Water-Soluble Pd–Imidate Complexes: Broadly Applicable Catalysts for the Synthesis of Chemically Modified Nucleosides via Pd-Catalyzed Cross-Coupling

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.

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.

One-pot expeditious synthesis of glycosylated esters through activation of carboxylic acids using trichloroacetonitrile

Acetimidates, a valuable intermediate has been well explored as versatile synthon in a number of organic transformations particularly as suitable donors in glycosylation reactions. Herein, we explored acetimidates to furnish high-to-excellent yield of diverse glycosylated esters under one-pot mild reaction condition. The commercially available trichloroacetonitrile is implemented for the activation of carboxylic acid via in situ generation of trichloroacetimidate, which was subsequently attacked by sugar alcohols to deliver high-to-excellent yields of desired glycosylated esters. The devised method has some notable features such as metal-free condition, one-pot mild reaction condition, easy-handling, high-to-excellent yields, and broad substrate scope.

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.

Trichloroacetimidate-Triggered Expeditious and Novel Synthesis of N-Acylbenzotriazoles

A facile route for the synthesis of a diverse range of N-acylbenzotriazole derivatives from the corresponding carboxylic acids has been established through a carbonyl activation pathway. In this method, trichloroacetonitrile is performed as an effective reagent for an easy access of N-acylbenzotriazoles which was simply proceeded through the activation of carboxylic acids via in situ imidate formation in anhydrous 1,2-dichloroethane followed by addition of 1H-benzotriazole at 80 °C for 3–4 h. Easy handling, one-pot, and metal-free conditions demonstrate the notable merits of the devised protocol.

A comprehensive review of caged phosphines: synthesis, catalytic applications, and future perspectives

Caged phosphines are versatile ligands due to their rigid backbones, exhibiting a range of catalytic activities, as depicted through the given pictorial representation.

Scale-Up of a Heck Alkenylation Reaction: Application to the Synthesis of an Amino-Modifier Nucleoside ‘Ruth Linker’

Ruth linker is a C5 pyrimidine modified nucleoside analogue widely utilized for the incorporation of a primary amine in a synthetic oligonucleotide. The increasing demand for non-radioactive labeling, detection of biomolecules, and assembly of COVID-19 test kits has triggered a need for scale-up of Ruth linker. Herein, an efficient protocol involving a palladium-catalyzed Heck alkenylation is described. The synthesis has been optimized with a goal of low catalyst concentration, column-free isolation, high product purity, reproducibility, and shorter reaction time. The scalability and utility of the process have been demonstrated successfully on a 100 g scale (starting material). Additionally, for scale-up of the Heck alkenylation protocol, 7-phospha-1,3,5-triaza-adamantanebutane sulfonate (PTABS) as the coordinating caged phosphine ligand was also synthesized on a multigram scale after careful optimization of the conditions.

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.

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.

Microwave-Assisted Palladium-Catalyzed Cross-Coupling Reactions: Generation of Carbon–Carbon Bond

Cross-coupling reactions furnishing carbon–carbon (C–C) bond is one of the most challenging tasks in organic syntheses. The early developed reaction protocols by Negishi, Heck, Kumada, Sonogashira, Stille, Suzuki, and Hiyama, utilizing palladium or its salts as catalysis have, for decades, attracted and inspired researchers affiliated with academia and industry. Tremendous efforts have been paid to develop and achieve more sustainable reaction conditions, such as the reduction in energy consumption by applying the microwave irradiation technique. Chemical reactions under controlled microwave conditions dramatically reduce the reaction time and therefore resulting in increase in the yield of the desired product by minimizing the formation of side products. In this review, we mainly focus on the recent advances and applications of palladium catalyzed cross-coupling carbon–carbon bond formation under microwave technology.

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.

Homogeneous Catalysis: A Powerful Technology for the Modification of Important Biomolecules

Homogeneous catalysis plays an important and ubiquitous role in the synthesis of simple and complex molecules, including drug compounds, natural products, and agrochemicals. In recent years, the wide-reaching importance of homogeneous catalysis has made it an indispensable tool for the modification of biomolecules, such as carbohydrates (sugars), amino acids, peptides, nucleosides, nucleotides, and steroids. Such a synthetic strategy offers several advantages, which have led to the development of new molecules of biological relevance at a rapid rate relative to the number of available synthetic methods. Given the powerful nature of homogeneous catalysis in effecting these synthetic transformations, this Focus Review has been compiled to highlight these important developments.

Facile one-pot nanocatalysts encapsulation of palladium–NHC complexes for aqueous Suzuki–Miyaura couplings

Pd–NHC loaded nanocatalysts (NCs) were readily constructed by a facile one-pot self-assembly approach. These nanoparticles exhibited excellent catalytic activity in aqueous Suzuki–Miyaura couplings.

Crystal structure of 8-(4-methyl-phen-yl)-2'-de-oxy-adenosine hemihydrate

In the asymmetric unit, equalling the unit cell (triclinic, P1, Z = 1), two mol-ecules of the title compound, 8-(4-methyl-phen-yl)-d-2'-de-oxy-adenosine, C17H19N5O3, are present, with distinct conformations of the two sugar moieties, together with one solvent water mol-ecule. All three ribose O atoms are involved in hydrogen bonding and the crystal packing is largely determined by hydrogen-bonding or hydrogen-heteroatom inter-actions (O-H⋯O, O-H⋯N, N-H⋯O, C-H⋯O and C-H⋯N) with one independent mol-ecule directly linked to four neighbouring mol-ecules and the other mol-ecule directly linked to six neighbouring mol-ecules. The two independent mol-ecules of the asymmetric unit display three weak intra-molecular C-H-to-heteroatom contacts, two of which are very similar despite the different conformations of the deoxyribosyl moieties. The aromatic ring systems of both mol-ecules are in proximity to each other and somehow aligned, though not coplanar. The absolute structures of the two mol-ecules were assumed with reference to the reactant 8-bromo-d-2'-de-oxy-adenosine as they could not be determined crystallographically.

Crystal structure of 5-(dibenzo-furan-4-yl)-2'-deoxy-uridine

The mol-ecule of the title compound, C21H18N2O6, has a bent rather than a linear conformation supported by three intra-molecular C-H⋯O hydrogen bonds. The packing in the crystal lattice is largely determined by inter-actions between hydrogen atoms with oxygen atom lone pairs with one mol-ecule inter-acting with neigbouring mol-ecules via O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds. The title compound crystallizes in the chiral ortho-rhom-bic space group P212121. Its absolute structure could not be determined crystallographically and was assumed with reference to that of the reactant 5-iodo-2'-de-oxy-uridine.

Synthesis of zwitterionic palladium complexes and their application as catalysts in cross-coupling reactions of aryl, heteroaryl and benzyl bromides with organoboron reagents in neat water

Imidazolium substituted quinoxaline based zwitterionic Pd(ii) complexes were synthesized and found to be excellent catalysts for carrying out Suzuki–Miyaura cross-coupling reactions in neat water.

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.