Comparative analysis of clinically approved lipid nanoparticles for intranasal siRNA delivery against SARS-CoV-2

SARS-CoV-2 continues to circulate globally, with persistent hospitalizations, despite a successful global vaccination strategy. We have developed highly conserved, antiviral short interfering (si)RNA and demonstrated in vivo antiviral efficacy following intranasal treatment of mice with naked siRNA. To enhance antiviral efficacy and siRNA protection, in this study we investigated the use of LNP packaging to improve delivery and efficacy. We examined three clinically approved lipid nanoparticle (LNP) formulations that mimic the compositions of Alnylam's Onpattro (MC3), Moderna's Spikevax (SM-102), and Pfizer-BioNTech's Comirnaty (ALC-0315) RNA-based therapeutics, to identify the optimal formulation for antiviral siRNA therapeutic respiratory delivery and antiviral efficacy. All LNP formulations assessed showed successful delivery of siRNA to respiratory cells in vitro and provided effective silencing of siRNA targeted SARS-CoV-2 genes. However, the MC3-based LNP-siRNA (MC3 LNP-siRNA) treatment elicited the least off-target immune activation, with no induction of interferon stimulated genes. Additionally, the MC3 LNP-siRNA remained effective when administered 24 h post-infection, significantly reducing viral RNA levels in vitro. Chemical modification of siRNA with 2'‑O‑methyl incorporation further attenuated immune activation, without compromising efficacy. In vivo intranasal delivery of MC3 LNP-siRNA was generally well tolerated, with no adverse effects on body weight or pulmonary function at therapeutic doses, although mild pulmonary leukocyte infiltration was observed at higher or repeated doses. Our study demonstrates that LNP-encapsulated and chemically modified siRNAs can provide an effective and mutation-resilient antiviral strategy. This study compares clinically relevant LNP formulations for siRNA delivery to the respiratory tract, demonstrating that MC3-based LNPs offer a promising platform for safe and effective RNA therapeutic delivery.