Cathepsin-Targeting SARS-CoV‑2 Inhibitors: Design, Synthesis, and Biological Activity

Cathepsins
(Cats) are proteases that mediate the successful entry
of SARS-CoV-2 into host cells. We designed and synthesized a tailored
series of 21 peptidomimetics and evaluated their inhibitory activity
against human cathepsins L, B, and S. Structural diversity was realized
by combinations of different C-terminal warhead functions and N-terminal
capping groups, while a central Leu-Phe fragment was maintained. Several
compounds were identified as promising cathepsin L and S inhibitors
with Ki values in the low nanomolar to
subnanomolar range, for example, the peptide aldehydes 9a and 9b (9a, 2.67 nM, CatL; 0.455 nM, CatS; 9b, 1.76 nM, CatL; 0.512 nM, CatS). The compounds’
inhibitory activity against the main protease of SARS-CoV-2 (Mpro) was additionally investigated. Based on the results at
CatL, CatS, and Mpro, selected inhibitors were subjected
to investigations of their antiviral activity in cell-based assays.
In particular, the peptide nitrile 11e exhibited promising
antiviral activity with an EC50 value of 38.4 nM in Calu-3
cells without showing cytotoxicity. High metabolic stability and favorable
pharmacokinetic properties make 11e suitable for further
preclinical development.