Modification of purine and pyrimidine nucleosides by direct C-H bond activation

6-azido and 6-azidomethyl uracil nucleosides

Azido nucleosides have been utilized for click reactions, metabolic incorporation into cellular DNA, and fluorescent imaging of live cells. Two classes of 6-azido modified uracil nucleosides; one with azido group directly attached to uracil ring and second with azido group attached via methylene linker are described. The 6-azido-2'-deoxyuridine (6-AdU) was prepared in 55% overall yield by lithiation-based regioselective C6-iodination of silyl protected 2'-deoxyuridine followed by treatment with sodium azide and deprotection with TBAF. Lithiation-based C6-alkylation of the protected uridine with methyl iodide followed by the oxidation of the 6-methyl product with selenium dioxide and the subsequent mesylation and azidation of the resulting 6-hydroxymethyl group gave after deprotection 6-azidomethyluridine (6-AmU) in 61% overall yield. Direct lithiation-based C6-hydroxymethylation followed by mesylation/azidation sequence and deprotection provided 6-AmU or 6-azidomethyl-2'-deoxyuridine (6-AmdU). Yields for the lithiation-based regioselective C6-iodination and alkylation were higher for uridine than 2'-deoxyuridine derivatives and they appear to be less dependent on the sugar protection group used. Strain promoted click reactions of 6-AdU and 6-AmdU with symmetrically fused cyclopropyl cyclooctyne (OCT) provided fluorescent triazoles. DFT-calculated dihedral angles and energy differences for the favored anti and syn conformation of 6-AdU and 6-AmdU versus their C5 azido counterparts are discussed.

Dual ligand approach increases functional group tolerance in the Pd-catalysed C-H arylation of N-heterocyclic pharmaceuticals

The excellent functional group tolerance of the Suzuki-Miyaura cross-coupling reactions has been decisive for their success in the pharmaceutical industry. Highly diversified (hetero)aromatic scaffolds can be effectively coupled in the final step(s) of a convergent synthetic route. In contrast, electrophilic Pd catalysts for non-directed C-H activation are particularly sensitive to inhibition by coordinating groups in pharmaceutical precursors. While C-H arylation enables the direct conversion of (hetero)aromatics without preinstalled functional or directing groups, its functional group tolerance should be increased to be viable in late-stage cross-couplings. In this work, we report on a dual ligand approach that combines a strongly coordinating phosphine ligand with a chelating 2-hydroxypyridine for the highly robust C-H coupling of bicyclic N-heteroaromatics with aryl bromide scaffolds. The catalyst speciation was studied via in situ XAS measurements, confirming the coordination of both ligands under the reaction conditions. The C-H activation catalyst was shown to be tolerant to a wide range of pharmaceutically relevant scaffolds, including examples of late-stage functionalization of known drug molecules.

Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts

Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.

Palladium-Catalysed Intermolecular Direct C–H Bond Arylation of Heteroarenes with Reagents Alternative to Aryl Halides: Current State of the Art

Abstract:

Abstract: This unprecedented review with 322 references provides a critical up-to-date picture of the Pd-catalysed intermolecular direct C–H bond arylation of heteroarenes with arylating reagents alternative to aryl halides that include aryl sulfonates (aryl triflates, tosylates, mesylates, and imidazole-1-sulfonates), diaryliodonium salts, [(diacetoxy)iodo]arenes, arenediazonium salts, 1-aryltriazenes, arylhydrazines and N’-arylhydrazides, arenesulfonyl chlorides, sodium arenesulfinates, arenesulfinic acids, and arenesulfonohydrazides. Particular attention has been paid to summarise the preparation of the various arylating reagents and to highlight the practicality, versatility, and limitations of the various developed arylation protocols, also comparing their results with those achieved in analogous Pd-catalysed arylation reactions involving the use of aryl halides as electrophiles. Mechanistic proposals have also been briefly summarised and discussed. However, data concerning Pd-catalysed direct C–H bond arylations involving the C–H bonds of aryl substituents of the examined heteroarene derivatives have not been taken into account.

Synthesis of Platinum(II) N-Heterocyclic Carbenes Based on Adenosine

Organometallic derivatization of nucleosides is a highly promising strategy for the improvement of the therapeutic profile of nucleosides. Herein, a methodology for the synthesis of metalated adenosine with a deprotected ribose moiety is described. Platinum(II) N-heterocyclic carbene complexes based on adenosine were synthesized, namely N-heterocyclic carbenes bearing a protected and unprotected ribose ring. Reaction of the 8-bromo-2′,3′,5′-tri-O-acetyladenosine with Pt(PPh₃)₄ by C8−Br oxidative addition yielded complex 1, with a Pt^II centre bonded to C-8 and an unprotonated N7. Complex 1 reacted at N7 with HBF₄ or methyl iodide, yielding protic carbene 2 or methyl carbene 3, respectively. Deprotection of 1 to yield 4 was achieved with NH₄OH. Deprotected compound 4 reacted at N7 with HCl solutions to yield protic NHC 5 or with methyl iodide yielding methyl carbene 6. Protic N-heterocyclic carbene 5 is not stable in DMSO solutions leading to the formation of compound 7, in which a bromide was replaced by chloride. The cis-influence of complexes 1–7 was examined by ³¹P{¹H} and ¹⁹⁵Pt NMR. Complexes 2, 3, 5, 6 and 7 induce a decrease of ¹J_Pt,P of more than 300 Hz, as result of the higher cis-influence of the N-heterocyclic carbene when compared to the azolato ligand in 1 and 4.

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

Extended fluorescent uridine analogues: synthesis, photophysical properties and selective interaction with BSA protein

The improvement in fluorescence properties of 2′-deoxyuridine was made possible by the introduction of (hetero)aromatic moieties at the C–5 position of uridine with alkenyl/phenyl/styryl linkers to create a library of useful fluorescent nucleosides.

An efficient synthesis of 3'-O-triazole modified guanosine-5'-O-monophosphate using click chemistry

First chemical synthesis of 3'-O-1,2,3-triazolyl-guanosine-5'-O-monophosphate by copper catalyzed click chemistry is described. The present cycloaddition reaction involves, in situ generation of azide from the corresponding bromide followed by copper catalyst cycloaddition with 3'-O-propargyl guanosine monophosphate in water, in the presence of catalytic amount of β-cyclodextrin. The CuAAC reaction is highly regioselective forming 1,4-cycloadduct with good yield and high purity. The final compound, 3'-O -triazole substituted guanosine monophosphate has the potential to use in various biomolecules such as labeled nucleic acids, mRNA dinucleotide cap analogs for molecular biology and their applications in the therapeutic field.

An Expeditious Total Synthesis of 5'-Deoxy-toyocamycin and 5'-Deoxysangivamycin

In present paper, an expeditious total synthesis of naturally occurring 5′-deoxytoyocamycin and 5′-deoxysangivamycin was accomplished. Because of the introduction of a benzoyl group at N-6 of 4-amino-5-cyano-6-bromo-pyrrolo[2,3-d]pyrimidine, a Vorbrüggen glycosylation with 1,2,3-tri-O-acetyl-5-deoxy-β-D-ribofuranose afforded a completely regioselective N-9 glycosylation product, which is unambiguously confirmed by X-ray diffraction analysis. All of the involved intermediates were well characterized by various spectra.

Synthesis, Optoelectronic Properties, Self-Association, and Base Pairing of Nucleobase-Functionalized Oligothiophenes

Device-relevant π-conjugated oligothiophenes with the canonical nucleobases directly embedded into the π-framework have been designed, synthesized, and characterized. These oligomers offer the ability to tune optoelectronic properties via the intimate merging of the nucleobase molecular electronic structure with base-pairing fidelity. Analysis of their optical and electronic properties in a hydrogen-bond-disrupting solvent (DMF) indicates that the nucleobase identity influences the intrinsic electronic properties of the semiconductors. These differences are supported by DFT calculations which demonstrate that the HOMO/LUMO orbitals are distributed differently for each compound. The solubility and competition between self-association and base pairing in a hydrogen-bond-supporting solvent (chloroform) was studied to better understand the oligomer behavior under conditions relevant for downstream solution processing into thin-film devices. These solution studies reveal that in each case base-pairing is preferred to self-aggregation; the relatively weak heteroassociation of 1A-1U (35 ± 5 M^-1) should be amenable to facile solution processing and successive hydrogen bond formation in the solid state, while the strong heteroassociation between 1G and 1C (>10⁴ M^-1) should enable assemblies to be preformed in solution. These results are expected to enable the synthesis of more complex π-conjugated architectures and facilitate their extension to optoelectronic devices.

C-H Imidation of 7-Deazapurines

We developed and presented here a ferrocene-catalyzed C-H imidation of 7-deazapurines (pyrrolo[2,3-d]pyrimidines) with N-imidyl peroxyesters. The reactions occur regioselectively at position 8 in 7-deazapurines, leading to a series of 8-succinimido-, phtalimido-, or naphthalimido-7-deazapurine derivatives. Attempted hydrazinolysis of resulting 8-imidyl-7-deazapurines led to corresponding 8-amino-7-deazapurine, which was very unstable and quickly decomposed.

Regioselective C–H and N–H functionalization of purine derivatives and analogues: a synthetic and mechanistic perspective

This perspective provides a systematic and concise overview of the recent development in C–H/N–H bond functionalization in purine derivatives and analogues.

Synthesis of Arylated Nucleobases by Visible Light Photoredox Catalysis

Arylated nucleobases were synthesized by visible light photocatalysis using rhodamine 6G as photoredox catalyst and N,N-diisopropylethylamine as sacrificial electron donor. The high redox potential of this catalyst system is achieved by a consecutive photoinduced electron transfer process (conPET) and allows the room temperature conversion of brominated and chlorinated nucleobases or nucleobase precursors as starting materials. In contrast to many transition-metal-based syntheses, a direct C-H arylation of nitrogen-containing halogenated heterocycles is possible without protection of the N-H groups. The method provides a simple, metal-free alternative for the synthesis of biologically interesting arylated heterocycles under mild conditions.

Combination of RuCl3·xH2O with PEG – a simple and recyclable catalytic system for direct arylation of heteroarenes via C–H bond activation

A simple and recyclable catalytic system for direct arylation of heteroarenes via C–H bond activation was developed with a relatively inexpensive RuCl₃·xH₂O as a catalyst and PEG-400 as a green medium without any additive or ligand.

Synthesis of 8-(1,2,3-triazol-1-yl)-7-deazapurine nucleosides by azide-alkyne click reactions and direct C-H bond functionalization

Treatment of toyocamycin or sangivamycin with 1,3-dibromo-5,5-dimethylhydantoin in MeOH (r.t./30 min) gave 8-bromotoyocamycin and 8-bromosangivamycin in good yields. Nucleophilic aromatic substitution of 8-bromotoyocamycin with sodium azide provided novel 8-azidotoyocamycin. Strain promoted click reactions of the latter with cyclooctynes resulted in the formation of the 1,2,3-triazole products. Iodine-mediated direct C8-H bond functionalization of tubercidin with benzotriazoles in the presence of tert-butyl hydroperoxide gave the corresponding 8-benzotriazolyltubercidin derivatives. The 8-(1,2,3-triazol-1-yl)-7-deazapurine derivatives showed moderate quantum yields and a large Stokes shifts of ~ 100 nm.

Purinyl N(3)-Directed Palladium-Catalyzed C-H Alkoxylation of N(9)-Arylpurines: A Late-Stage Strategy to Synthesize N(9)-(ortho-Alkoxyl)arylpurines

A palladium-catalyzed alkoxylation of N(9)-arylpurines with primary or secondary alcohols has been developed successfully, which is a rare C-H activation reaction of polynitrogenated purines and offers a late-stage strategy to synthesize N(9)-(ortho-alkoxyl)arylpurines. Although there are more than four nitrogen atoms present in the purine moiety, the reaction can be effectively conducted by sterically blocking the N(1) site for catalyst coordination and first employing the purinyl N(3) atom as a directing group.

Ruthenium-Catalyzed C-H Bond Activation Approach to Azolyl Aminals and Hemiaminal Ethers, Mechanistic Evaluations, and Isomer Interconversion

C(sp³)-N bond-forming reactions between benzotriazole and 5,6-dimethylbenzotriazole with N-methylpyrrolidinone, tetrahydrofuran, tetrahydropyran, diethyl ether, 1,4-dioxane, and isochroman have been conducted using RuCl₃•3H₂O/t-BuOOH in 1,2-dichloroethane. In all cases, N1 and N2 alkylation products were obtained, and these are readily separated by chromatography. One of these products, 1-(isochroman-1-yl)-5,6-dimethyl-1H-benzotriazole, was examined by X-ray crystallography. It is the first such compound to be analyzed by this method, and notably, the benzotriazolyl moiety is quasi-axially disposed, consistent with the anomeric effect. This has plausible consequences, not observed previously. In contrast to other hemiaminal ether-forming reactions, which proceed via radicals, this Ru-catalyzed process is not suppressed in the presence of a radical inhibitor. Therefore, an oxoruthenium-species-mediated rapid formation of an oxocarbenium intermediate is believed to occur. In the radical-trapping experiment, previously unknown products containing both the benzotriazole and the TEMPO unit have been identified. In these products, it is likely that the benzotriazole is introduced via a Ru-catalyzed C-N bond formation, whereas C-O bond-formation with TEMPO occurs via a radical reaction. We show that reactions of THF with TEMPO are influenced by ambient light. A competitive reaction of THF and THF-d₈ with benzotriazole indicated that C-H bond cleavage occurs ca. 5 times faster than C-D cleavage. This is comparable to other metal-mediated radical reactions of THF, but lower than that observed for a reaction catalyzed by n-Bu₄N⁺I^-. Detailed mechanistic experiments and comparisons are described. The catalytic system was also evaluated for reactions of benzimidazole, imidazole, 1,2,4-triazole, and 1,2,3-triazole with THF, and successful reactions were achieved in each case. In the course of our studies, we discovered an unexpected but significant isomerization of some of the benzotriazolyl hemiaminal ethers. This is plausibly attributable to the pseudoaxial orientation of the heterocycle in the products and the stability of oxocarbenium ions, both of which can contribute to C-N bond cleavage and reformation. Predominantly, the N2-isomers rearrange to the N1-isomers even upon storage at low temperature! This previously unknown phenomenon has also been studied and described.