Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches

Abstract

The recently emerged COVID-19 has been declared a pandemic by the World Health Organization as to date; no therapeutic drug/vaccine is available for the treatment. Due to the lack of time and the urgency to contain the pandemic, computational screening appears to be the best tool to find a therapeutic solution. Accumulated evidence suggests that many phyto-compounds possess anti-viral activity. Therefore, we identified possible phyto-compounds that could be developed and used for COVID-19 treatment. In particular, molecular docking was used to prioritize the possible active phyto-compounds against two key targets namely RNA dependent RNA polymerase (RdRp) and main protease (M^pro) of SARS-CoV-2. In this study, an antiviral drug- Remdesivir (RdRp inhibitor) and Darunavir (M^pro inhibitor) are used as reference drugs. This study revealed that phyto-molecules- Mulberroside-A/C/E/F, Emblicanin A, Nimbolide, and Punigluconin showed high binding affinity against RdRp while Andrographolides, Mulberrosides, Anolignans, Chebulic acid, Mimusopic acid, and Punigluconin showed better binding affinity against M^pro as compared with the reference drug. Furthermore, ADME profiles validated the drug-likeness properties of prioritized phyto-compounds. Besides, to assess the stability, MD simulations studies were performed along with reference inhibitors for M^pro (Darunavir) and RdRp (Remdesivir). Binding free energy calculations (MM-PBSA) revealed the estimated value (ΔG) of M^pro_Darunavir; M^pro_Mulberroside E; RdRp_Remdesivir and RdRp_Emblicanin A were -111.62 ± 6.788, -141.443 ± 9.313, 30.782 ± 5.85 and -89.424 ± 3.130 kJmol^-1, respectively. Taken together, the study revealed the potential of these phyto-compounds as inhibitors of RdRp and M^pro inhibitor that could be further validated against SARS-CoV-2 for clinical benefits.Communicated by Ramaswamy H. Sarma.

Keywords: COVID-19; MM-PBSA; SARS-CoV-2; molecular docking; molecular dynamics; phyto-compounds.

Figure 1.

Top docked natural ligands and standard inhibitor with RNA dependent RNA Polymerase (RdRp). (a) 2D ligand interaction of Emblicanin A in the active site of RdRp (b) interaction of Mulberroside A in RdRp active site (c) interaction of Mulberroside E in RdRp active site (d) interaction of Mulberroside F in RdRp active site (e) interaction of Punigluconin in RdRp active site (f) interaction of Remdesivir in RdRp active site.

Figure 2.

Top docked natural ligands and standard inhibitor with Main Protease (M^pro). (a) 2 D ligand interaction of Mulberroside E in the active site of M^pro (b) interaction of Oxo-andrographolide in M^pro active site (c) interaction of Mulberroside F in M^pro active site (d) interaction of Punigluconin in M^pro active site (e) interaction of Chebulic acid in M^proactive site (f) interaction of Darunavir in M^pro active site.

Figure 3.

RMSD of M^pro and RdRp with inhibitors computing the deviation (nm) vs. function of time (50 ns):(A) RMSD of the protein Cα backbone atoms M^pro_Darunavir (Black); M^pro_MulberrosideE (Red) (B) RMSD of the protein Cα backbone atoms RdRp_Remdesivir (Black) and RdRp_EmblicaninA (Red) (C) RMSD of the inhibitor atoms of M^pro_Darunavir (Black) and M^pro_MulberrosideE (Red)(D) RMSD of the inhibitor atoms of RdRp_Remdesivir (Black)and RdRp_EmblicaninA (Red).

Figure 4.

Residue-wise RMSF deviations (nm) of M^pro and RdRp with inhibitors: (A) RMSF of the protein Cα backbone atoms of M^pro_Darunavir (black); M^pro_MulberrosideE (red) (B) RMSF of the protein Cα backbone atoms ofRdRp_Remdesivir (black) and RdRp_EmblicaninA (red).

Figure 5.

Radius of Gyration of the protein Cα backbone atoms of (A) M^pro_Darunavir(black); M^pro_MulberrosideE (red) (B) RdRp_Remdesivir (black) and RdRp_EmblicaninA (red).

Figure 6.

H-bonds of M^pro and RdRp with inhibitors: (A)Inter H-bond formation between M^pro and Darunavir (black) and Mulberroside E (red); (B) Inter H-bond formation between RdRp and Remdesivir (black) and Emblicanin A (red).

Figure 7.

2D representation of M^pro interactions with Mulberroside E. M ^pro_Mulberroside E interactions analyzed at every 10 ns interval. Residues mainly contributing in H-bond formation with the Mulberroside E are circled in each inset diagram with red colour.

Figure 8.

2D representation of RdRp interactions with Emblicanin A. RdRp_ Emblicanin A interactions analyzed at every 10 ns interval. Residues mainly contributing in H-bond formation with the Emblicanin A are circled in each inset diagram with red colour.

Figure 9.

PCA, 2D projection scatter plot (A) Overlay of 2D scatter plot projection the motion of the proteins in phase space for the two principle components, PC1 and PC3 derived for of M^pro_Darunavir (black); M^pro_Mulberroside E (red); (B) Overlay of 2D scatter plot projection the motion of the proteins in phase space for the two principle components, PC1 and PC3 derived for of RdRp_Remdesivir (black) and RdRp_Emblicanin A (red).

Figure 10.

MM-PBSA Calculation of binding free energy.(A) The total binding free energy for all the M^pro and RdRp inhibitor complexes calculated for last 30 ns stable trajectory for a total of 150 frames, each at 200 ps interval. (B) Representative contributions of each energy component for binding free energy for M^pro and RdRp interactions with inhibitors. (C) The contribution of important binding residues of M^pro with Mulberroside E to the total binding free energy. (D) The contribution of important binding residues of RdRp with Emblicanin A to the total binding free energy. The (-ve) values indicate stable complex formation for PfCDPK2_inhibitor complexes, while the (+ve) values indicate a destabilizing effect.