrrolo[3,2-d]pyrimidin-4(3H)-one ( 12 ). Finally, the α anomer in the guanosine series, 16 , was prepared from 5 by the same procedure as that used to prepare 12 . The structural assignments were made on the basis of ultraviolet and proton nmr spectroscopy. In particular, the isopropylidene intermediates 9 and 14 were used to assign the proper configuration as β and α, respectively, according to Imbach's rule.     

Single-molecule fluorescence detection of a tricyclic nucleoside analogue

Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε₄₄₂ = 20 000 M⁻¹ cm⁻¹ and Φ_em,540 = 0.39 in water, increasing to Φ_em = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities.

Fluorescent nucleoside analogue ABN is readily detected at the single-molecule level and retains a quantum yield >50% in duplex DNA oligonucleotides.     

Synthesis, structure, and biological evaluation of C-2 sulfonamido pyrimidine nucleosides

The C-2 sulfonamido pyrimidine nucleosides were prepared by opening the 2,2′- or 2,3′-bond in anhydronucleosides under nucleophilic attack of sulfonamide anions. Reaction of the sodium salt of p-toluenesulfonamide or 2-(aminosulfonyl)-N,N-dimethylnicotinamide with 2,2′-anhydro-1-(β-d-arabinofuranosyl)cytosine gave the C-2 sulfonamido derivatives in excellent yields. Ring opening of the less reactive 2,2′-anhydrouridine and 2,3′-anhydrothymidine could be accomplished with DBU/CH₃CN activation of p-toluenesulfonamide, giving moderate yields for C-2 sulfonamido derivatives. The action of acetic acid or ZnBr₂/CH₂Cl₂ on 5-methyl-N²-tosyl-1-(2-deoxy-5-O-trityl-β-d-threo-pentofuranosyl)isocytosine led to the cleavage of both the protection group and the nucleoside bond, yielding 5-methyl-N²-tosylisocytosine as the major product. Structures of the prepared C-2 sulfonamido nucleosides were confirmed by the 1D and 2D NMR experiments, and X-ray structural analysis of 4-imino-N²-tosylamino-1-(β-d-arabinofuranosyl)pyrimidine. Both methods confirmed β-configuration and anti-conformation of the 2-sulfonamido nucleosides. The investigated compounds displayed moderate inhibition of tumor cell growth in vitro, as determined by the MTT assay using six different human tumor cell lines.     

Efficient desulfurization of 2-thiopyrimidine nucleosides to the corresponding 4-pyrimidinone analogues using trans-2-(phenylsulfonyl)-3-phenyloxaziridine

A brief treatment of 2-thiopyrimidine nucleosides (s²U^∗) with trans-2-phenylsulfonyl-3-phenyloxaziridine (PSO) results in efficient substrate desulfurization leading to the corresponding 4-pyrimidinone analogues (H²U^∗). The key transformation proceeds through oxidation of the 2-thiocarbonyl group to a sulfur oxyacid derivative and subsequent elimination of sulfur dioxide. 4-Pyrimidinone 1-β-d-riboside (H²U) has been transformed into the respective phosphoramidite, a ready-to-use monomer for the introduction of a modified nucleoside into an oligonucleotide chain. Moreover, the effective desulfurization of the 2-thiouridine nucleotide could be achieved directly at the oligonucleotide level, by treatment of the TdA(s²U)dGdC oligonucleotide with PSO, as verified by MALDI-TOF mass spectrometry.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

嘧啶并呋咱核苷衍生物的制备及其活性初探

4H,6H-[1,2,5]噁二唑并[3,4-d]嘧啶-5,7-二酮1-氧化物(1)和6-甲基-4H,6H-[1,2,5]噁二唑并[3,4-d]嘧啶-5,7-二酮1-氧化物(2)是一氧化氮(NO)供体, 将它们分别在无溶剂条件下与高温熔融的全乙酰基保护的核糖、木糖、葡萄糖进行糖基化反应, 分别得到相应的噁二唑并[3, 4-d]嘧啶核苷类化合物7, 9～12, 化合物7经NH₃-MeOH处理, 去O-乙酰基制得8, 这些新型核苷化合物可作为潜在的NO供体. 部分此类化合物的生物活性研究表明, 嘧啶并呋咱核苷衍生物具有抗病毒、抗肿瘤活性, 为研究抗病毒、抗肿瘤药物提供了新结构类型的候选化合物.     

Azetidines-Containing Fluorescent Purine Analogs: Synthesis and Photophysical Properties

Analogues of N,N-dimethyladenine exploiting both thieno-and isothiazolo-pyrimidine cores were modified with 3-subsituted azetidines to yield visibly emissive and responsive fluorophores. The emission quantum yields, among the highest seen for purine analogues (0.64 and 0.77 in water and dioxane respectively), correlated with the Hammett inductive constants of the substituents on the azetidine ring. Ribosylation of the difluoroazetidino-modified nucleobase yielded an emissive nucleoside that displayed a substantially lower emission quantum yield in water, compared to the precursor nucleobase. Importantly, high emission quantum yield was restored in deuterium oxide, which highlights the potential impact of the sugar moiety on the photophysical features of fluorescent nucleosides, a functionality usually considered non-chromophoric and photophysically benign.     

Conformation of nucleoside antibiotics

Minor modifications or substitutions in the sugar or in the base part of pyrimidine and purine nucleosides have a profound effect on their biological activity. These modified nucleosides usually become antiviral, antibacterial, or cancerostatic agents and they are collectively called nucleoside antibiotics. The conformational properties of some of these nucleoside antibiotics have been studied by the PCILO method. The results obtained from such study indicate that the conformational preferences of these nucleoside antibiotics are very similar to those of their parent nucleosides and especially so in the situations that occur in aqueous solutions. The important biological significance of these results is that these nucleoside antibiotics can easily get incorporated into growing chains of DNA and RNA by mimicking their parent nucleosides and can interfere with the protein synthesis of RNA or DNA synthesis.     

Synthesis of a novel uridine analogue and its use in attempts to form new cyclonucleosides using ring-closing metathesis

One novel nucleoside analogue having a hex-5-enyl group and an allyl group in the 5′-C and 3-N position was synthesized regio- and diastereoselectively from d-glucose in twelve steps. In order to reach a particular conformation of nucleosides the nucleoside formation of restricted cyclonucleoside analogues was studied via Ring-Closing Metathesis.     

3′-Selective modification of a 4′,5′-didehydro-5′-deoxy-2′,3′-epoxyuridine using nucleophiles

1-(2,3-Anhydro-5-deoxy-4,5-didehydro-α-l-erythro-pent-4-enofuranosyl)uracil 4 was obtained by the treatment of 5′-iodo-2′,3′-epoxyuridine 5 with LiHMDS in excellent yield. The pyrimidine nucleoside 4 possesses quite unique vinyl epoxide moiety within the molecules. The reactions of 4 with a variety of nucleophiles gave 3′-substituted pyrimidine nucleosides without the formation of the corresponding 2′-substituted isomers. In the case of NaN₃ or PhSH, the corresponding 5′-adduct was obtained as a minor product together with the expected 3′-adduct.