3-Chymotrypsin-like protease (also known as main protease) (3CLpro)

The 3-chymotrypsin-like protease (3CLpro), also known as the main protease (Mpro) or nonstructural protein 5 (nsp5), is a highly conserved cysteine protease essential for coronavirus replication.[1][3] This enzyme catalytically cleaves the viral polyproteins pp1a and pp1ab at 11 conserved sites, liberating 11 individual non-structural proteins (nsp4-16) required for viral transcription, replication, and recombination.[1][3] The protease operates through a unique cysteine-histidine catalytic dyad (C145-H41 in SARS-CoV-2) that performs peptide bond hydrolysis, with strict substrate specificity requiring glutamine at the P1 position and a small amino acid at the P1' position.[3][5] Because coronaviruses are absolutely dependent on 3CLpro for viral replication and humans lack a homologous protease, 3CLpro represents one of the most pursued targets for antiviral drug development.[1][2] Multiple classes of 3CLpro inhibitors have demonstrated potent antiviral activity against SARS-CoV-2, MERS-CoV, and other coronaviruses in cell culture and animal models, with lead compounds showing IC₅₀ values in the submicromolar range and proof-of-concept efficacy in vivo.[2][4] Structure-guided optimization efforts continue to enhance inhibitor potency and selectivity while addressing challenges related to drug bioavailability, metabolic stability, and resistance development.

Other names

Main protease (Mpro)C30 endopeptidaseNonstructural protein 5 (nsp5)3C-like protease

Irreversible active site inhibition; Hydrogen bonding with substrate-binding pocket residues; Cysteine-histidine dyad inhibition; Blocking peptide bond hydrolysis at specific cleavage sites