Seed-Region Modified siRNA Oligonucleotides for Lower Off-Target Toxicity
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Solution Overview
Problem
Existing siRNA drugs face issues with off-target toxicity due to incomplete pairing in the seed region, leading to unpredictable toxic side effects, while chemical modifications to reduce off-target effects often compromise on-target activity.
Innovation Solution
Introduce specific chemical modifications, such as Ago, Ggo, Cgo, Ugo, Ggs, or Tgo, at nucleotide positions 2 to 8 of the siRNA antisense strand, combined with other modifications like 2'-fluoro or phosphorothioate linkages, to minimize off-target effects while maintaining on-target activity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Object-affected harmful factors
If chemical modifications are introduced to the 5' end seed region of the siRNA antisense strand to reduce off-target toxicity, then off-target effects are reduced, but on-target activity is significantly lost
Solution Approach 1:
The patent applies local quality by introducing chemical modifications specifically at certain positions within the seed region (positions 2-8) rather than uniformly across the entire sequence. Different modifications are placed at different positions to achieve position-specific effects: some positions are modified to reduce off-target binding while other positions maintain strong target recognition. This localized modification strategy allows the seed region to simultaneously achieve both reduced off-target toxicity and maintained on-target activity.
Solution Approach 2:
The patent employs parameter changes by systematically varying the type of chemical modification at different positions within the seed region. Multiple modification types (e.g., 2'-fluoro, 2'-methoxy, phosphorothioate linkages) are used at different positions to optimize the balance between off-target reduction and on-target activity. This parameter optimization allows fine-tuning of the seed region's binding characteristics to achieve the desired therapeutic effect.
2Object-affected harmful factors
If chemical modifications are introduced to adjust the interaction strength between the seed region and target gene, then off-target effects are reduced, but the silencing effect on target mRNA may be compromised
Solution Approach 1:
The patent applies segmentation by dividing the seed region into multiple positions (2-8) and applying different modifications to different segments. This allows each segment to perform its specific function: some segments are optimized for reducing off-target binding while other segments maintain strong complementary pairing with the target mRNA. This segmented approach ensures that the overall silencing effect is preserved while off-target effects are reduced.
Solution Approach 2:
The patent uses local quality by making position-specific modifications within the seed region. Each position is modified according to its specific functional requirements: positions that contribute to off-target binding are modified to reduce such binding, while positions critical for target recognition maintain their original or slightly modified structure. This localized optimization ensures both reduced off-target effects and maintained silencing activity.
Data Source
Figure 1
AI summary
The present disclosure relates to an oligonucleotide and a preparation method and use thereof. The present disclosure provides a single-stranded or double-stranded oligonucleotide, wherein each strand has 15 to 35 nucleotides, and at least one nucleotide position of the oligonucleotide other than the termini comprises a chemical modification represented by formula (II) or a tautomer modification thereof. The modification method of the present disclosure can minimize the impact on the on-target activity of siRNA while reducing its off-target effect.