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.

Aqueous and Visible-Light-Promoted C-H (Hetero)arylation of Uracil Derivatives with Diazoniums

Direct C5 (hetero)arylation of uracil and uridine substrates with (hetero)aryl diazonium salts under photoredox catalysis with blue light was reported. The coupling proceeds efficiently with diazonium salts and heterocycles in good functional group tolerance at room temperature in aqueous solution without transition-metal components. A plausible radical mechanism has been proposed.

Recent Advances in the Microwave-Assisted Production of Hydroxymethylfurfural by Hydrolysis of Cellulose Derivatives-A Review

The concepts of sustainable development, bioeconomy, and circular economy are being increasingly applied for the synthesis of molecules of industrial interest. Among these molecules, hydroxymethylfurfural as a platform molecule is the subject of various research approaches to improve its synthesis and productivity, and extend its potential uses. Accordingly, this review paper aims essentially at outlining recent breakthroughs obtained in the field of hydroxymethylfurfural production from sugars and polysaccharide feedstocks under microwave-assisted technology. The review discusses advances obtained via microwave activation in major production pathways recently explored, split into the following categories: (i) use of various homogeneous catalysts like mineral or organic acids, metal salts, or ionic liquids; (ii) feedstock dehydration making use of various solid acid catalysts; and (iii) non-catalytic routes.

Modification of oligodeoxynucleotides by on-column Suzuki cross-coupling reactions

The on-column functionalization of oligodeoxynucleotides via base-free Suzuki cross-coupling reactions is reported herein. These cross-coupling reactions were carried out with various boronic acids and either full-length modified oligonucleotides containing one or more 2'-deoxy-5-iodouridine (5IdU) monomer(s) or on oligonucleotide fragments immediately after incorporation of 5IdU. Five different functionalities were coupled to oligonucleotides containing one or three attachment points.

Sensing the impact of environment on small molecule differentiation of RNA sequences

Using pattern recognition of RNA with small molecules (PRRSM) with fluorescent RNA chemosensors and aminoglycosides, we reveal the impact of changing environmental conditions on the differentiation of a range of RNA structures as well as the ability to predict different sequence/size compositions of five canonical RNA motifs.

One-step highly selective borylation/Suzuki cross-coupling of two distinct aryl bromides in pure water

A one-step borylation/Suzuki cross-coupling of two distinct aryl bromides by Na₂PdCl₄ catalysis mediated by B₂(OH)₄ was developed in pure water, allowing the synthesis of various biaryls and heterobiaryls.

Small Molecule-Based Pattern Recognition To Classify RNA Structure

Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes. Complete (100%) predictive ability for this RNA training set was achieved by incorporating two exhaustively guanidinylated aminoglycosides into the receptor library. The PCA was then externally validated using biologically relevant RNA constructs. In bulge-stem-loop constructs of HIV-1 transactivation response element (TAR) RNA, we achieved nucleotide-specific classification of two independent secondary structure motifs. Furthermore, examination of cheminformatic parameters and PCA loading factors revealed trends in aminoglycoside:RNA recognition, including the importance of shape-based discrimination, and suggested the potential for size and sequence discrimination within RNA structural motifs. These studies present a new approach to classifying RNA structure and provide direct evidence that RNA topology, in addition to sequence, is critical for the molecular recognition of RNA.

Design for carbon–carbon bond forming reactions under ambient conditions

The carbon–carbon (C–C) bond forms the ‘backbone’ of nearly every organic molecule, and lies at the heart of the chemical sciences! Let us explore designing of carbon–carbon frameworks at ambient conditions.

An efficient water-soluble surfactant-type palladium catalyst for Suzuki cross-coupling reactions in pure water at room temperature

An in situ-generated Pd catalyst with a bidentate phosphine-type zwitterionic surfactant as a ligand showed high catalytic activity in the Suzuki reactions.

A 2-((4-Arylpiperazin-1-yl)methyl)phenol ligated Pd(ii) complex: an efficient, versatile catalyst for Suzuki–Miyaura cross-coupling reactions

N,N,O-Tridentate palladium(ii) complex 4a was found to be an efficient catalyst for the Suzuki cross-coupling reaction of aryl halides (iodo-, bromo- and chloro-), which afforded cross-coupling products in good to excellent yields.

Analysis of the water extract of waste papaya bark ash and its implications as an in situ base in the ligand-free recyclable Suzuki–Miyaura coupling reaction

The conversion of waste papaya-bark to ash–water extract via low-temperature combustion, and its utilization as an efficient and eco-friendly in situ basic medium for Suzuki–Miyaura cross-coupling reaction at room temperature are reported.

Increasing the Stability of DNA:RNA Duplexes by Introducing Stacking Phenyl-Substituted Pyrazole, Furan, and Triazole Moieties in the Major Groove

Consecutive incorporations of our previously published thymidine analogue, 5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W in oligonucleotides, has demonstrated significant duplex-stabilizing properties due to its efficient staking properties in the major groove of DNA:RNA duplexes. The corresponding 2'-deoxycytidine analogue is not as well-accommodated in duplexes, however, due to its clear preference for the ring-flipped coplanar conformation. In our present work, we have used ab initio calculations to design two new building blocks, 5-(5-phenylfuran-2-yl)-2'-deoxycytidine monomer Y and 5-(1-phenyl-1H-pyrazol-3-yl)-2'-deoxycytidine monomer Z, that emulate the conformation of W. These monomers were synthesized by Suzuki-Miyaura couplings, and the pyrazole moiety was obtained in a cycloaddition from N-phenylsydnone. We show that the novel analogues Y and Z engage in efficient stacking either with themselves or with W due to a better overlap of the aromatic moieties. Importantly, we demonstrate that this translates into very thermally stable DNA:RNA duplexes, thus making Y and especially Z good candidates for improving the binding affinities of oligonucleotide-based therapeutics. Since we now have both efficiently stacking T and C analogues in hand, any purine rich stretch can be effectively targeted using these simple analogues. Notably, we show that the introduction of the aromatic rings in the major groove does not significantly change the helical geometry.

Pd(OAc)2 in WERSA: a novel green catalytic system for Suzuki-Miyaura cross-coupling reactions at room temperature

A recyclable/reusable Pd(OAc)2 catalysed Suzuki-Miyaura cross-coupling reaction condition in neat "Water Extract of Rice Straw Ash" (WERSA) at room temperature was developed. This is a ligand/base/promoter/additive/organic media free protocol.

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.

First pinacol coupling in emulsified water: key role of surfactant and impact of alternative activation technologies

For the first time, the influence of surfactants on the radical pinacol coupling reaction is investigated. The rate and selectivity of this reductive C-C coupling are compared under three different activation technologies: thermal activation, microwave irradiation, and sonication. The use of IgepalCO520, a neutral surfactant, led to the successful conversion of aromatic or α,β-unsaturated aliphatic carbonyl compounds in moderate to excellent yield (55-90 %). An insight on the potential mechanism involved in the reaction is also proposed, based on microscopic observations and particle size measurement.

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.

‘On-water’ organic synthesis: a green, highly efficient, low cost and reusable catalyst system for biaryl synthesis under aerobic conditions at room temperature

The PdCl₂/sucrose/K₂CO₃/H₂O system showed the superb catalytic activity towards the Suzuki reaction of a wide range of aryl/heteroaryl halides with diverse phenylboronic acids at room temperature with operational simplicity and shorter reaction time.

Pd(OAc)2 and (DHQD)2PHAL as a simple, efficient and recyclable/reusable catalyst system for Suzuki–Miyaura cross-coupling reactions in H2O at room temperature

Suzuki–Miyaura cross-coupling reaction catalyzed by Pd(OAc)₂–(DHQD)₂PHAL is a very simple, mild, efficient and recyclable/reusable protocol for the synthesis of biaryls/heterobiaryls in neat H₂O at room temperature.

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.

Quinoline and phenanthroline preparation starting from glycerol via improved microwave-assisted modified Skraup reaction

An efficient “green” modified Skraup reaction in neat water was developed using inexpensive, abundant and environmentally-friendly glycerol under microwave irradiation conditions.

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.

First ligand-free, microwave-assisted, Heck cross-coupling reaction in pure water on a nucleoside – application to the synthesis of antiviral BVDU

For the first time, a palladium catalyzed Heck cross-coupling reaction between 5-iodo-2′-deoxyuridine and various acrylate derivatives was performed using ligand-free conditions and microwave assistance in pure water.

Original access to 5-aryluracils from 5-iodo-2′-deoxyuridine via a microwave assisted Suzuki-Miyaura cross-coupling/deglycosylation sequence in pure water

A facile and efficient methodology to obtain various 5-aryluracil derivatives was developed through a two steps sequence: a ligand-free Suzuki-Miyaura cross-coupling reaction starting from totally deprotected 5-iodo-(2′-deoxy)uridine followed by a very simple deglycosylation procedure in pure water with assistance of microwave irradiation.

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.

Micellar catalysis using a photochromic surfactant: application to the Pd-catalyzed Tsuji-Trost reaction in water

The first example of a Pd-catalyzed Tsuji-Trost reaction, applied in a photochromic micellar media under conventional heating and microwave irradiation, is reported. The surfactant activity and recycling ability were investigated and compared with those of a few commercially available surfactants. The synthetic photochromic surfactant proved to be efficient, recyclable, and versatile for Pd-catalyzed coupling reactions.