Chemical synthesis of 4′-thio and 4′-sulfinyl pyrimidine nucleoside analogues

Guinan, Mieke; Huang, Ningwu; Hawes, Chris S.; Lima, Marcelo A.; Smith, Mark E.; Miller, Gavin J.

doi:10.1039/d1ob02097h

Cited by 15 publications

(8 citation statements)

References 27 publications

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“…Considering the importance of chemical modifications to the D-ribose core in developing nucleoside analogue therapeutics, we recently disclosed an efficient gram-scale synthetic entry to 4'-thioribopyrimidines, where the furanose ring oxygen is substituted with a sulfur atom. [13][14][15] This work complimented wider attention from several academic and industrial groups exploring the chemical synthesis of 4′-thionucleosides, since the first disclosure of 4′-thioadenosine in the early 1960s. [16][17][18][19] Bioisosteric replacement of furanose oxygen with larger sulfur can impart changes to the furanose ring conformation, improving the hydrolytic stability of the glycosidic linkage and has delivered several biologically active 4'-thionucleosides (Figure 1a).…”

Section: Introductionmentioning

confidence: 85%

Biocatalytic nucleobase diversification of 4’-thionucleosides and de novo RNA synthesis using 5-ethynyl-4’-thiouridine

Westarp,

Benckendorff,

Motter

et al. 2024

Preprint

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Nucleoside and nucleotide analogues have proven transformative in the treatment of viral infections and cancer. One branch of structural modification to deliver new nucleoside analogue classes explores replacement of canonical ribose oxygen with a sulfur atom. Whilst biological activity of such analogues has been shown in some cases, widespread exploration of this class of analogue is hitherto hampered by the lack of a straightforward and universal nucleobase diversification strategy. Herein, we present a synergistic platform enabling both biocatalytic nucleobase diversification from 4'-thiouridine in a one-pot process, and chemical functionalization to access new functional entities. This methodology delivers entry across pyrimidine and purine 4'-thionucleosides, paving a way for wider synthetic and biological exploration. We exemplify our approach by enzymatic synthesis of 5-iodo-4'-thiouridine on multi-milligram scale and from here switch to the chemical synthesis of a novel nucleoside analogue probe, 5-ethynyl-4'-thiouridine. Finally, we demonstrate the utility of this probe to monitor RNA synthesis de novo in proliferating HeLa cells, validating its capability as a new metabolic RNA labelling tool.

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Section: Introductionmentioning

confidence: 85%

Biocatalytic nucleobase diversification of 4’-thionucleosides and de novo RNA synthesis using 5-ethynyl-4’-thiouridine

Westarp,

Benckendorff,

Motter

et al. 2024

Preprint

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“…Difluorinated uridine 9 was also converted into its cytidine form by following established protocols. 32,33 Briefly, 9 was treated with POCl 3 followed by triazole, furnishing a C4-triazolyl intermediate that, after amination with NH 4 OH, afforded 6′,6′-gem-difluorocytidine 12 in 61% yield, over two steps.…”

Section: Cluster Synlettmentioning

confidence: 99%

Chemical Diversification of Carbocyclic Fluorinated Pyrimidine Nucleosides: Introducing 2′-Arabino Analogues and Ring Unsaturation

Benckendorff

Hawes

Smith

et al. 2023

Synlett

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Analogues of the canonical nucleosides have a longstanding presence and proven capability within medicinal chemistry and drug discovery research. Herein we report chemical diversification of carbocyclic pyrimidine nucleosides, containing CF2 and CHF in place of furanose oxygen, to introduce ring unsaturation and 2’-epimers. Utilising gram-scale access to 6’-(R)-monofluoro- and 6’-gem-difluorouridine we explore provision of 2’,3’-didehydro-2’,3’-dideoxy and 1’,2’-didehydro-2’-deoxy analogues, alongside the first example of 6’-(R)-fluoroarabino carbauridine. Key stereochemistries and the presence of unsaturation are confirmed using X-ray crystallography and NMR, and an indicative conformational preference for a monofluoro 2’,3’-didehydro-2’,3’-dideoxy system is presented. This synthetic blueprint offers potential to explore biological activity for these hitherto unavailable materials, including for direct comparison to established nucleoside analogue drugs.

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“…Examples here include the following: 1) incorporation of 4-thioribose within canonical nucleosides, noting conformational changes within related RNA sequences following solid-phase synthesis (Haeberli, 2005); 2) improved thermal stability and reduced susceptibility toward nucleases for 2 -modified-4 -thioRNA (Takahashi et al, 2009); 3) improved RNA interference in mammalian cells using 4thio-modified siRNA (Dande et al, 2006); 4) 4 -thio-LNA/BNA building blocks introduced within oligonucleotide sequences, seeking to provide new motifs in the advent of mRNA-based vaccines (Maeda et al, 2021); 5) preparation and exploration of nucleotide triphosphates of 4 -thionucleosides for SELEX (systematic evolution of ligands by exponential enrichment) (Kato, 2005). Accordingly, access to appropriate 4 -thionucleoside substrates for the purpose of oligonucleotide synthesis is of continued interest, and in relation to our own programs (Benckendorff et al, 2023(Benckendorff et al, , 2022, we have recently developed a reliable and robust synthesis method delivering multi-gram access to 4 -thiouridine 5 and derivatives therefrom (Guinan et al, 2022a(Guinan et al, , 2022b. From this, we wished to gain entry to a 4 -thiouridine phosphoramidite, appropriately protected for solid-phase nucleic acid synthesis.…”

Section: Introductionmentioning

confidence: 99%

Preparation of a 4′‐Thiouridine Building‐Block for Solid‐Phase Oligonucleotide Synthesis

Benckendorff,

Sanghvi,

Miller

2023

Current Protocols

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Starting from a commercially available thioether, we report a nine‐step synthesis of a 4′‐thiouridine phosphoramidite building‐block. We install the uracil nucleobase using Pummerer‐type glycosylation of a sulfoxide intermediate followed by a series of protecting group manipulations to deliver the desired phosphite. Notably, we introduce a 3′,5′‐O‐di‐tert‐butylsilylene protecting group within a 4′‐thiosugar framework, harnessing this to ensure regiospecific installation of the 2′‐O‐silyl protecting group. We envisage this methodology will be generally applicable to other 4′‐thionucleosides and duly support the exploration of their inclusion within related nucleic acid syntheses. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: (2R,3S,4R)‐2,3‐O‐Isopopropylidene‐5‐O‐tert‐butyldiphenylsilyl‐1‐(4‐sulfinyl)cyclopentane: SulfoxidationBasic Protocol 2: 2′,3′‐O‐Isopropylidene‐5′‐O‐tert‐butyldiphenylsilyl‐4′‐thiouridine: Pummerer glycosylationBasic Protocol 3: 4′‐Thiouridine: DeprotectionBasic Protocol 4: 2′‐O‐tert‐Butyldimethylsilyl‐3′,5′‐di‐tert‐butylsiloxy‐4′‐thiouridine: 2′,3′,5′‐O‐silylationBasic Protocol 5: 2′‐O‐tert‐Butyldimethylsilyl‐4′‐thiouridine: Selective 3′‐5′‐desilylationBasic Protocol 6: 2′‐O‐tert‐Butyldimethylsilyl‐5′‐O‐dimethoxytrityl‐4′‐thiouridine: 5′‐O‐dimethoxytritylationBasic Protocol 7: 2′‐O‐tert‐butyldimethylsilyl‐3′‐O‐[(2‐cyanoethoxy)(N,N‐diisopropylamino)phosphino]‐5′‐O‐dimethoxytrityl‐4′‐thiouridine: 3′‐O‐phosphitylation

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Chemical synthesis of 4′-thio and 4′-sulfinyl pyrimidine nucleoside analogues

Abstract: Synthesis of 4-thioribose building blocks and related 4′-thio and 4′-sulfinyl nucleoside analogues.

Cited by 15 publications

References 27 publications

Biocatalytic nucleobase diversification of 4’-thionucleosides and de novo RNA synthesis using 5-ethynyl-4’-thiouridine

Biocatalytic nucleobase diversification of 4’-thionucleosides and de novo RNA synthesis using 5-ethynyl-4’-thiouridine

Chemical Diversification of Carbocyclic Fluorinated Pyrimidine Nucleosides: Introducing 2′-Arabino Analogues and Ring Unsaturation

Preparation of a 4′‐Thiouridine Building‐Block for Solid‐Phase Oligonucleotide Synthesis

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