Circular siRNA Design for Metabolic Stability and RISC Loading
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Solution Overview
Problem
Current RNA interference therapies using siRNAs face challenges in achieving potent, metabolically stable, and targeted gene silencing due to limitations in three-dimensional structure design, chemical modifications, and delivery methods, leading to inefficiencies and off-target effects.
Innovation Solution
Development of small circular interfering RNAs (sciRNAs) with chemically modified nucleotides and circular structures, featuring phosphate mimics, ligand conjugation, and specific linkers to enhance stability and targeting, allowing for efficient gene silencing by forming stable complexes with the Argonaute 2 protein.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Stability of the object's composition
If circular siRNA structures are formed using natural ribonucleotides and phosphodiester linkages, then the structural integrity is maintained, but the metabolic stability is poor and off-target effects increase
Solution Approach 1:
The patent applies parameter changes by modifying the chemical composition of the siRNA molecule. Specifically, it incorporates chemically modified nucleotides (such as 2′-O-methyl, 2′-fluoro, LNA) and alternative phosphate linkages (phosphorothioate, phosphordithioate) to enhance metabolic stability and reduce off-target effects while maintaining the circular structure's gene silencing function.
Solution Approach 2:
The patent employs composite materials by combining multiple types of chemically modified nucleotides and linkage types within the same circular siRNA structure. This composite approach creates a hybrid molecule that leverages the stabilizing effects of different modifications simultaneously, achieving both enhanced potency and reduced off-target effects.
2Stability of the object's composition
If chemical modifications are introduced to enhance stability, then metabolic stability improves, but the loading efficiency onto RISC complex decreases
Solution Approach 1:
The patent applies local quality by strategically placing chemical modifications at specific positions within the circular siRNA sequence rather than uniformly modifying all nucleotides. The 5′-end phosphate mimic is positioned at a critical location to ensure proper RISC loading, while other modifications are distributed to provide stability without interfering with complex formation.
Solution Approach 2:
The patent uses parameter changes by selecting specific types of chemical modifications that balance stability enhancement with RISC compatibility. The 5′-end phosphate mimic parameter is specifically chosen to mimic natural phosphate groups, ensuring proper recognition by RISC while providing enhanced stability compared to standard phosphodiester linkages.
3Device complexity
If linear siRNA structures are used, then the simplicity of design is maintained, but the potency and duration of gene silencing are limited
Solution Approach 1:
The patent applies spheroidality by transforming the linear siRNA structure into a circular topology. This cyclic structure eliminates free ends, preventing exonuclease degradation and significantly extending the duration of gene silencing activity while maintaining relatively simple design principles based on standard nucleotide sequences.
4Ease of manufacture
If standard siRNA sequences are used, then the ease of synthesis is maintained, but the potency and metabolic stability are insufficient
Solution Approach 1:
The patent applies parameter changes by incorporating chemically modified nucleotides and linkage types that enhance potency and metabolic stability. These modifications are integrated into standard synthesis protocols, maintaining relative ease of manufacture while dramatically improving therapeutic performance through enhanced resistance to nucleases and improved target binding affinity.
Data Source
AI summary
One aspect of the present invention relates to a small circular interfering RNA (sciRNA) comprising a sense strand and an antisense strand, each of said sense and antisense strands comprising at least one nucleic acid modification, optionally wherein the sense strand has a circular or substantially circular structure. Other aspects of the invention relate a pharmaceutical composition and a method for inhibiting the expression of a target gene in a subject using the sciRNA.