2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)amino]-1-propyn-1-yl]uridine
[CAS# 115899-40-6]

Identification

• Classification: Pharmaceutical intermediate >> Heterocyclic compound intermediate >> Pyrimidine compound
• Name: 2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)amino]-1-propyn-1-yl]uridine
• Synonyms: 2,2,2-trifluoro-N-[3-[1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]prop-2-ynyl]acetamide
• Molecular Formula: C₁₄H₁₄F₃N₃O₆
• Molecular Weight: 377.27
• CAS Registry Number: 115899-40-6
• SMILES: C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C#CCNC(=O)C(F)(F)F)CO)O

Properties

• Solubility: Very slightly soluble (0.13 g/L) (25 ºC), Calc.^*
• Density: 1.6±0.1 g/cm³ Calc.^*
• Index of refraction: 1.587 (Calc.)^*

^* Calculated using Advanced Chemistry Development (ACD/Labs) Software.

Safety Data

• Hazard Symbols: GHS07 Warning
• Hazard Statements: H302
• Precautionary Statements: P280-P305+P351+P338

Discovory and Applicatios

2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)amino]-1-propyn-1-yl]uridine is a modified nucleoside analog derived from 2'-deoxyuridine. It features a substitution at the 5-position of the uracil base with a propynyl group carrying a 2,2,2-trifluoroacetyl-protected amino functionality. This chemical modification imparts distinct properties compared to the natural nucleoside, influencing its chemical reactivity and biological interactions.

The compound was synthesized to investigate how incorporation of trifluoroacetyl-protected amino groups affects nucleoside behavior. The trifluoroacetyl group is commonly used in organic synthesis as a protecting group for amino moieties, providing stability during multi-step chemical reactions and allowing selective deprotection when needed. The presence of the propynyl substituent at the 5-position of uridine can enhance base stacking and affect nucleic acid duplex stability.

Applications of 2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)amino]-1-propyn-1-yl]uridine are primarily in the fields of nucleic acid chemistry and medicinal research. This analog can be incorporated into synthetic oligonucleotides for studying nucleic acid structure, hybridization properties, and molecular recognition. Modifications at the 5-position of pyrimidine nucleosides like uridine are known to influence DNA and RNA duplex stability and specificity, making such analogs useful in antisense technologies and nucleic acid-based diagnostics.

In therapeutic research, modified nucleosides like this compound are explored for their potential to interfere with nucleic acid metabolism in viruses or cancer cells. The trifluoroacetyl group may also improve the compound’s stability and bioavailability by affecting its interaction with cellular enzymes and transporters. These features can contribute to the development of novel nucleoside-based drugs with enhanced efficacy and selectivity.

The synthesis of this nucleoside analog generally involves introducing the propynyl substituent at the 5-position of 2'-deoxyuridine through palladium-catalyzed coupling reactions. Subsequently, the amino group is protected with the 2,2,2-trifluoroacetyl moiety to prevent unwanted side reactions during further synthetic steps. This method provides a controlled and efficient route to obtain modified nucleosides suitable for biochemical and pharmaceutical applications.

Due to its unique chemical structure, 2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)amino]-1-propyn-1-yl]uridine is valuable for investigating the effects of base modifications on nucleic acid properties. Its incorporation into oligonucleotides aids in the design of molecular probes with improved binding affinity and specificity. Additionally, it serves as a scaffold for developing new nucleoside analogs with potential therapeutic uses.

In summary, 2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)amino]-1-propyn-1-yl]uridine is a chemically tailored nucleoside with applications in nucleic acid research, diagnostics, and drug development, offering advantages in stability, specificity, and functional versatility.