Structure-based lead optimization of peptide-based vinyl methyl ketones as SARS-CoV-2 main protease inhibitors

In March 2020, a global pandemic of COVID-19 caused by SARS-CoV-2 was declared. The huge efforts to restrict the impact on public health led to the approval of different vaccines and antiviral drugs. Among the latter, Nirmatrelvir, a reversible inhibitor of SARS-CoV-2 main protease (Mpro), an essential viral cysteine protease, was the first drug approved for non-severe forms of the disease.[1] Despite the relevant achieved results, the fight against SARS-CoV-2 and health problems accompanying COVID-19 is still ongoing. Recently, a virtual screening analysis for inhibitors of SARS-CoV-2 Mpro using a set of in-house compounds allowed us to identify two hits (i.e., 1 and 2), which bear a methyl vinyl ketone warhead.[2] Starting from these compounds, a series of novel Michael acceptors harbouring the methyl vinyl ketone warhead was developed. The analogues differ from each other for the amino acids at the P2 site, meanwhile, the effect of vinyl methyl ester warhead was also assessed. The vinyl methyl ketone-containing analogues exhibited sub-micromolar activity against the viral protease. SPR38, SPR39, and SPR41 were fully characterized, and hCatL, which plays a key role in the virus entry into host cells, resulted to be sensitive to SPRs. Additionally, dose-dependent enzyme inhibition was observed. Lastly, SPR39 and SPR41 showed single-digit micromolar EC50 values against infected cells. All in all, the vinyl methyl ketone moiety resulted to be a valid warhead for SARS-CoV-2 Mpro inhibition, meanwhile, bulky aliphatic amino acids at the P2 site resulted to be well-tolerated. Starting from these findings, further SAR studies will be carried out to improve the inhibitory properties.