Design and systematic evaluation of novel chemical modification patterns enable the identification of a potent siRNA targeting PCSK9

Fully modified small interfering RNAs (siRNAs) have demonstrated remarkable advantages in medicine development since they enable the knockdown of the majority of disease-related proteins. However, unmodified siRNAs usually cannot be used for medications due to their biochemical instability. siRNA modification patterns are engineered to enhance both structural stability and pharmacodynamic efficacy, thus being vital in the development of potent siRNA drugs. However, most modification patterns of approved or clinically investigated siRNAs are protected by patents, significantly restricting their broader application. Therefore, the development of proprietary modification patterns has been essential for siRNA therapeutics companies. Here, based on a comprehensive analysis of existing studies, we designed novel modification patterns by altering 2'-F moiety positions at critical sites on sense or antisense strands to enhance siRNA efficacy. Experiments indicate that these modification patterns improve the in vitro activity of an approved siRNA drug targeting proprotein convertase subtilisin/kexin type 9 (PCSK9) mRNA, which lowers plasma low-density lipoprotein cholesterol (LDL-C) levels. Furthermore, by optimizing sequence modification combinations, we identified a promising siRNA drug (YK1597-DV29PG5) targeting PCSK9, which has advanced to clinical trials with favorable preclinical efficacy and safety. This study offers valuable insights for designing novel, efficient modification patterns for siRNA drugs.