Cysteine proteases
(CPs) are an important class of enzymes, many
of which are responsible for several human diseases. For instance,
cruzain of protozoan parasiteTrypanosoma cruziis responsible for the Chagas disease, while the role of human cathepsin
L is associated with some cancers or is a potential target for the
treatment of COVID-19. However, despite paramount work carried out
during the past years, the compounds that have been proposed so far
show limited inhibitory action against these enzymes. We present a
study of proposed covalent inhibitors of these two CPs, cruzain and
cathepsin L, based on the design, synthesis, kinetic measurements,
and QM/MM computational simulations on dipeptidyl nitroalkene compounds.
The experimentally determined inhibition data, together with the analysis
and the predicted inhibition constants derived from the free energy
landscape of the full inhibition process, allowed describing the impact
of the recognition part of these compounds and, in particular, the
modifications on the P2 site. The designed compounds and, in particular,
the one with a bulky group (Trp) at the P2 site show promisingin vitroinhibition activities against cruzain and cathepsin
L for use as a starting lead compound in the development of drugs
with medical applications for the treatment of human diseases and
future designs.