Phloretin targeting the 3CLpro Cys144 exhibits broad-spectrum antiviral activity against swine enteric coronavirus

Swine enteric coronaviruses (SECoVs) cause severe watery diarrhea and high mortality in piglets, resulting in significant economic losses to the global pig industry. However, frequent mutations in SECoVs significantly compromise vaccine-induced immunity and limit cross-protection against emerging variants. Therefore, there is an urgent need to develop new broad-spectrum antiviral drugs to be the last line of defense to supplement vaccine immunity. In this study, we utilized molecular docking and molecular dynamics simulations to identify phloretin as a broad-spectrum SECoV inhibitor. Phloretin has demonstrated prophylactic and therapeutic efficacy in vitro and in vivo, improving the survival of SECoV-infected piglets. It was further found that phloretin exerts a broad-spectrum antiviral effect by acting on the conserved 3CLpro Cys144 site of three SECoVs. It is worth noting that derivative A12, designed on the basis of the structure-activity relationship (SAR) between phloretin and 3CLpro, showed a 15.7, 2.6, and 8.4-fold increase in antiviral effect against porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine delta coronavirus (PDCoV), respectively. This study reveals a 3CLpro Cys144 targeting broad-spectrum strategy for use against SECoVs, providing a candidate drug to bridge the vaccine immunity gap.