<p>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 <i>in vitro</i>. This blockade may be achieved <i>in vivo</i> 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 <i>in vitro</i>. 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 <i>in vitro</i> 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 <i>in
vivo</i> 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. <br></p>