Rational Design and Screening of Chemically Modified Anti-SARS-CoV-2 siRNA

To realize the therapeutic potential of RNA interference against severe acute respiratory syndrome coronavirus 2, strategic chemical modifications are crucial for enhancing the siRNA stability and potency. In this study, 200 siRNAs were screened to identify effective candidates that targeted the highly conserved RNA-dependent RNA polymerase gene and identified VS-38m as a lead compound. Building on this scaffold, we systematically evaluated a series of modification patterns by introducing 2'-fluoro (2'-F) and 2'-O-methyl (2'-OMe) substitutions at specific positions on both the guide and sense strands. To further improve guide strand selection, asymmetric 3'-end modifications, including glycol nucleic acid, threose nucleic acid, and unlocked nucleic acid, were incorporated at the 3' end of the sense strand. The optimized siRNA VS-159m102 demonstrated superior gene-silencing efficacy at picomolar concentrations, along with reduced cytotoxicity and improved serum stability. Our findings on optimal modification patterns provide valuable insights for the future development and application of siRNA therapeutics.