posted on 2021-02-05, 17:03authored byKas Steuten, Heeyoung Kim, John C. Widen, Brett M. Babin, Ouma Onguka, Scott Lovell, Oguz Bolgi, Berati Cerikan, Christopher J. Neufeldt, Mirko Cortese, Ryan K. Muir, John M. Bennett, Ruth Geiss-Friedlander, Christoph Peters, Ralf Bartenschlager, Matthew Bogyo
Two proteases produced by the SARS-CoV-2
virus, the main protease
and papain-like protease, are essential for viral replication and
have become the focus of drug development programs for treatment of
COVID-19. We screened a highly focused library of compounds containing
covalent warheads designed to target cysteine proteases to identify
new lead scaffolds for both Mpro and PLpro proteases.
These efforts identified a small number of hits for the Mpro protease and no viable hits for the PLpro protease. Of
the Mpro hits identified as inhibitors of the purified
recombinant protease, only two compounds inhibited viral infectivity
in cellular infection assays. However, we observed a substantial drop
in antiviral potency upon expression of TMPRSS2, a transmembrane serine
protease that acts in an alternative viral entry pathway to the lysosomal
cathepsins. This loss of potency is explained by the fact that our
lead Mpro inhibitors are also potent inhibitors of host
cell cysteine cathepsins. To determine if this is a general property
of Mpro inhibitors, we evaluated several recently reported
compounds and found that they are also effective inhibitors of purified
human cathepsins L and B and showed similar loss in activity in cells
expressing TMPRSS2. Our results highlight the challenges of targeting
Mpro and PLpro proteases and demonstrate the
need to carefully assess selectivity of SARS-CoV-2 protease inhibitors
to prevent clinical advancement of compounds that function through
inhibition of a redundant viral entry pathway.