Protegrin-2, a potential inhibitor for targeting SARS-CoV-2 main protease M(pro)

BACKGROUND: SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat SARS-CoV-2 and its variants. The main protease (M(pro)) of SARS-CoV-2 is a promising therapeutic target due to its crucial role in viral replication and its conservation in all the variants. Therefore, the aim of this work was to identify an effective inhibitor of M(pro). METHODS: We studied around 200 antimicrobial peptides using in silico methods including molecular docking and allergenicity and toxicity prediction. One selected antiviral peptide was studied experimentally using a Bioluminescence Resonance Energy Transfer (BRET)-based M(pro) biosensor, which reports M(pro) activity through a decrease in energy transfer. RESULTS: Molecular docking identified one natural antimicrobial peptide, Protegrin-2, with high binding affinity and stable interactions with M(pro) allosteric residues. Furthermore, free energy calculations and molecular dynamics simulation illustrated a high affinity interaction between the two. We also determined the impact of the binding of Protegrin-2 to M(pro) using a BRET-based assay, showing that it inhibits the proteolytic cleavage activity of M(pro). CONCLUSIONS: Our in silico and experimental studies identified Protegrin-2 as a potent inhibitor of M(pro) that could be pursued further towards drug development against COVID-19 infection.