Fig 1.
The virtual screening scheme of molecular docking of SAR-CoV-2 3CLpro inhibitors from the crystal structures of potent peptidomimetic inhibitors (N3, 13b, and 11a) using the DrugBank database. The screened compounds were selected, and the common drugs were later included for testing the SAR-CoV-2 3CLpro inhibitory activity by enzyme-based assay.
Fig 2.
Binding energy (kcal/mol) of approved drugs against three X-ray structures of SARS-CoV-2 3CLpro (PDB entry codes: 6LU7, 6LZE, and 6Y2F) derived from molecular docking.
Fig 3.
Binding energy heatmap (kcal/mol) of top 60 screened compounds against three X-ray structures of SARS-CoV-2 3CLpro (PDB entry codes: 6LU7, 6LZE, and 6Y2F) resulted from molecular docking.
The compounds in the blue and green highlight are the reference compounds used for screening and the selected compounds for enzyme-based assay, respectively.
Fig 4.
Heat map of the top compounds interacting with SARS-CoV-2 3CLpro derived from Fig 3 relative to the known inhibitors derived from LigPlot version 2.2.
Table 1.
The selected compounds and common drugs for SAR-CoV-2 3CLpro inhibitory activity assay.
Fig 5.
(A) Relative activity of 3CLpro in the presence of 100 μM of compounds and (B) inhibition of 3CLpro by lapatinib at various concentrations.
Fig 6.
Dynamics analysis of lapatinib with SARS-CoV-2 3CLpro.
(A) Distance between the Cm of lapatinib and the Cm of SARS-CoV-2 3CLpro active site residues, (B) # H-bonds, (C) # atom contacts, (D) RMSD plot for protein backbone (CA, C, O, and N atoms) and lapatinib, (E) interaction energy, and (F) radius of gyration (Rg) of 3CLpro in each chain plotted along with the 500-ns MD simulation.
Fig 7.
Key binding residues and protein motions of SARS-CoV-2 3CLpro/lapatinib complex.
(A) Binding free energy contribution per residue () for lapatinib binding derived from the last 100 ns, colored from dark red to green according to the highest to lowest free energies. The residues with
≤ −0.5 kcal/mol and ≥ 0.5 kcal/mol are labeled. The key residues are colored according to their
values. The representative structure was taken from the last MD snapshot. Noted that the quinazoline scaffold of lapatinib highly interacted with L141 at the S1 site (
of -3.33 kcal/mol). Their percentages of hydrogen bond occupation are shown in (B). (C) 2D projection of MD trajectories on the first two PC modes and PCA scree plot, (D) PC1 porcupine plot of the holo and apo forms, where the arrowhead and length represent the direction and amplitude of motion, respectively, and (E) RMSF plot of 3CLpro in each chain.
Fig 8.
The pharmacophore models of lapatinib and peptidomimetic inhibitor(s) in complex with SAR-CoV-2 3CLpro.
The 2D and 3D pharmacophore models of the first representative frame of lapatinib at 401 ns, and peptidomimetic inhibitors N3, 13b, and 11a at 81 ns, where RPMs derived from MD trajectories of lapatinib-3CLpro complex (401–500 ns), and peptidomimetic inhibitor(s)-3CLpro complex (81–100 ns) are illustrated on the right column. The green arrow, red arrow, purple arrow, and yellow color sphere (or circle in 2D) are pharmacophore features of hydrogen bond donor (HBD) and acceptor (HBA), halogen bond donor (XBD), and hydrophobic interaction properties, respectively.
Fig 9.
Interaction map of four inhibitors against SAR-CoV-2 3CLpro derived from 401–500 ns MD trajectories for lapatinib 81–100 ns, and MD trajectories for peptidomimetic inhibitors N3, 13b, and 11a. The abbreviations of H, HBA, and HBD represent the pharmacophore features of hydrophobic interaction, hydrogen bond acceptor, and hydrogen bond donor properties. The numbers in the blue box are the percentage of appearance in each interaction per residue.
Fig 10.
Rational design of lapatinib against the SARS-CoV-2 3CLpro.
(A) 2D structure of lapatinib and designed lapatinibs, (B) predicted binding affinity of the designed compounds A-H against SARS-CoV-2 3CLpro in comparison with lapatinib using LigandScout 4.4.2 program, (C) the binding free energy per residue of modified lapatinib, compound F/SARS-CoV-2 3CLpro complex, and its hydrogen bond interactions (D). The results were obtained from one snapshot of the complex after system minimization.