Around three billion people are at risk of infection
by the dengue
virus (DENV) and potentially other flaviviruses. Worldwide outbreaks
of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack
of antiviral drugs, and limitations on vaccine usage emphasize the
need for novel antiviral research. Here, we propose a consensus virtual
screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in
silico combination of a hologram quantitative structure–activity
relationship (HQSAR) model and molecular docking on characterized
binding sites followed by molecular dynamics (MD) simulations, which
filtered a data set of 7.6 million compounds to 2,775 hits. Lastly,
docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five
compounds had their antiviral activity confirmed against ZIKV, YFV,
DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ±
0.8 μM), displaying aggregator characteristics for enzymatic
inhibition against ZIKV NS3pro (ranging from 28 ±
7 to 70 ± 7 μM). Taken together, the compounds identified
in this approach may contribute to the design of promising candidates
to treat different flavivirus infections.