3-Chymotrypsin-like protease (also referred to as Middle East respiratory syndrome coronavirus 3C-like protease or MERS-CoV 3C-like protease) (3CLpro or Mpro)

The 3-chymotrypsin-like protease (3CLpro), also known as the main protease (Mpro), is a 306 amino acid cysteine protease encoded in the coronavirus replicase gene that plays an indispensable role in the viral life cycle. This enzyme specifically recognizes and cleaves viral polyproteins (pp1a and pp1ab) at conserved sequences (Leu-Gln↓[Ser, Ala, Gly]), generating mature non-structural proteins essential for viral replication. The protease consists of three domains: catalytic domains I and II that form an antiparallel β-barrel structure responsible for enzymatic activity, and domain III containing α-helices responsible for protease dimerization. The active site features a catalytic dyad composed of histidine and cysteine residues that execute proteolytic cleavage through nucleophilic-type reactions. Because the 3CLpro is essential for coronavirus replication and is highly conserved among coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2, it represents an attractive and viable therapeutic target for developing broad-spectrum antiviral agents. Numerous structure-guided inhibitors have been developed that bind competitively to the enzyme's active site, with compounds like 6j and 6e demonstrating potent activity and in vivo efficacy in animal models of coronavirus infection. This target offers significant promise for the development of effective treatments against coronavirus infections.

Other names

Main protease (Mpro)3C-like proteaseNsp5Chymotrypsin-like cysteine proteaseMERS-CoV 3CLpro

Competitive inhibition of the active site, which contains a catalytic dyad composed of histidine and cysteine residues. Inhibitors bind to substrate-binding pockets located in the cleft between catalytic domains I and II, forming hydrogen bonding interactions with key active site residues (e.g., Gln 192, Gln 167, Phe 143). This action blocks viral polyprotein cleavage to prevent processing of viral proteins required for replication.