Exploring bifunctional molecules for anti-SARS-CoV-2 and anti-inflammatory activity through structure-based virtual screening, SAR investigation, and biological evaluation

As new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge, they raise increasing concerns about the efficacy of neutralizing antibodies and vaccines. This situation underscores the urgent need for specific drugs against the coronavirus disease 2019 (COVID-19). Given that COVID-19 is particularly associated with substantial inflammation, the development of novel, effective antiviral and anti-inflammatory agents represents a promising research direction. In this study, we virtually screened a library consisting of 2900 anti-inflammatory small molecules for their inhibitory effects on the 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2 and selected 23 promising candidates for further testing using a fluorescence resonance energy transfer (FRET) assay. The results indicated that Gnetol had the most potent inhibitory effect against SARS-CoV-2 3CL^pro. Further structural modifications led to the identification of compounds 38 and 39, which displayed superior inhibitory activity. Compound 39 showed good selectivity for host proteases. Subsequently, Gnetol and its structural analogs, which demonstrated SARS-CoV-2 3CL^pro inhibitory activity, were tested for their anti-inflammatory effects. Among these, Piceatannol and compound 39 exhibited enhanced anti-inflammatory effects, with compound 39 alone showing the most potent antiviral and anti-inflammatory activity. Thus, our study has explored a new research strategy for discovering antiviral and anti-inflammatory bifunctional molecules. The discovery of Gnetol and its structural analogs has provided new lead candidates for the development of COVID-19 therapeutics.