Fig 1.
Ribbon representation of coronavirus Mpro structures in complex with ligands/inhibitors superposed, showing the main ligand binding site, using SARS-CoV-2 sequence as the query.
The main ligands/inhibitors are circled in red. The water molecules are shown as small red balls. The figure was generated in Chimera. PDB information about the Mpro structures used for superposition in this figure are given in S1 Table in S1 File.
Table 1.
Molecular docking results of top ranking compounds savinin, betulinic acid, and curcumin with (A) SARS-CoV-2 Mpro monomer and (B) SARS-CoV-2 Mpro dimer, respectively, based on affinity of binding.
The top-energy pose (according to Total Energy) of each compound is presented (with an RMSD of 0.0). The DockThor molecular docking program was used for analysis of interactions between SARS-CoV-2 Mpro monomer and dimer and the three compounds, using default settings. Ligplot was used to reveal the residues involved in binding and the mode of interaction with the ligands. The SARS-CoV-2 Mpro monomer and SARS-CoV-2 Mpro dimer (chain A) used in this study were from PDB IDs 6yb7 and 7ali, respectively.
Fig 2.
Hydrophobic surface representation of the highest scoring herbal compound-SARS-CoV-2 Mpro monomer complexes.
(a-c) Savinin, betulinic acid and curcumin, respectively, in complex with SARS-CoV-2 Mpro monomer using DockThor. The phytochemicals are shown in ball and stick representation. The figure was generated using Chimera.
Fig 3.
Structural analysis of savinin-, betulinic acid- and curcumin-SARS-CoV-2 Mpro monomer complexes as revealed by molecular docking, with the highest scores in terms of affinity.
(a, d and g) Ligplot analyses of the savinin-, betulinic acid- and curcumin-SARS-CoV-2 Mpro monomer complexes, respectively, showing Mpro residues involved in hydrogen bonding and hydrophobic interactions. (b, e and h) Hydrophobic representation of the savinin-, betulinic acid- and curcumin-SARS-CoV-2 Mpro monomer complexes, respectively. (c, f and i) Electrostatic potential representation of the savinin-, betulinic acid- and curcumin-SARS-CoV-2 Mpro monomer complexes, respectively. The residues involved in interaction with savinin, betulinic acid and curcumin are labelled. The figure was generated using the Ligplot and Chimera programs.
Fig 4.
Hydrophobic surface representation of the highest scoring herbal ligand-SARS-CoV-2 Mpro dimer complexes.
(a-c) Curcumin, betulinic acid and savinin, respectively, in complex with SARs-CoV-2 Mpro dimer using DockThor. The herbal ligands are shown in ball and stick representation. The figure was generated using Chimera.
Fig 5.
Structural analysis of the curcumin- and betulinic acid- and savinin-SARS-CoV-2 Mpro dimer complexes as revealed by molecular docking, with the highest scores in terms of affinity.
(a, d and g) Ligplot analyses of the curcumin- and betulinic acid- and savinin-SARS-CoV-2 Mpro dimer complexes, respectively, showing Mpro residues involved in hydrogen bonding and hydrophobic interactions. (b, e and h) Hydrophobic representation of the curcumin-, betulinic acid- and savinin-SARS-CoV-2 Mpro dimer complexes, respectively. (c, f and i) Electrostatic potential representation of curcumin-, betulinic acid- and savinin-SARS-CoV-2 Mpro dimer complexes, respectively. The residues involved in interaction with either curcumin, betulinic acid or savinin are labelled. The figure was generated using the Ligplot and Chimera programs.
Fig 6.
RMSD plots of ligands from both monomeric and dimeric states of SARS-CoV-2 Mpro and the RMSD plots of the apo and ligand-bound SARS-CoV-2 Mpro complexes in the dimeric state.
(A) RMSD of the ligands from the ligand-monomeric SARS-CoV-2 Mpro complexes. Betulinic acid (green) showed the highest stability followed by Nirmatrelvir (red), Savinin (yellow) and Curcumin (navy blue). (B) RMSD of the ligands from the ligand-dimeric SARS-CoV-2 Mpro complexes. Both chains A and B of Betulinic acid, Savinin, Curcumin and Nirmatrelvir are presented. (C) RMSD of the ligand-monomeric SARS-CoV-2 Mpro complexes. (D) RMSD of the ligand-dimeric SARS-CoV-2 Mpro complexes. Apo SARS-CoV-2 Mpro (green); Betulinic acid-SARS-CoV-2 Mpro (yellow), Savinin-SARS-CoV-2 Mpro (red), Nirmatrelvir-SARS-CoV-2 Mpro (dark blue) and curcumin-SARS-CoV-2 Mpro (light blue). Apo-SARS-CoV-2 Mpro (Apo), Betulininc acid-SARS-CoV-2 Mpro complex (BET), Savinin-SARS-CoV-2 Mpro complex (SAV), Curcumin-SARS-CoV-2 Mpro complex (CUR) and Nirmatrelvir-SARS-CoV-2 Mpro complex (NIR).
Fig 7.
Overlay of ligand-dimeric SARS-CoV-2 Mpro complexes at 0, 50 and 100 ns intervals of MD simulations.
(a) Savinin- SARS-CoV-2 Mpro complex, (b) Betulinic acid-SARS-CoV-2 Mpro complex, (c) Curcumin-SARS-CoV-2 Mpro complex and (d) Nirmatrelvir-SARS-CoV-2 Mpro at 0, 50 and 100 ns (in grey, pink and green, respectively) of the MD simulation.
Fig 8.
RMSF analysis of apo- and ligand-bound SARS-CoV-2 Mpro structures, in both the monomeric and dimeric states.
(A) RMSF values of apo- and ligand- bound SARS-CoV-2 Mpro structures, in the monomeric state. (B) RMSF values of apo- and ligand-bound SARS-CoV-2 Mpro structures, in the dimeric state. Chains A and B of SARS-CoV-2 Mpro in the dimeric state were analysed separately.
Fig 9.
Radius of Gyration of apo- and ligand-bound SARS-CoV-2 Mpro structures, both in the monomeric and dimeric states.
Apo-SARS-CoV-2 Mpro (Mpro), Betulininc acid-SARS-CoV-2 Mpro complex (BET), Savinin-SARS-CoV-2 Mpro complex (SAV), Curcumin-SARS-CoV-2 Mpro complex (CUR) and Nirmatrelvir-SARS-CoV-2 Mpro complex (NIR). Dimer denotes the dimeric form of the SARS-CoV-2 Mpro protein, either in apo or halo forms.
Fig 10.
Hydrogen bonding analysis between the ligands and the monomeric state of SARS-CoV-2 Mpro as revealed by MD.
(a, b and c) Hydrogen bonds formed between betulinic acid and SARS-CoV-2 Mpro. (d, e and f) Hydrogen bonds formed between savinin and SARS-CoV-2 Mpro. (g, h and i) Hydrogen bonds formed between curcumin and SARS-CoV-2 Mpro. (j, k and l) Hydrogen bonds formed between Nirmatrelvir and SARS-CoV-2 Mpro. (a) Thr25 and His41, (b) Thr190 and His41 and (c) Gln192 and His41 participated in hydrogen bonding with betulinic acid. (d) Ser46 and main chain of Thr26, (e) Thr25, Cys145 and main chain of Gln189 and (f) Asn142, Cys145 and main chain of Gln189 formed hydrogen bonded with savinin. (g) His41, (h) Gln189, Asp187, Thr26 and (i) Gly143 and Cys145 formed hydrogen bonds with curcumin. (j) Cys44, (k) Asn119 and (l) His41 hydrogen bonded with Nirmatrelvir.
Fig 11.
Hydrogen bonding analysis between the ligands and the dimeric state of SARS-CoV-2 Mpro as revealed by MD.
(a) Hydrogen bonding formed between savinin and Glu166 of SARS-CoV-2 Mpro. (b and c) Hydrogen bondings formed between betulinic acid and residues Thr25, Thr26 and His164 of SARS-CoV-2 Mpro. (d, e and f) Hydrogen bondings formed between curcumin and residues Thr26 and Gln189 of SARS-CoV-2 Mpro, as well as Ser301 of the adjacent monomer. (g, h and i) Hydrogen bondings formed between Nirmatrelvir and residues Thr25, Thr45, Ser46, Asn142 and Gln189 of SARS-CoV-2 Mpro.
Table 2.
Summary of the MM/PBSA results of the ligand-bound SARS-CoV-2 Mpro dimeric complexes.
The values are given in kJ/mol.
Fig 12.
Contribution energy of residues from the ligand-bound SARS-CoV-2 Mpro complexes, in the dimeric state of the protein.
The contribution energies of residues from SARS-CoV-2 Mpro in the betulinic acid-, Savinin-, Curcumin- and Nirmatrelvir-bound SARS-CoV-2 Mpro complexes are given. The positive values in kJ/mol indicates the negative contribution of the residue for ligand binding and the negative values represent the probable positive role of the residues in stabilisation of the ligand binding to the SARS-CoV-2 Mpro.
Fig 13.
Buried Surface Area analysis of ligand-bound SARS-CoV-2 Mpro complexes, in the dimeric state of the protein.
This figure compared the BSA value of each ligand in relation to the chain it was bound to. Nirmatrelvir (NIR) exhibited the highest BSA values indicating more area covered by this ligand. Savinin (SAV) presented the lowest values and hence higher access of solvent molecules to the binding pocket. Betulinic acid (BET) and curcumin (CUR) stood in middle, with betulinic acid covering more buried surface area than curcumin.