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

Cu(II)/PTABS-Promoted, Regioselective SNAr Amination of Polychlorinated Pyrimidines with Mechanistic Understanding

Regioselective amination of polyhalogenated heteroarenes (especially pyrimidines) has extensive synthetic and commercial relevance for drug synthesis applications but is plagued by the lack of effective synthetic strategies. Herein, we report the Cu(II)/PTABS-promoted highly regioselective nucleophilic aromatic substitution (S_NAr) of polychlorinated pyrimidines assisted by DFT predictions of the bond dissociation energies of different C-Cl bonds. The unique reactivity of Cu(II)-PTABS has been attributed to the coordination/activation mechanism that has been known to operate in these reactions, but further insights into the catalytic species have also been provided.

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.

Suzuki-Miyaura Coupling, Heck Alkenylation, and Amidation of DMTr-Protected 5-Iodo-2'-Deoxyuridine via Palladium-catalyzed Reactions

Modification of nucleosides via cross-coupling processes has been carried out extensively on unprotected halonucleosides to produce functionalized nucleosides that are often developed for incorporation into oligonucleotides or used as fluorescent probes. This approach requires protection of the 5'-OH with the 4,4'-dimethoxytrityl (DMTr) group, which is complicated and a common cause of reaction failure. Here we report a method for direct functionalization of 5'-O-DMTr-5-iodo-2'-deoxyuridine via Suzuki-Miyaura cross-coupling, Heck alkenylation, and carboamidation. This approach facilitates rapid synthesis of a variety of C5-substituted 5'-O-DMTr-2'-deoxyuridine derivatives. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the SerrKap palladacycle complex Basic Protocol 2: Suzuki-Miyaura coupling of 5'-O-DMTr-5-iodo-2'-deoxyuridine using SerrKap palladacycle Basic Protocol 3: Heck coupling of 5'-O-DMTr-5-iodo-2'-deoxyuridine using SerrKap palladacycle Basic Protocol 4: Heck coupling of 5'-O-DMTr-5-iodo-2'-deoxyuridine with Ruth linker using Pd(OAc)₂ /PTABS Basic Protocol 5: Carbonylative amidation of 5'-O-DMTr-5-iodo-2'-deoxyuridine using Pd(OAc)₂ /PTABS.