The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands
novel direct antiviral treatments. The main protease (M
pro
) and papain-like
protease (PL
pro
) are attractive drug targets among coronaviruses due to their
essential role in processing the polyproteins translated from the viral RNA. In this
study, we virtually screened 688 naphthoquinoidal compounds and derivatives against
M
pro
of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in
biochemical assays against M
pro
using a novel fluorogenic substrate. In
parallel, these compounds were also assayed with SARS-CoV-2 PL
pro
. Four
compounds inhibited M
pro
with half-maximal inhibitory concentration
(IC
50
) values between 0.41 μM and 9.0 μM. In addition, three
compounds inhibited PL
pro
with IC
50
ranging from 1.9 μM to
3.3 μM. To verify the specificity of M
pro
and PL
pro
inhibitors, our experiments included an assessment of common causes of false positives
such as aggregation, high compound fluorescence, and inhibition by enzyme oxidation.
Altogether, we confirmed novel classes of specific M
pro
and PL
pro
inhibitors. Molecular dynamics simulations suggest stable binding modes for
M
pro
inhibitors with frequent interactions with residues in the S1 and S2
pockets of the active site. For two PL
pro
inhibitors, interactions occur in
the S3 and S4 pockets. In summary, our structure-based computational and biochemical
approach identified novel naphthoquinonal scaffolds that can be further explored as
SARS-CoV-2 antivirals.