Statine-based peptidomimetic compounds as inhibitors for SARS-CoV-2 main protease (SARS-CoV‑2 Mpro)

Abstract

COVID-19 is a multisystemic disease caused by the SARS-CoV-2 airborne virus, a member of the Coronaviridae family. It has a positive sense single-stranded RNA genome and encodes two non-structural proteins through viral cysteine-proteases processing. Blocking this step is crucial to control virus replication. In this work, we reported the synthesis of 23 statine-based peptidomimetics to determine their ability to inhibit the main protease (Mpro) activity of SARS-CoV-2. Among the 23 peptidomimetics, 15 compounds effectively inhibited Mpro activity by 50% or more, while three compounds (7d, 8e, and 9g) exhibited maximum inhibition above 70% and IC₅₀ < 1 µM. Compounds 7d, 8e, and 9g inhibited roughly 80% of SARS-CoV-2 replication and proved no cytotoxicity. Molecular docking simulations show putative hydrogen bond and hydrophobic interactions between specific amino acids and these inhibitors. Molecular dynamics simulations further confirmed the stability and persisting interactions in Mpro's subsites, exhibiting favorable free energy binding (ΔG_bind) values. These findings suggest the statine-based peptidomimetics as potential therapeutic agents against SARS-CoV-2 by targeting Mpro.

Figure 1

Synthesis of the β-hydroxy-γ-amino acid intermediate (1).

Figure 2

Synthesis of the statine-based peptidomimetics (7a-h, 8a-g, 9a-g, and 10).

Figure 3

The dose-dependent curves of the statine-based peptidomimetics 7d, 8e, and 9g (and atazanavir, ATV, as positive control) against SARS-CoV-2. Calu-3 cells infected with SARS-CoV-2 MOI 0.01 were treated with the compounds 7d, 8e, 9g, and ATV at a semi-log curve of concentration (10, 3.16, 1, 0.316, and 0.1 µM) for 24 h at 37 ºC, 5% CO₂ (n = 3).

Figure 4

Best pose by molecular docking simulations of statine-like derivatives on the SARS-CoV-2 Mpro active site (PDB ID: 6LU7): (A) 7d; (B) 8e, and (C) 9g. The residues involved in H-bond interactions (dashed black lines) with the ligands are in ball-and-line model (cyan color) and residues involved in hydrophobic interactions are in stick models (light green color). In 2D structures, the atoms (or groups) of the ligands involved in H-bond interactions are circled in yellow.

Figure 5

RMSD analysis of the 7d (A), 8e (B), and 9g (C) relative to the Mpro-Cα atoms.

Figure 6

Cα-RMSD analysis per Mpro subsites S1 + S1’ (red line), S2 (green line), S4 (purple line), and S5 (blue line) that are relative to the simulations by molecular dynamics of the ligand-Mpro complex. Ligands: 7d (A), 8e (B), and 9g (C).

Figure 7

Cα-RMSF analysis at different times relative to the simulations by molecular dynamics of the ligand-Mpro complex. Ligands: 7d (A), 8e (B) and 9g (C).