5′-Cyclo-Phosphonate Nucleotides for Nuclease-Stable RNAi Agents
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
There is a need for novel modified nucleotides that can provide improved stability and/or potency to oligomeric compounds, such as RNAi agents, particularly enhancing the stability of the phosphate moiety on the terminal nucleotide of RNAi agents to increase their effectiveness in RNA interference pathways.
Innovation Solution
The development of 5′-cyclo-phosphonate modified nucleotides, which are incorporated into oligonucleotides, including RNAi agents, to enhance stability against endonucleases and exonucleases, and improve the likelihood of strand incorporation into the RNA-induced silencing complex (RISC) by maintaining a phosphorylated terminal end.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If standard phosphodiester bonds are used in oligonucleotides, then the structure is simple and easy to synthesize, but the stability against nucleases is poor
Solution Approach 1:
The patent applies parameter changes by modifying the chemical structure of the phosphate moiety at the 5′ terminal end of the oligonucleotide. Specifically, it introduces a cyclo-phosphonate group with cyclic structures (such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl rings) replacing the standard phosphodiester bond configuration. This structural parameter change significantly enhances resistance to endonucleases and exonucleases while maintaining synthetic feasibility through established phosphoramidite chemistry methods.
Solution Approach 2:
The patent employs composite materials by combining the cyclo-phosphonate modified nucleotide structure with existing oligonucleotide frameworks. The modified 5′ terminal nucleotide incorporates a composite structure featuring a cycloalkyl or cycloalkenyl ring fused with a phosphonate group, creating a hybrid structure that integrates the stability benefits of cyclic carbonates with the functional properties of phosphonate bonds, thereby achieving enhanced nuclease resistance without completely redesigning the entire oligonucleotide molecule.
2Reliability
If the 5′ terminal phosphate moiety is left unmodified, then synthesis is simpler, but the likelihood of strand incorporation into RISC is reduced
Solution Approach 1:
The patent applies preliminary action by incorporating the cyclo-phosphonate modification at the 5′ terminal end during the oligonucleotide synthesis process itself, rather than requiring post-synthesis modification. The phosphoramidite building blocks containing the cyclo-phosphonate group are introduced directly during solid-phase synthesis, ensuring the modified structure is established beforehand. This preliminary incorporation facilitates efficient loading into RISC while avoiding additional complex post-synthesis steps.
3Duration of action of moving object
If standard nucleotides are used, then the oligonucleotide has natural structure, but the duration and potency of expression-inhibiting activity is reduced
Solution Approach 1:
The patent applies parameter changes by systematically varying the cyclic group parameters (ring size from cyclopropyl to cycloheptyl, saturation level, and substitution patterns) to optimize both the duration of action and chemical stability. These parameter modifications in the cyclo-phosphonate structure enhance resistance to hydrolysis and enzymatic degradation, thereby extending the half-life and potency of expression-inhibiting oligomeric compounds in biological systems while maintaining structural diversity for further optimization.
Data Source
AI summary
Described are 5′-cyclo-phosphonate modified nucleotides, and oligonucleotides, such as interference (RNAi) agents, containing 5′-cyclo-phosphonate modified nucleotides. The RNAi agents having either double-stranded or single-stranded oligonucleotides described herein comprising 5′cyclo-phosphonate modified nucleotides are useful in modulating gene expression as well as therapeutic, diagnostic, target validation, and genomic discovery applications. The RNAi agents and single-stranded antisense oligonucleotides comprising 5′-cyclo-phosphonate modified nucleotides are useful in the treatment of diseases or conditions that respond to inhibition of gene expression or activity in a cell, tissue, or organism.