ArticleMolecular therapy. Nucleic acids2024
ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulation.
Article in Molecular therapy. Nucleic acids, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antisense Versus Antigene in the Computer-Aided Design of Triplex-Forming Oligonucleotides (TFO): Insights from a Dual-Method Review, Combining Bibliometric and Systematic Review.International journal of molecular sciences · 2025Pooled it
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- Accurately modeling RNase H-mediated antisense oligonucleotide efficacy.Molecular therapy. Nucleic acids · 2026Article
- Safety and toxicity assessment of antisense oligonucleotides in brain-relevant human cellular models.Molecular therapy. Nucleic acids · 2026Review
- To scramble or not: Steric blocking 2'-MOE/PS control antisense oligonucleotides across cellular models.Molecular therapy. Nucleic acids · 2026Article
- Survivin-Targeting Antisense Oligonucleotides in Cancer Therapy.Molecules (Basel, Switzerland) · 2026Review
- Landscape and biogenesis of piRNAs in HBV-associated hepatocarcinogenesis: from repetitive elements to oncogenic circuits.Discover oncology · 2026Review
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- QStrain: an interactive platform for viral genome analysis and nucleic acid therapeutic design.BMC bioinformatics · 2026Article
- Functional characterization of dynamic nascent RNA folding ensembles in real time.Science advances · 2026Article
- Review
- ASOptimizer: optimizing chemical diversity of antisense oligonucleotides through deep learning.Nucleic acids research · 2025Article
- Review
- ASOG: AntiSense Oligonucleotide Generator.Computational and structural biotechnology journal · 2025Article
- Deep learning facilitates efficient optimization of antisense oligonucleotide drugs.Molecular therapy. Nucleic acids · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have highlighted the effectiveness of using antisense oligonucleotides (ASOs) for cellular RNA regulation, including targets that are considered undruggable; however, manually designing optimal ASO sequences can be labor intensive and time consuming, which potentially limits their broader application. To address this challenge, we introduce a platform, the ASOptimizer, a deep-learning-based framework that efficiently designs ASOs at a low cost. This platform not only selects the most efficient mRNA target sites but also optimizes the chemical modifications for enhanced performance. Indoleamine 2,3-dioxygenase 1 (IDO1) promotes cancer survival by depleting tryptophan and producing kynurenine, leading to immunosuppression through the aryl-hydrocarbon receptor (Ahr) pathway within the tumor microenvironment. We used ASOptimizer to identify ASOs that target IDO1 mRNA as potential cancer therapeutics. Our methodology consists of two stages: sequence engineering and chemical engineering. During the sequence-engineering stage, we optimized and predicted ASO sequences that could target IDO1 mRNA efficiently. In the chemical-engineering stage, we further refined these ASOs to enhance their inhibitory activity while reducing their potential cytotoxicity. In conclusion, our research demonstrates the potential of ASOptimizer for identifying ASOs with improved efficacy and safety.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.