The SARS-CoV-2 main protease as drug target

Abstract

The unprecedented pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. The virus emerged in late 2019 and can cause a severe disease associated with significant mortality. Several vaccine development and drug discovery campaigns are underway. The SARS-CoV-2 main protease is considered a promising drug target, as it is dissimilar to human proteases. Sequence and structure of the main protease are closely related to those from other betacoronaviruses, facilitating drug discovery attempts based on previous lead compounds. Covalently binding peptidomimetics and small molecules are investigated. Various compounds show antiviral activity in infected human cells.

Keywords: Antivirals; COVID-19; Coronavirus; Peptidomimetics; Protease inhibitors.

Graphical abstract

Fig. 1

(a) Organisation of the RNA genome of SARS-CoV-2 with selected genes (Wuhan-Hu-1 isolate MN908947). (b) Schematic representation of polyprotein cleavage sites of SARS-CoV-2. The papain-like protease PL^pro cleaves at 3 distinct sites. The main protease M^pro (also referred to as 3CL^pro) cleaves at 11 distinct sites.

Fig. 2

Alignment of the amino acid sequences of crystallised main proteases of SARS-CoV-2 (PDB: 6Y2E), SARS-CoV (PDB: 2BX4) and MERS-CoV (PDB: 5C3N). Domains I, II and III comprise residues 8–101, 102–184 and 201–306, respectively. The catalytic dyads are indicated by asterisks. The alignment was generated using T-Coffee and shaded with Boxshade.

Fig. 3

Superimposition of X-ray crystal structures of the main proteases of SARS-CoV (pink, PDB: 2BX4), MERS-CoV (cyan, PDB: 5C3N) and SARS-CoV-2 (green, PDB: 6Y2E). Only the monomers are shown. Residues of the catalytic dyad are indicated (His41/Cys145 for SARS-CoV and SARS-CoV-2 and His41/Cys148 for MERS-CoV). The root-mean-square deviation (RMSD) of the superimpositions is 0.934 Å for SARS-CoV/MERS-CoV, 0.532 Å for SARS-CoV/SARS-CoV-2 and 0.905 Å for MERS-CoV/SARS-CoV-2. This figure was generated with UCSF Chimera.

Fig. 4

X-ray crystal structure of the M^pro homodimer of SARS-CoV-2 (PDB: 6Y2E). Residues of the catalytic dyad (His41/Cys145) are indicated. (a) Protomers are indicated. (b) Protomer domains are indicated. This figure has been generated with UCSF Chimera.

Fig. 5

Polyprotein cleavage sites recognised by M^pro of SARS-CoV-2, SARS-CoV and MERS-CoV. Peptide sequences cover residues P₅ to P₅′ according to the nomenclature of Schechter and Berger. Data were generated from pp1ab polyprotein sequences reported in the UniProt database with the accession codes P0DTD1 (SARS-CoV-2), P0C6X7 (SARS-CoV) and K9N7C7 (MERS-CoV). The consensus sequence over all cleavage sites was plotted using WebLogo.

Fig. 6

X-ray co-crystal structures of SARS-CoV-2 M^pro with covalently binding peptidomimetic inhibitors. M^pro is shown as hydrophobicity surface (red indicating hydrophobic and blue hydrophilic surface areas) and grey ribbon with amino acid side chains (UCSF Chimera). Inhibitor groups binding to protease subsites are indicated according to the Schechter Berger nomenclature. Electrophilic warheads covalently binding to Cys145 are circled. (a) Compound 3 with an α-ketoamide warhead (PDB: 6Y2F). (b) Compound 4 with a Michael acceptor warhead (PDB: 7BQY). (c) Compound 5 with a C-terminal aldehyde warhead (PDB: 6LZE).

Fig. 7

Inhibitors of the SARS-CoV-2 main protease M^pro. IC₅₀ indicates enzymatic inhibition. EC₅₀ indicates antiviral activity in cells.