In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro)

Abstract

The ongoing Coronavirus Disease 19 (COVID-19) pandemic has had a profound impact on the global healthcare system. As the SARS-CoV-2 virus, responsible for this pandemic, continues to spread and develop mutations in its genetic material, new variants of interest (VOIs) and variants of concern (VOCs) are emerging. These outbreaks lead to a decrease in the efficacy of existing treatments such as vaccines or drugs, highlighting the urgency of new therapies for COVID-19. Therefore, in this study, we aimed to identify potential SARS-CoV-2 antivirals using a virtual screening protocol and molecular dynamics simulations. These techniques allowed us to predict the binding affinity of a database of compounds with the virus M^pro protein. This in silico approach enabled us to identify twenty-two chemical structures from a public database (QSAR Toolbox Ver 4.5 ) and ten promising molecules from our in-house database. The latter molecules possess advantageous qualities, such as two-step synthesis, cost-effectiveness, and long-lasting physical and chemical stability. Consequently, these molecules can be considered as promising alternatives to combat emerging SARS-CoV-2 variants.

Keywords: 3CLpro; Mpro; Nsp5; SARS-CoV-2; antivirals.

Figure 1

General workflow diagram.

Figure 2

Structure of the SARS-CoV-2 M^pro protein. The possible interaction sites are colored green, and the rest of the protein is blue. Image created in the Molecular Operating Environment, MOE 2022.02.

Figure 3

Potential binding site evaluated by SiteFinder. The size of the sphere represents how tightly packed the atoms are in the receptor; the larger the volume, the more accessible the atoms become. Spheres are colored by hydrophobic (gray) and hydrophilic (red). Image generated in MOE, 2022.02.

Figure 4

M^pro 7TOB potential interaction site, in green, defined by “ProteinsPlus” online server.

Figure 5

Consensus amino acids belonging to M^pro 7TOB site identified with DoGSiteScorer and SiteFinder from MOE 2022 tools.

Figure 6

The crystal structure of M^pro. Depiction of the M^pro amino acid substitutions in the SARS-CoV-2 variants of concern. The purple residue represents the K90R substitution present in the beta B.1.351 variant, whereas the green residue represents the P132H substitution present in the Omicron variants BA.1, BA.2, BA.4, BA.5, BA.2.12.1, BA.2.75, BQ.1, and XBB. Defining amino acid changes are those that appear at the phylogenetic root of a variant. Figure made with BioRender with a purchased license.

Figure 7

Grid of the 7TOB protein of SARS-CoV-2 in which the area where interactions with ligands were calculated is presented.

Figure 8

M^pro–Ensitrelvir complex active site. The direct protein–ligand interactions are represented in the dotted line. Three-dimensional (left) and two-dimensional (right) representations.

Figure 9

M^pro–Atazanavir complex active site. The direct protein–ligand interactions are represented in the dotted line. Three-dimensional (left) and two-dimensional (right) representations.

Figure 10

M^pro–LQM 778 complex active site. The direct protein–ligand interactions are represented in the dotted line. Three-dimensional (left) and two-dimensional (right) representations.

Figure 11

RMSD of M^pro systems: apo-form (in blue) and with the ligands M^proL6 (in red) and LQM 778 (in yellow).

Figure 12

RMSF of the M^pro protein in its apo-form in blue, compared to the ligands M^proL6 in red and LQM 778 in purple.

Figure 13

Radius of gyration of the ligands M^proL6 and LQM 778 and the apo-protein M^pro.