Efficient synthesis of unprotected C-5-aryl/heteroaryl-2'-deoxyuridine via a Suzuki-Miyaura reaction in aqueous media

Rapid plugged flow synthesis of nucleoside analogues via Suzuki-Miyaura coupling and heck Alkenylation of 5-Iodo-2'-deoxyuridine (or cytidine)

Nucleosides modification via conventional cross-coupling has been performed using different catalytic systems and found to take place via long reaction times. However, since the pandemic, nucleoside-based antivirals and vaccines have received widespread attention and the requirement for rapid modification and synthesis of these moieties has become a major objective for researchers. To address this challenge, we describe the development of a rapid flow-based cross-coupling synthesis protocol for a variety of C5-pyrimidine substituted nucleosides. The protocol allows for facile access to multiple nucleoside analogues in very good yields in a few minutes compared to conventional batch chemistry. To highlight the utility of our approach, the synthesis of an anti-HSV drug, BVDU was also achieved in an efficient manner using our new protocol.

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Supplementary Information

The online version contains supplementary material available at 10.1007/s41981-023-00265-1.

Water-Soluble Pd-Imidate Complexes as Versatile Catalysts for the Modification of Unprotected Halonucleosides

Modification of unprotected nucleosides has been attracting continuous interest, since these building blocks themselves and their phosphate-upgraded corresponding nucleotides have shown a plethora of uses in fields like biochemistry or pharmacy. Pd-catalyzed cross-coupling reactions, conducted in water or its mixtures with polar organic solvents, have frequently been the researchers' choice for the functionalization of the purine/pyrimidine base of the unprotected nucleosides. In this scenario, the availability of hydrophilic ligands and its water-soluble palladium complexes has markedly set the pace of the advances. The approach of our group to the synthesis of such complexes, Pd-imidates specifically, has faced critical stages, namely the jump to synthesize water soluble complexes from our experience working in conventional solvents, the preparation of phosphine free complexes and the overall goal of getting catalytic systems able to work close to room temperature. The continuous feedback with Kapdi's group, experienced in the chemistry of nucleosides, has produced over the last decade the interesting results in both fields presented here.

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.

Prospects and Applications of Palladium Nanoparticles in the Cross-coupling of (hetero)aryl Halides and Related Analogues

Discovering efficient methods for the formation of carbon-carbon bonds is a central ongoing theme in organic synthesis. Cross-coupling reactions catalysed by metal nanoparticles are attractive alternatives to the traditional use of metal counterparts due to the catalytic tunability, selectivity, recyclability and reusability of the nanoparticles. The ongoing search for sustainable processes demands that reusable and environmentally benign catalysts are used. While the advantages of nanoparticles catalysts over bulk catalysts cannot be overemphasised, the problem of sintering, agglomeration and leaching are drawbacks to their full industrial applications. Hence, efforts are being made towards advancing the efficiency of the catalytic nanoparticle systems over the years. This review presents the progress, the challenges and the prospects of palladium nanoparticle with focus on Heck, Suzuki, Hiyama and Sonogashira cross-coupling reactions involving (hetero) aryl halides and the analogues.

Eucalyptol: A Bio-Based Solvent for the Synthesis of O,S,N-Heterocycles. Application to Hiyama Coupling, Cyanation, and Multicomponent Reactions

We report here the use of eucalyptol as a bio-based solvent for Hiyama coupling, cyanation, and multicomponent reactions on O,S,N-heterocycles. These heterocycles were chosen as targets or as starting materials given their biological potential; they play an important role in therapeutically active compounds. Once again, eucalyptol proved to be a credible and sustainable alternative to common solvents.

Laser synthesis: a solvent-free approach for the preparation of phenylthiazolo[5,4-b]pyridine derivatives

We describe here a rapid and straightforward solvent-free method to access phenylthiazolo[5,4-b]pyridines using a Nd-YAG laser NANO-NY81-10 (λ = 355 nm, 10 Hz pulse frequency; 8 ns pulse duration).

Eucalyptol as a Bio-Based Solvent for Buchwald-Hartwig Reaction on O,S,N-Heterocycles

We report here the use of eucalyptol as a bio-based solvent for the Buchwald–Hartwig reaction on O,S,N-heterocycles. These heterocycles containing oxygen, sulfur and nitrogen were chosen as targets or as starting materials. Once again, eucalyptol demonstrated to be a possible sustainable alternative to common solvents.

Novel Carbazole-Based N-Heterocyclic Carbene Ligands to Access Synthetically Relevant Stilbenes in Pd-Catalyzed Coupling Processes

A series of new carbazole-based N-heterocyclic carbene (NHC) ligands have been synthesized in a simple and facile synthetic route and subsequently used in a Pd/carbazole-based NHC catalytic system, which was found to be effective in catalyzing Heck reactions to provide substituted stilbene derivatives in good yields. Several bioactive stilbenes, including pterostilbene, pinosylvin, trimethoxy resveratrol, and resveratrol, were synthesized in good yields, and a 10 mmol scale-up was also performed for trimethoxy resveratrol. The synthetic application was also extended by performing a double-tandem chemoselective Heck reaction followed by Miyaura borylation in a one-pot procedure to give single-step access to synthetically useful stilbenyl boronate esters. Similarly, a unique triple-tandem protocol of a chemoselective Heck reaction/Miyaura borylation/Suzuki-Miyaura coupling reaction sequence was performed for the one-pot modification of biologically relevant molecules.

First Metal-Free Synthesis of Tetracyclic Pyrido and Pyrazino Thienopyrimidinone Molecules

We report herein a new metal free synthetic pathway to generate tetracyclic compounds from 3-aminothieno[3,2-b]pyridine-2-carboxylate. To enlarge the molecular diversity, we studied the Suzuki coupling of 9-chloro-6H-pyrido[1,2-a]pyrido[2′,3′:4,5]thieno[3,2-d]pyrimidin-6-one and several boronic acids were easily introduced.

A Greener and Efficient Method for Nucleophilic Aromatic Substitution of Nitrogen-Containing Fused Heterocycles

A simple and efficient methodology for the nucleophilic aromatic substitution of nitrogen-containing fused heterocycles with interesting biological activities has been developed in an environmentally sound manner using polyethylene glycol (PEG-400) as the solvent, leading to the expected compounds in excellent yields in only five minutes.

An expedient synthesis of flexible nucleosides via a regiocontrolled enzymatic glycosylation of functionalized imidazoles

A versatile two-step synthesis of C4- and C5-arylated 2′-deoxyribosylimidazoles was elaborated by enzymaticN-transglycosylation followed by microwave-assisted Pd-catalysed arylation reactions.

C-C Bond Formation: Synthesis of C5 Substituted Pyrimidine and C8 Substituted Purine Nucleosides Using Water Soluble Pd-imidate Complex

The synthesis of a highly efficient, water soluble [Pd(Sacc)2 (TPA)2 ] complex for C-C bond formation is described. Additionally, application of the [Pd(Sacc)2 (TPA)2 ] complex for Suzuki-Miyaura arylation of all four nucleosides (5-iodo-2'-deoxyuridine [5-IdU], 5-iodo-2'-deoxycytidine [5-IdC], 8-bromo-2'-deoxyadenosine, and 8-bromo-2'-deoxyguanosine) with various aryl/heteroaryl boronic acids in plain water under milder conditions is demonstrated. © 2016 by John Wiley & Sons, Inc.

Novel water-soluble phosphatriazenes: versatile ligands for Suzuki–Miyaura, Sonogashira and Heck reactions of nucleosides

Two new water-soluble phosphatriazene as versatile ligands for catalyzing Suzuki–Miyaura reactions of purines and pyrimidines in neat water with the possibility of recycling. Copper-free Sonogashira and Heck reaction were also made possible.

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides

Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

Aqueous microwave-assisted cross-coupling reactions applied to unprotected nucleosides

Metal catalyzed cross-coupling reactions have been the preferred tools to access to modified nucleosides (on the C5-position of pyrimidines and on the C7- or C8-positions of purines). Our objective is to focus this mini-review on the Suzuki-Miyaura and on the Heck cross-couplings of nucleosides using microwave irradiations which is an alternative technology compatible with green chemistry and sustainable development.

Catalytic C–H bond functionalisation of purine and pyrimidine nucleosides: a synthetic and mechanistic perspective

C–H bond functionalisation of heteroarenes, especially nucleosides, has received a lot of attention in the past few years. This review describes the state-of the art in this area with a global aspiration for possibly functionalising purine and pyrimidine moieties in complex biomolecular systems.

Pd–imidate complexes as recyclable catalysts for the synthesis of C5-alkenylated pyrimidine nucleosides via Heck cross-coupling reaction

Pd–imidate complexes as recyclable catalysts for Heck alkenylation of pyrimidine nucleosides. Pd–imidate complexes have been employed as efficient catalysts for the Heck alkenylation of unprotected 5-iodo-2′-deoxyuridine in acetonitrile.

Palladium-catalyzed direct arylation of 5-halouracils and 5-halouracil nucleosides with arenes and heteroarenes promoted by TBAF

The 1-N-benzyl-5-iodo(or bromo)uracil undergoes Pd-catalyzed [Pd₂(dba)₃] direct arylation with benzene and other simple arenes in the presence of TBAF in DMF without the necessity of adding any ligands or additives to give 5-arylated uracil analogues. The TBAF-promoted coupling also occurs efficiently with electron rich heteroarenes at 100 °C (1 h) even with only small excess of heteroarenes. The protocol avoids usage of the arylboronic acid or stannane precursors for the synthesis of 5-(2-furyl, or 2-thienyl, or 2-pyrrolyl)uracil nucleosides, which are used as important RNA and DNA fluorescent probes. The fact that 1-N-benzyl-3-N-methyl-5-iodouracil did not undergo the TBAF-promoted couplings with arenes or heteroarenes suggests that the C4-alkoxide (enol form of uracil) facilitates coupling by participation in the intramolecular processes of hydrogen abstraction from arenes. TBAF-promoted arylation was extended into the other enolizable heterocyclic systems such as 3-bromo-2-pyridone. The π-excessive heteroarenes also coupled with 5-halouracils in the presence of Pd(OAc)₂/Cs₂CO₃/PivOH combination in DMF (100 °C, 2 h) to yield 5-arylated uracils.

High-affinity RNA targeting by oligonucleotides displaying aromatic stacking and amino groups in the major groove. Comparison of triazoles and phenyl substituents

Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.

Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides

Nucleoside analogues have attracted much attention due to their potential biological activities.

New water soluble Pd-imidate complexes as highly efficient catalysts for the synthesis of C5-arylated pyrimidine nucleosides

Recyclable water-soluble Pd complexes were revealed as excellent catalysts for Suzuki–Miyaura cross-coupling of challenging substrates like the antiviral nucleoside analogue 5-iodo-20-deoxyuridine.