Hörberg Johanna, Carlesso Antonio, Reymer Anna
Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden.
Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Box 431, SE-405 30 Gothenburg, Sweden.
Mol Ther Nucleic Acids. 2024 Oct 4;35(4):102351. doi: 10.1016/j.omtn.2024.102351. eCollection 2024 Dec 10.
Oligonucleotide drugs, an emerging modulator class, hold promise for targeting previously undruggable biomacromolecules. To date, only 18 oligonucleotide drugs, including sought-after antisense oligonucleotides (ASOs) and splice-switching oligonucleotides, have approval from the U.S. Food and Drug Administration. These agents effectively bind mRNA, inducing degradation or modulating splicing. Current oligonucleotide drug design strategies prioritize full Watson-Crick base pair (bp) complementarity, overlooking mRNA target three-dimensional shapes. Given that mRNA conformational diversity can impact hybridization, incorporating mRNA key structural properties into the design may expedite ASO lead discovery. Using atomistic molecular dynamics simulations inspired by experimental data, we demonstrate the advantages of incorporating common triple bps into the design of ASOs targeting RNA hairpin motifs, which are highly accessible regions for interactions. By using an RNA pseudoknot modified into an ASO-hairpin complex, we investigate the effects of ASO length and hairpin loop mutations. Our findings suggest that ASO-mRNA complex stability is influenced by ASO length, number of common triple bps, and the dynamic accessibility of bases in the hairpin loop. Our study offers new mechanistic insights into ASO-mRNA complexation and underscores the value of pseudoknots in constructing training datasets for machine learning models aimed at designing novel ASO leads.
寡核苷酸药物是一类新兴的调节剂，有望靶向以前难以成药的生物大分子。迄今为止，只有18种寡核苷酸药物，包括备受追捧的反义寡核苷酸（ASO）和剪接转换寡核苷酸，获得了美国食品药品监督管理局的批准。这些药物能有效结合mRNA，诱导其降解或调节剪接。目前的寡核苷酸药物设计策略优先考虑完全的沃森-克里克碱基对（bp）互补性，而忽略了mRNA靶标的三维形状。鉴于mRNA的构象多样性会影响杂交，将mRNA的关键结构特性纳入设计中可能会加快ASO先导物的发现。利用受实验数据启发的原子分子动力学模拟，我们证明了将常见的三碱基对纳入靶向RNA发夹基序的ASO设计中的优势，RNA发夹基序是易于相互作用的区域。通过将RNA假结修饰成ASO-发夹复合物，我们研究了ASO长度和发夹环突变的影响。我们的研究结果表明，ASO-mRNA复合物的稳定性受ASO长度、常见三碱基对的数量以及发夹环中碱基的动态可及性影响。我们的研究为ASO-mRNA复合作用提供了新的机制见解，并强调了假结在构建机器学习模型训练数据集以设计新型ASO先导物方面的价值。
