Heck and Sonogashira couplings in aqueous media – application to unprotected nucleosides and nucleotides

Ubiquitous Role of Phosphine-Based Water-Soluble Ligand in Promoting Catalytic Reactions in Water

Catalysis has been at the forefront of the developments that has revolutionised synthesis and provided the impetus in the discovery of platform technologies for efficient C-C or C-X bond formation. Current environmental situation however, demands a change in strategy with catalysis being promoted more in solvents that are benign (Water) and for that the development of hydrophilic ligands (especially phosphines) is a necessity which could promote catalytic reactions in water, allow recyclability of the catalytic solutions and make it possible to isolate products using column-free techniques that involve lesser usage of hazardous organic solvents. In this review, we therefore critically analyse such catalytic processes providing examples that do follow the above-mentioned parameter.

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.

Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling

New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.

Novel Highly Efficient Green and Reusable Cu(II)/Chitosan-Based Catalysts for the Sonogashira, Buchwald, Aldol, and Dipolar Cycloaddition Reactions

In this study, new Cu(II)/chitosan-based systems were designed via (i) the treatment of chitosan with sodium sulfate (1a) or sodium acetate (1b); (ii) the coating of 1a or 2a with a sodium hyaluronate layer (2a and 2b, correspondingly); (iii) the treatment of a cholesterol–chitosan conjugate with sodium sulfate (3a) or sodium acetate (3b); and (iv) the succination of 1a and 1b to afford 4a and 4b or the succination of 2a and 2b to yield 5a and 5b. The catalytic properties of the elaborated systems in various organic transformations were evaluated. The use of copper sulfate as the source of Cu2+ ions results in the formation of nanoparticles, while the use of copper acetate leads to the generation of conventional coarse-grained powder. Cholesterol-containing systems have proven to be highly efficient catalysts for the cross-coupling reactions of different types (e.g., Sonogashira, Buchwald–Hartwig, and Chan–Lam types); succinated systems coated with a layer of hyaluronic acid are promising catalysts for the aldol reaction; systems containing inorganic copper(II) salt nanoparticles are capable of catalyzing the nitrile-oxide-to-nitrile 1,3-dipolar cycloaddition. The elaborated catalytic systems efficiently catalyze the aforementioned reactions in the greenest solvent available, i.e., water, and the processes could be conducted in air. The studied catalytic reactions proceed selectively, and the isolation of the product does not require column chromatography. The product is separated from the catalyst by simple filtration or centrifugation.

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.

Quadrol-Pd(II) complexes: phosphine-free precatalysts for the room-temperature Suzuki-Miyaura synthesis of nucleoside analogues in aqueous media

Commercially available Quadrol, N,N,N',N'-tetrakis(2-hydroxypropyl)ethylenediamine (THPEN), has been used for the first time as a N^N-donor neutral hydrophilic ligand in the synthesis and characterization of new water soluble palladium(II) complexes containing chloride, phthalimidate or saccharinate as co-ligands. [PdCl2(THPEN)] (1) [Pd(phthal)2(THPEN)] (2), [Pd(sacc)2(THPEN)] (3) and the analogous complex with the closely related N,N,N',N'-tetrakis(2-hydroxyethyl)ethylenediamine (THEEN) [Pd(sacc)2(THEEN)] (4) were efficiently prepared in a one-pot reaction from [PdCl2(CH3CN)2] or Pd(OAc)2. Structural characterization of 1 and 3 by single crystal X-ray diffraction produced the first structures reported to date of palladium complexes with Quadrol. The resultant palladium complexes are highly soluble in water and were found to be effective as phosphine-free catalysts for the synthesis of functionalized nucleoside analogues under room-temperature Suzuki-Miyaura cross-coupling conditions between 5-iodo-2'-deoxyuridine (& 5-iodo-2'-deoxycytidine) with different aryl boronic acids in neat water. This is the first report of the coupling process performed on nucleosides in water at room temperature.

Palladium Catalyst Recycling for Heck-Cassar-Sonogashira Cross-Coupling Reactions in Green Solvent/Base Blend

The identification of a green, versatile, user-friendly, and efficient methodology is necessary to facilitate the use of Heck-Cassar-Sonogashira (HCS) cross-coupling reaction in drug discovery and industrial production in the pharmaceutical segment. The Heck-Cassar and Sonogashira protocols, using N-hydroxyethylpyrrolidone (HEP)/water/N,N,N',N'-tetramethyl guanidine (TMG) as green solvent/base mixture and sulfonated phosphine ligands, allowed to recycle the catalyst, always guaranteeing high yields and fast conversion under mild conditions, with aryl iodides, bromides, and triflates. No catalyst leakage or metal contamination of the final product were observed during the HCS recycling. To our knowledge, a turnover number (TON) up to 2375, a turnover frequency (TOF) of 158 h-1 , and a process mass intensity (PMI) around 7 that decreased around 3 after solvent, base, and palladium recovery, represent one of the best results to date using a sustainable protocol. The Heck-Cassar protocol using sSPhos was successfully applied to the telescoped synthesis of Erlotinib (TON: 1380; TOF: 46 h-1 ).

Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications

The encoding of chemical compounds with amplifiable DNA tags facilitates the discovery of small-molecule ligands for proteins. To investigate the impact of stereo- and regiochemistry on ligand discovery, we synthesized a DNA-encoded library of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids. The library was selected against multiple proteins and yielded specific ligands. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, which was experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and binders to tumour-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumour targeting.

1,3,5-Triaza-7-phosphaadamantane (PTA) Derived Caged Phosphines for Palladium-Catalyzed Selective Functionalization of Nucleosides and Heteroarenes

Phosphines have, in combination with transition metals, played a pivotal role in the rapid development of efficient catalytic processes. Caged phosphines constitute a class of three-dimensional scaffolds providing unique control over steric and electronic properties. The versatility of the caged phosphine ligands has been demonstrated elegantly by the groups of Verkade, Gonzalvi as well as Stradiotto. Our research group has also been working extensively for the past several years in the development of 1,3,5-triaza-7-phosphaadamantane-based caged ligands and in this personal note we have summarized these applications pertaining to the modification of biologically useful nucleosides and heteroarenes.

Fast Heck-Cassar-Sonogashira (HCS) Reactions in Green Solvents

The replacement of toxic solvents with greener alternatives in Heck–Cassar–Sonogashira (HCS) cross-couplings was investigated. The fine-tuning of the HCS protocol allowed to achieve complete conversions and high speed under mild conditions. N-Hydroxyethylpyrrolidone (HEP) gave the best results. Moreover, the methodology was successfully applied to the synthesis of an intermediate of the anticancer drug Erlotinib, demonstrating the versatility of the new green protocol.

Discovery, Synthesis, and Scale-up of Efficient Palladium Catalysts Useful for the Modification of Nucleosides and Heteroarenes

Nucleic acid derivatives are imperative biomolecules and are involved in life governing processes. The chemical modification of nucleic acid is a fascinating area for researchers due to the potential activity exhibited as antiviral and antitumor agents. In addition, these molecules are also of interest toward conducting useful biochemical, pharmaceutical, and mutagenic study. For accessing such synthetically useful structures and features, transition-metal catalyzed processes have been proven over the years to be an excellent tool for carrying out the various transformations with ease and under mild reaction conditions. Amidst various transition-metal catalyzed processes available for nucleoside modification, Pd-catalyzed cross-coupling reactions have proven to be perhaps the most efficient, successful, and broadly applicable reactions in both academia and industry. Pd-catalyzed C-C and C-heteroatom bond forming reactions have been widely used for the modification of the heterocyclic moiety in the nucleosides, although a single catalyst system that could address all the different requirements for nucleoside modifications isvery rare or non-existent. With this in mind, we present herein a review showcasing the recent developments and improvements from our research groups toward the development of Pd-catalyzed strategies including drug synthesis using a single efficient catalyst system for the modification of nucleosides and other heterocycles. The review also highlights the improvement in conditions or the yield of various bio-active nucleosides or commercial drugs possessing the nucleoside structural core. Scale ups wherever performed (up to 100 g) of molecules of commercial importance have also been disclosed.

Screening of copper and palladium-mediated reactions compatible with DNA-encoded chemical libraries

The construction of DNA-encoded chemical libraries (DECLs) crucially relies on the availability of chemical reactions, which are DNA-compatible and which exhibit high conversion rates for a large number of diverse substrates. In this work, we present our optimization and validation procedures for three copper and palladium-catalyzed reactions (Suzuki cross-coupling, Sonogashira cross-coupling and copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC)), which have been successfully used by our group for the construction of large encoded libraries.

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.