Oligonucleotide End Modifications for TLR7/8 Response Control
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Solution Overview
Problem
Existing therapeutic oligonucleotides induce potent immune responses and immunosuppressive effects through Toll-Like Receptor 7 (TLR7) and TLR8 engagement, necessitating a need for oligonucleotides with limited immunosuppressive effects.
Innovation Solution
Designing oligonucleotides with specific structural features, such as three continuous pyrimidine bases at the 5′ and/or 3′ ends, or two continuous cytosine bases at the 5′ end, along with modified backbones, to maintain or potentiate TLR7 and TLR8 responses.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If chemical modifications (phosphorothioate backbone, 2'-O-methyl, 2'-MOE, 2'-F, LNA) are incorporated to stabilize the oligonucleotide and prevent degradation, then the stability and binding affinity are improved, but the immune response through TLR7 and TLR8 engagement increases
Solution Approach 1:
The patent applies local quality by incorporating specific base modifications (2'-O-methyl, 2'-MOE, 2'-F, or LNA) at particular positions within the oligonucleotide sequence, particularly at the 5' and 3' ends, to locally enhance stability and binding affinity while controlling immune engagement. This localized modification strategy allows different regions of the oligonucleotide to serve different functions: stability enhancement at the ends and targeted mRNA binding in the middle region.
Solution Approach 2:
The patent employs parameter changes by systematically varying chemical modification parameters (type of backbone modification, type of base modification, position of modifications) to optimize the balance between stability, binding affinity, and immune response. The invention evaluates different modification combinations to achieve the desired therapeutic profile with minimal immunosuppression.
2Reliability
If 2'-O-methyl bases are incorporated to stabilize the oligonucleotide, then the binding affinity to target mRNA is improved, but the TLR7 and TLR8 sensing is inhibited
Solution Approach 1:
The patent applies local quality by strategically positioning 2'-O-methyl modifications at specific locations (5' and 3' ends) where they provide maximum stability benefit with minimal impact on TLR sensing. The middle region of the oligonucleotide maintains natural RNA-like structures to preserve TLR engagement while the modified ends provide stability and binding affinity.
Solution Approach 2:
The patent employs asymmetry by using different modification strategies at the 5' and 3' ends compared to the middle region. The ends incorporate stabilizing modifications (2'-O-methyl, phosphorothioate) while the middle region maintains sequences and structures that promote TLR7/8 sensing, creating an asymmetric modification pattern that balances competing requirements.
3Reliability
If phosphorothioate backbone modification is used to prevent degradation, then the stability is improved, but the TLR9, TLR7, AIM2, and cGAS sensing is antagonized
Solution Approach 1:
The patent applies local quality by limiting phosphorothioate backbone modifications to specific regions (particularly the 5' and 3' ends) rather than applying them uniformly throughout the entire oligonucleotide. This localized approach provides stability enhancement at the termini while preserving TLR sensing capability in the middle region where mRNA binding occurs.
Solution Approach 2:
The patent employs segmentation by dividing the oligonucleotide into distinct functional regions with different chemical properties: modified ends for stability and unmodified or differently modified middle regions for TLR engagement and mRNA binding. This segmented architecture allows each region to optimize its specific function without compromising the other.
4Reliability
If extensive chemical modifications are applied to all regions of the oligonucleotide, then the stability and binding affinity are maximized, but the immune response and immunosuppressive effects increase
Solution Approach 1:
The patent applies local quality by concentrating chemical modifications (phosphorothioate backbone, 2'-O-methyl, 2'-MOE, 2'-F, or LNA) primarily at the 5' and 3' ends of the oligonucleotide, while leaving the middle region less modified or with different modifications. This localized modification strategy maximizes stability and binding affinity at the termini where they are most critical, while preserving TLR7 and TLR8 sensing capability in the middle region that interacts with target mRNA.
Solution Approach 2:
The patent employs segmentation by dividing the oligonucleotide into distinct functional zones with different modification densities: highly modified ends for stability and binding, and less modified middle regions for TLR engagement. This segmented architecture allows the oligonucleotide to simultaneously achieve therapeutic stability and maintain immune recognition, avoiding the immunosuppressive effects of uniform modification.
Data Source
AI summary
The present invention relates to oligonucleotides that maintain a Toll-Like Receptor 7 (TLR7) response and/or which potentiate Toll-Like Receptor 8 (TLR8) sensing.