Polysaccharides from Syzygium aromaticum binding to 3CLpro contain glycoproteins interacting with RdRp against SARS-CoV-2

Abstract

The development of anti-SARS-CoV-2 drugs remains important for strategic medicine reserves. 3-chymotrypsin-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp) are key targets for new COVID-19 drugs. Previously, we showed polysaccharides bound 3CLpro to impede SARS-CoV-2 replication. We further hypothesized that natural polysaccharides might block viral replication by binding to both 3CLpro and RdRp. Here, we showed that crude polysaccharide 922 from Syzygium aromaticum almost completely blocked viral replication, while glycoprotein fractions 9222P and 9224P from 922 also showed potent antiviral effects. Although pectic polysaccharide 922211 from 922 interacted with 3CLpro, it showed no antiviral effect. Mechanism studies revealed that 922211, 9221S from 922, and 922 bound 3CLpro; however, only 9222P and 9224P bound RdRp. Further analysis suggested that 9222P and 9224P might suppress RNA elongation. Overall, the antiviral activity of 922 was likely mainly derived from its 9222P and 9224P targeting RdRp, with partial contribution from components interacting with 3CLpro. Additional investigations showed that 922, 9222P, and 9224P were internalized by Vero E6 cells. Intranasal administration of fluorescence and radiolabeled 922 demonstrated efficient pulmonary delivery and sustained retention in vivo. These findings suggest 922 holds promise for further development as an antiviral candidate.

Keywords: 3CL protease; Pectin; Polysaccharide; RdRp; SARS-CoV-2; Syzygium aromaticum.