The zymogenic form of SARS-CoV-2 main protease: A discrete target for drug discovery.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M) autocatalytically releases itself out of the viral polyprotein to form a fully active mature dimer in a manner that is not fully understood. Here, we introduce several tools to help elucidate differences between cis (intramolecular) and trans (intermolecular) proteolytic processing and to evaluate inhibition of precursor M. We found that many mutations at the P1 position of the N-terminal autoprocessing site do not block cis autoprocessing but do inhibit trans processing. Notably, substituting the WT glutamine at the P1 position with isoleucine retains M in an unprocessed precursor form that can be purified and further studied. We also developed a cell-based reporter assay suitable for compound library screening and evaluation in HEK293T cells. This assay can detect both overall M inhibition and the fraction of uncleaved precursor form of M through separable fluorescent signals. We observed that inhibitory compounds preferentially block mature M. Bofutrelvir and a novel compound designed in-house showed the lowest selectivity between precursor and mature M, indicating that inhibition of both forms may be possible. Additionally, we observed positive modulation of precursor activity at low concentrations of inhibitors. Our findings help expand understanding of the SARS-CoV-2 viral life cycle and may facilitate development of strategies to target precursor form of M for inhibition or premature activation of M.