Macrocyclic Azapeptide Nitriles: Structure-Based Discovery of Potent SARS-CoV‑2 Main Protease Inhibitors as Antiviral Drugs

Given the crucial role of the main protease (Mpro) in
the replication cycle of SARS-CoV-2, this viral cysteine protease
constitutes a high-profile drug target. We investigated peptidomimetic
azapeptide nitriles as auspicious, irreversibly acting inhibitors
of Mpro. Our systematic approach combined an Mpro active-site scanning by combinatorially assembled azanitriles with
structure-based design. Encouraged by the bioactive conformation of
open-chain inhibitors, we conceptualized the novel chemotype of macrocyclic
azanitriles whose binding mode was elucidated by cocrystallization.
This strategy provided a favorable entropic contribution to target
binding and resulted in the development of the extraordinarily potent
Mpro inhibitor 84 with an IC50 value
of 3.23 nM and a second-order rate constant of inactivation, kinac/Ki, of 448,000
M–1s–1. The open-chain Mpro inhibitor 58, along with the macrocyclic compounds 83 and 84, a broad-spectrum anticoronaviral agent,
demonstrated the highest antiviral activity with EC50 values
in the single-digit micromolar range. Our findings are expected to
promote the future development of peptidomimetic Mpro inhibitors
as anti-SARS-CoV-2 agents.