Peptide Nucleic Acid Derivatives for Low-Toxicity Exon Skipping
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Solution Overview
Problem
Current antisense oligonucleotides, such as phosphorothioate oligonucleotides (PTOs) and 2′-O-alkyl-RNA, face challenges with poor cell permeability and toxicity, limiting their therapeutic efficacy, particularly in conditions like Duchenne Muscular Dystrophy (DMD) and other diseases where exon skipping is desired to produce functional proteins.
Innovation Solution
Development of peptide nucleic acid (PNA) derivatives that are designed to target specific splice sites in pre-mRNA, enhancing exon skipping efficiency and cellular uptake without the need for toxic delivery agents, thereby promoting the production of functional proteins.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional antisense oligonucleotides are used for exon skipping, then sequence-specific modulation of gene expression is achieved, but cell permeability is poor leading to high doses and toxicities
Solution Approach 1:
The patent modifies the chemical structure of the oligonucleotide by incorporating peptide nucleic acid (PNA) backbone instead of traditional phosphodiester backbone. This structural parameter change transforms the molecule from a negatively charged phosphodiester chain to a neutral PNA backbone, which fundamentally alters cell membrane permeability characteristics and enables efficient cellular uptake without requiring high doses that cause toxicity.
Solution Approach 2:
The invention creates a hybrid molecule combining PNA backbone with nucleobase modifications. The PNA backbone provides cell permeability while the modified nucleobases (such as 2'-O-alkyl, 2'-O-methoxyethyl, or locked nucleic acid modifications) enhance affinity for the target pre-mRNA. This composite structure integrates the advantages of both components to achieve potent exon skipping with improved pharmacokinetic properties.
2Ease of operation
If lipofection formulation is used to improve cell permeability, then delivery efficiency increases, but cytotoxicity occurs
Solution Approach 1:
The PNA derivative is designed to be self-delivering without requiring external formulation agents. The neutral PNA backbone inherently facilitates cell membrane permeability through passive diffusion or receptor-mediated endocytosis, eliminating the need for lipofection complexes. This self-service delivery mechanism avoids the cytotoxicity associated with lipofection while maintaining efficient cellular uptake.
3Reliability
If high doses of traditional oligonucleotides are administered to overcome poor permeability, then therapeutic activity is achieved, but toxicity increases
Solution Approach 1:
The patent changes the fundamental chemical parameter of the oligonucleotide backbone from phosphodiester to PNA. This structural transformation improves cell membrane permeability by eliminating the negative charge that hinders passive diffusion. As a result, the molecule achieves therapeutic efficacy at much lower doses, directly resolving the contradiction between therapeutic activity and dose requirement.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
PNA derivatives effectively induce exon skipping in target genes, improving protein expression and functional activity, offering a safer and more efficient alternative to traditional oligonucleotides by overcoming cell membrane penetration barriers.
Implementation Method 1
Peptide nucleic acids (PNAs) are synthetic polypeptides that have the ability to hybridize with complementary nucleic acids, including DNA and RNA
Implementation Method 2
Oligonucleotides with good cell permeability are able to modulate such biological processes within cell in a sequence predictable manner
Data Source
AI summary
A peptide nucleic acid derivative of Formula I is provided to tightly bind to a splice site within a pre-mRNA in a sequence specific manner. Given with excellent cell membrane permeability and strong affinity for RNA, the peptide nucleic acid derivative induces exon skipping in cells treated with the peptide nucleic acid at sub-femtomolar concentration as “naked” oligonucleotide. The compound shows therapeutic activity in subjects upon systemic administration even at 1 μg/Kg or less, and therefore is useful to treat a disease or symptom at affordable treatment cost.