Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M ^pro and cathepsin L

TLDR

The main protease (Mpro) of SARS‑CoV‑2 is a key antiviral drug target. The study aims to guide the development of dual inhibitors that target both viral Mpro and host cathepsin L as antiviral agents. X‑ray crystallography of Mpro bound to calpain inhibitors II and XII and GC‑376 analogs revealed that the S1 pocket accommodates hydrophobic methionine side chains and that inhibitor XII binds in an inverted pose. These structural insights demonstrate that hydrophobic P1 moieties can be exploited for dual inhibition and provide a basis for designing more effective SARS‑CoV‑2 antivirals.

Abstract

The main protease (Mpro) of SARS-CoV-2 is a key antiviral drug target. While most Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently found that several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II and XII, which are also active against human cathepsin L, a host protease that is important for viral entry. In this study, we solved x-ray crystal structures of Mpro in complex with calpain inhibitors II and XII and three analogs of GC-376 The structure of Mpro with calpain inhibitor II confirmed that the S1 pocket can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. The structure of calpain inhibitor XII revealed an unexpected, inverted binding pose. Together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of dual inhibitors as SARS-CoV-2 antivirals.