Abstract

Gapmer antisense oligonucleotides (ASOs) enable sequence-specific degradation of target mRNAs, offering therapeutic access to previously “undruggable” genes and holding great promise for treating chronic and genetic diseases. However, the rapid development of ASO therapeutics remains limited by challenges in rational sequence design and translational validation. Here, we present ClinASO, an integrated computational–experimental platform that unifies key determinants of ASO efficacy—including RNase H cleavage preference, SNP avoidance, off-target filtering, and cross-species conservation—into a single, data-driven workflow. This system enables rapid identification of potent ASO leads and direct in vivo validation in wild-type animal disease models. Using ClinASO, we efficiently identified potent ASOs against PCSK9 and IRS1 , both exhibiting superior silencing activity compared to their clinical counterparts. Furthermore, ClinASO generated a potent ASO targeting ACSL4 genes implicated in metabolic dysfunction-associated liver disease (MASLD). In multiple human cells the ASO achieved robust silencing effect. Notably, by conjugating GalNAc, this ASO demonstrated durable, liver-specific knockdown, significantly ameliorating hepatic steatosis and normalizing systemic lipid profiles in MASLD mouse model. Together, these findings establish ClinASO as an efficient, experimentally validated online tool for the rational design and rapid development of translatable ASO therapeutics.