Targeting coronaviral inflammation: aptamer-based strategies for emerging threats

Coronaviruses have repeatedly emerged in recent years, causing significant and ongoing threats to global public health. The development of therapeutic agents and strategies capable of responding to future outbreaks caused by emerging coronavirus variants remain an ongoing priority. Here, we engineered a single-stranded DNA aptamer (NApt8-3) that selectively binds to the conserved nucleocapsid (N) protein shared among multiple coronaviruses, including SARS-CoV-2 (wild-type, beta, omicron variant), SARS-CoV, MERS-CoV, HCoV-OC43 and HCoV-229E, and strongly inhibits N protein-induced inflammatory cytokine expression. Mechanistically, NApt8-3 effectively binds to the N protein and blocks its interaction with the NLRP3 inflammasome, a key mediator of coronavirus-induced inflammation. To enable intracellular delivery and evaluate its therapeutic potential, we developed a proof-of-concept anti-SARS-CoV-2 agent-circSASON, a circular trivalent aptamer-antisense oligonucleotide (ASO) chimera-combining NApt8-3, an antispike protein aptamer, and an ASO that silences the N gene. In vitro experiments demonstrated that circSASON effectively inhibits SARS-CoV-2 replication and suppresses N protein-induced cytokine expression in host cells. The intranasal administration of circSASON significantly decreased the level of SARS-CoV-2 and alleviated SARS-CoV-2-induced pulmonary inflammation and inflammatory cytokine expression in mice. Therefore, our findings highlight NApt8-3 as a broad-spectrum anti-inflammatory agent that targets the conserved coronavirus N protein. The therapeutic design strategy employed, together with the N aptamer developed in this study, may offer a framework for the rapid development of treatments to combat future pandemics caused by emerging coronavirus variants.