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

Swine enteric coronavirus (SECoVs) infections 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 while limiting 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 simulation to identify phloretin as a broad-spectrum SECoVs inhibitor. Phloretin has demonstrated prophylactic and therapeutic efficacy in vitr o 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's worth noting that derivative A12, designed on the basis of the SAR between phloretin and 3CLpro, showed a 15.7-fold, 2.6-fold, 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 broad-spectrum targeting strategy for use against SECoVs, providing a candidate drug to bridge the vaccine immunity gap. This study reveals that phloretin has both prophylactic and therapeutic effects and exerts broad-spectrum antiviral activity both in vivo and in vitro by binding to the conserved amino acid site Cys144 in SECoV 3CLpro. The structural modification of phloretin has led to the discovery of derivative A12 enhanced the broad-spectrum anti-SECoV activity of phloretin. • Phloretin shows prophylactic and therapeutic broad-spectrum anti-SECoVs effect. • Phloretin targets Cys144 in the 3CLpro active pocket of SECoVs to exert its broad-spectrum antiviral activity. • The designed phloretin derivative A12 demonstrated at least a 2.6-fold increase in efficacy against SECoVs.