Efficient N-Arylation and N-Alkenylation of the Five DNA/RNA Nucleobases

Synthesis of Rigid Rod, Trigonal, and Tetrahedral Nucleobase-Terminated Molecules

An efficient fragment splicing method for the construction of multiple nucleobase-terminated monomers has been developed. Conformationally fixed rod, trigonal planar and tetrahedral thymine and adenine structures were generated in moderate to good yields, which will serve as inspiring examples for exploration of nucleobases as natural hydrogen-bond components in supramolecular chemistry.

Double-headed nucleosides: Synthesis and applications

Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.

Recent developments in selective N-arylation of azoles

Transition-metal based carbon-heteroatom (C-X) bond formation has attracted the attention of synthetic chemists over the past few years because the resultant aryl/heteroaryl motifs are important substructures in many natural products, pharmaceuticals, etc. Several efficient protocols such as Buchwald-Hartwig amination, Ullmann coupling, Chan-Lam coupling and metal-free approaches have proved beneficial in C-X bond formation. Selective arylation of one hetero-centre over other centres without protection/deprotection thus allowing minimum synthetic manipulation has been achieved for several substrates using these protocols. Azoles are one such novel five-membered heterocyclic core with huge pharmaceutical applications. Though N-arylation on azole-bearing analogues has been extensively practised, selective N-arylation either on one N-centre or the exocyclic N-site of the azole ring in competition with other hetero-centres in the framework has been recently explored for azole-carrying systems. Thus, this review would focus on recent advances in chemo- and regio-selective N-arylation (either on one N-centre or the exocyclic N-site of the azole ring) on azole-containing frameworks.

Chan-Evans-Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

The Chan–Evans–Lam reaction of 1-unsubstituted 4-fluoroalkylpyrimidin-2(1Н)-ones with arylboronic acids is reported as a facile synthetic route to hitherto unavailable N1-(het)aryl and N1-alkenyl derivatives of the corresponding pyrimidines. An efficient C–N bond-forming process is also observed by using boronic acid pinacol esters as coupling partners in the presence of Cu(II) acetate and boric acid. The 4-fluoroalkyl group on the pyrimidine ring significantly assists in the formation of the target N1-substituted products, in contrast to the 4-methyl and 4-unsubstituted substrates which do not undergo N1-arylation under similar reaction conditions.

A diversity of alkylation/acylation products of uracil and its derivatives: synthesis and a structural study

tert-Butyl dicarbonate (Boc2O) and ethyl iodide (EtI) reactions with uracil (U), thymine (T) and 6-methyluracil (6-MU) were performed following routine procedures in pyridine/DMF solvents and with DMAP as the catalyst. Among 20 synthesized compounds, a derivative of 6-methyluracil substituted by the Boc-pyridine moiety at the C5 position appeared unexpectedly. The NMR spectra confirmed the molecular structure of all uracil derivatives. Parallel quantum mechanical DFT calculations supported the experimental findings.

N,O-Bidentate ligand-tunable copper(ii) complexes as a catalyst for Chan-Lam coupling reactions of arylboronic acids with 1H-imidazole derivatives

An efficient procedure for Chan-Lam coupling reactions of arylboronic acids with 1H-imidazole derivatives using N,O-bidentate ligand-tunable copper(ii) complexes as a catalyst under base-free conditions has been developed. This protocol features mild reaction conditions, high yields and compatibility with different functional groups, providing a direct and facile strategy for the construction of C-N bonds and synthesis of heterocyclic compounds.

Benzene-glycol nucleic acid (BGNA)–DNA chimeras: synthesis, binding properties, and ability to elicit human RNase H activity

This paper describes the synthesis and properties of benzene-glycol nucleic acid (BGNA)–DNA chimeras containing four nucleoside analogs – thymidine, cytidine, adenosine, and guanosine – with a base-benzene-glycol structure.

Copper-Catalyzed Inter- and Intramolecular C-N Bond Formation: Synthesis of Benzimidazole-Fused Heterocycles

A Cu (II)-catalyzed, inter/intramolecular C-N bond formation for the synthesis of various benzimidazole-fused heterocycles in a concise manner has been reported. The robustness of this reaction is demonstrated by the synthesis of a series of benzimidazole-fused heteroaromatics (e.g., pyrido[1,2-a] benzimidazole, benzimidazo[1,2-a]quinolines, benzimidazo [1,2-a]pyrazine, benzo[4,5] imidazo[2,1-b]thiazoles) directly from 2-aminoheteroarenens and 2-iodoarylboronic acids in one-pot. The novel cascade protocol for C-N bond formation operates via unique combination of Chan-Lam type coupling followed by Ullmann-type reaction.

Double-headed nucleotides introducing thymine nucleobases in the major groove of nucleic acid duplexes

Four different double-headed nucleosides each combining two thymine nucleobases with different linkers were synthesised. The 5-position of 2'-deoxyuridine was connected to the N1-position of a thymine through either m- or p-disubstituted phenyl or phenylacetylene linkers by the use of Suzuki or Sonogashira couplings. When introduced into oligonucleotides, the thermal stability of dsDNA and DNA : RNA duplexes were determined and structural information was obtained from CD- and fluorescence spectroscopy. Also the recognition of abasic sites was studied. In general, the more stable duplexes were obtained with m- rather than p-substitution and with phenylacetylene rather than phenyl linkers.

Thymine functionalised porphyrins, synthesis and heteromolecular surface-based self-assembly

The synthesis and surface-based self-assembly of thymine-functionalised porphyrins is described. Reaction of 1-formylphenyl-3-benzoyl-thymine with suitable pyrollic species leads to the formation of tetra-(phenylthymine)porphyrin (tetra-TP) or mono-thymine-tri-(3,5-di-tert-butylphenyl)porphyrin (mono-TP). Single crystal X-ray diffraction studies demonstrate the self-association of mono-TP in the solid state through thymine···thymine hydrogen-bonding interactions but in solution this interaction (Kd = 6.1 ± 3.0 M-1) is relatively weak in comparison to the heteromolecular interaction between mono-TP and 9-propyladenine (K = 91.8 ± 20.5 M-1). STM studies of the tetratopic hydrogen-bonding tecton, tetra-TP, deposited on an HOPG substrate reveal the formation of an almost perfectly square self-assembled lattice through thymine···thymine hydrogen-bonding. Co-deposition of tetra-TP with 9-propyladenine leads to the adoption of preferable thymine···adenine interactions leading to the formation of a heteromolecular tetra-TP···9-propyladenine hydrogen bonded array including both Watson-Crick thymine···adenine interactions and adenine···adenine hydrogen-bonding. The studies demonstrate a pathway for the self-assembly of tetratopic hydrogen-bonding tectons and the use of preferential heteromolecular thymine···adenine interactions for the disruption of the homomolecular tetra-TP array. Studies of the self-assembly of tetra-TP and 9-propyladenine demonstrate a strong dependence on overall concentration and molar ratio of components indicating the importance of kinetic effects in surface self-assembly processes.

New developments in direct functionalization of C–H and N–H bonds of purine bases via metal catalyzed cross-coupling reactions

This review provides a concise overview on the cross-coupling reactions in direct functionalization of purine bases in recent years.

Direct N9-arylation of purines with aryl halides

The reported protocol is the first to be demonstrated to efficiently couple aryl halides to purines with predictable selectivity.

A convenient, highly selective and eco-friendly N-Boc protection of pyrimidines under microwave irradiation

A novel and practical microwave-assisted, highly selective N3-Boc protection of pyrimidine nucleobases in eco-friendly DEM/EtOH solvent, under mild conditions and moderate to high yield is described.

Synthesis and broad spectrum antiviral evaluation of bis(POM) prodrugs of novel acyclic nucleosides

A series of seventeen hitherto unknown ANP analogs bearing the (E)-but-2-enyl aliphatic side chain and modified heterocyclic base such as cytosine and 5-fluorocytosine, 2-pyrazinecarboxamide, 1,2,4-triazole-3-carboxamide or 4-substituted-1,2,3-triazoles were prepared in a straight approach through an olefin acyclic cross metathesis as key synthetic step.

All novel compounds were evaluated for their antiviral activities against a large number of DNA and RNA viruses including herpes simplex virus type 1 and 2, varicella zoster virus, feline herpes virus, human cytomegalovirus, hepatitis C virus (HCV), HIV-1 and HIV-2. Among these molecules, only compound 31 showed activity against human cytomegalovirus in HEL cell cultures with at EC₅₀ of ∼10 μM. Compounds 8a, 13, 14, and 24 demonstrated pronounced anti-HCV activity without significant cytotoxicity at 100 μM.

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The synthesis of new acyclonucleoside phosphonates is proposed.

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Challenging olefin acyclic cross metathesis is the key synthetic step.

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CuAAC reaction under microwave activation led to substituted-1,2,3-triazoles.

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Compounds exhibited pronounced anti-HCV activity.

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Compounds were also evaluated on a wide panel of other viral strains.

Steering supramolecular patterns by nucleobase-terminated molecules

Supramolecular patterns formed by adsorption from a liquid of nucleobase-terminated molecular rods on a graphite surface were investigated by scanning tunneling microscopy.

A click chemistry approach to pleuromutilin derivatives, part 2: conjugates with acyclic nucleosides and their ribosomal binding and antibacterial activity

Pleuromutilin is an antibiotic that binds to bacterial ribosomes and thereby inhibit protein synthesis. A new series of semisynthetic pleuromutilin derivatives were synthesized by a click chemistry strategy. Pleuromutilin was conjugated by different linkers to a nucleobase, nucleoside, or phenyl group, as a side-chain extension at the C22 position of pleuromutilin. The linkers were designed on the basis of the best linker from our first series of pleuromutilin derivatives following either conformational restriction or an isosteric methylene to oxygen exchange. The binding of the new compounds to the Escherichia coli ribosome was investigated by molecular modeling and chemical footprinting of nucleotide U2506, and it was found that all the derivatives bind to the specific site and most of them better than pleuromutilin itself. The effect of the side-chain extension was also explored by chemical footprinting of nucleotide U2585, and the results showed that all the compounds interact with this position to varying degrees. Derivatives with a conformational restriction of the linker generally had a higher affinity than derivatives with an isosteric exchange of one of the carbons in the linker with a hydrophilic oxygen. A growth inhibition assay with three different bacterial strains showed significant activity of several of the new compounds.

CuBr catalyzed C-N cross coupling reaction of purines and diaryliodonium salts to 9-arylpurines

CuBr was found to be an efficient catalyst for the C-N cross coupling reaction of purine and diaryliodonium salts. 9-Arylpurines were synthesized in excellent yields with short reaction times (2.5 h). The method represents an alternative to the synthesis of 9-arylpurines via Cu(II) catalyzed C-N coupling reaction with arylboronic acids as arylating agents.

Copper-catalyzed C-P bond construction via direct coupling of phenylboronic acids with H-phosphonate diesters

A mild and efficient method was developed for the copper-catalyzed additions of H-phosphonate diesters to boronic acids under the copper catalyst system Cu(2)O/1,10-phenanthroline. To the best of our knowledge this finding is the first example of a copper-catalyzed synthesis of aryl phosphonates from arylboronic acids and H-phosphonate dialkyl esters.

Design and synthesis of a beta-lactamase activated 5-fluorouracil prodrug

An efficient synthesis of a 5-fluorouracil-cephalosporin prodrug is described for use against colorectal and other cancers in antibody and gene-directed therapies. The compound shows stability in aqueous media until specifically activated by beta-lactamase (betaL). The kinetic parameters of the 5-fluorouracil-cephalosporin conjugate were determined in the presence of Enterobacter cloacae P99 betaL (ECl betaL) revealing a K(m)=95.4 microM and V(max)=3.21 microMol min(-1) mg(-1). The data compare favorably to related systems that have been reported and enable testing of this prodrug against cancer cell lines in vitro and in vivo.

N-Arylation of amines, amides, imides and sulfonamides with arylboroxines catalyzed by simple copper salt/EtOH system

The coupling of arylboroxines with a variety of amines, amides, imides and sulfonamides catalyzed by a copper salt/EtOH system has been developed. In the absence of a base or additive the corresponding N-arylation products were obtained in moderate to excellent yields.

Synthesis of rigid homo- and heteroditopic nucleobase-terminated molecules incorporating adenine and/or thymine

A series of homo- and heteroditopic thymine- and/or adenine-terminated molecules incorporating rigid aryl or oligo(phenylene ethynylene) linkers has been efficiently synthesized. The key steps involved in the synthesis are the construction of the N-arylated nucleobases using the Chan-Lam-Evans-modified Ullman coupling and their further elaboration using the Sonogashira coupling. Furthermore, the synthesis of a rigid tripodal thymine derivative is reported.