Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection

The entry of SARS-CoV-2 into target cells requires the activation of its surface spike protein, S, by host proteases. The host serine protease TMPRSS2 and cysteine proteases Cathepsin B/L can activate S, making two independent entry pathways accessible to SARS-CoV-2. Blocking the proteases prevents SARS-CoV-2 entry in vitro. This blockade may be achieved in vivo through 'repurposing' drugs, a potential treatment option for COVID-19 that is now in clinical trials. Here, we found, surprisingly, that drugs targeting the two pathways, although independent, could display strong synergy in blocking virus entry. We predicted this synergy first using a mathematical model of SARS-CoV-2 entry and dynamics in vitro. The model considered the two pathways explicitly, let the entry efficiency through a pathway depend on the corresponding protease expression level, which varied across cells, and let inhibitors compromise the efficiency in a dose-dependent manner. The synergy predicted was novel and arose from effects of the drugs at both the single cell and the cell population levels. Validating our predictions, available in vitro data on SARS-CoV-2 and SARS-CoV entry displayed this synergy. Further, analysing the data using our model, we estimated the relative usage of the two pathways and found it to vary widely across cell lines, suggesting that targeting both pathways in vivo may be important and synergistic given the broad tissue tropism of SARS-CoV-2. Our findings provide insights into SARS-CoV-2 entry into target cells and may help improve the deployability of drug combinations targeting host proteases required for the entry. Author summary The COVID-19 pandemic has triggered urgent efforts to repurpose available drugs for the treatment of SARS-CoV-2 infection. Synergistic drug combinations are particularly desirable because they allow the achievement of desired efficacies with minimal toxicities. Here, we predict that drugs targeting the host proteases, TMPRSS2 and Cathepsin B/L, which facilitate SARS-CoV-2 entry into cells through independent pathways, would be synergistic. We identified the synergy using a mathematical model and found evidence for it in available in vitro data. We found the estimated usage of the two pathways to vary vastly across cell types, highlighting the need to target both pathways. Our findings would help maximize the impact of combination therapies targeting host proteases involved in SARS-CoV-2 entry, which are currently in clinical trials.