Production of human cathepsins using <scp>Expi293™</scp> mammalian cell expression system for off‐target activity of cysteine protease inhibitor screening

Following the SARS-CoV-2 pandemic, many direct-acting antivirals targeting viral cysteine protease were developed. SARS-CoV-2, as well as other viruses, rely on cysteine proteases for their replication, suggesting future generations of antivirals targeting cysteine proteases will emerge. A major concern for these first-generation drugs is the off-target effects on host cysteine proteases. Therefore, screening for inhibitor specificity is a crucial step in antiviral drug development. Cathepsins are one of the most abundant human proteases, which have roles in maintaining cell health and are key to many physiological processes. Here we describe a general expression and purification protocol for cathepsins B, S, and L using the Expi293™ mammalian expression system. We characterized the glycosylation pattern and kinetic parameters of purified enzymes with commercially available cathepsin-specific fluorogenic substrates and also established cathepsin inhibition screen assays. We tested specificity indices of peptidic inhibitors of SARS-CoV-2 M^pro synthesized by our team and nirmatrelvir as a benchmark for all three cathepsins. Establishing a reliable cathepsin inhibition assay would assist with screening of newly developed cysteine protease inhibitors for off-target activity within the scope of pandemic preparedness.