In Silico Identification of Natural Compounds Against SARS-CoV-2 Main Protease From Chinese Herbal Medicines

Figures & data

Table 1. Docking scores of top 20 compounds with SARS-CoV-2 Mpro and their Chinese herbal medicine sources.

S. no.	Compound name	Docking score (kcal/mol)	Latin name
1	Japonicone G	-10.0	Inulae Herba
2	Bilobetin	-9.9	Ranunculus ternatus
3	Ternatoside D	-9.7	Ranunculus ternatus
4	Aristolochine	-9.6	Aristolochia debilis
5	Kumujansine	-9.6	Picrasma quassioides
6	Robustaflavone-4′-methyl ether	-9.6	Ranunculus ternatus
7	Amentoflavone	-9.5	Ranunculus ternatus
8	Podocarpusflavone A	-9.4	Ranunculus ternatus
9	Quassidine G	-9.3	Picrasma quassioides
10	Protostemonine	-9.3	Stemona japonica
11	Picrasidine N	-9.2	Picrasma quassioides
12	Stemocochinin	-9.2	Stemona japonica
13	4’,5-Dihydroxyflavanone	-9.1	Hydrangea febrifuga
14	Kayaflavone	-9.1	Ranunculus ternatus
15	Isoginkgetin	-9.1	Ranunculus ternatus
16	Picrasidine M	-9.1	Picrasma quassioides
17	5,6,9,11-tetradehydrotoonaciliatin K	-9.1	Picrasma quassioides
18	Picrasidine T	-9.0	Picrasma quassioides
19	Luteoloside	-9.0	Gleditsia sinensis
20	Ternatoside C	-9.0	Ranunculus ternatus

Figure 1. Distribution of docking energy between ∼1200 natural compounds and SARS-CoV-2 Mpro.

Figure 2. Docked comformations of six selected compounds with SARS-CoV-2 Mpro.

Docked comformations of (A) Japonicone G, (B) Kumujansine, (C) Quassidine G, (D) Picrasidine M and (E) Picrasidine T within the active site of SARS-CoV-2 Mpro along with their corresponding 2D interaction plots.

Figure 3. RMSD plot of two complexes.

RMSD plot of complex Japonicone G and Picrasidine T with SARS-CoV-2 Mpro during 100 ns MD simulation, respectively: (A) Mpro in complex with Japonicone G; (B) Japonicone G in complex; (C) Mpro in complex with Picrasidine T; (D) Picrasidine T in complex.

Figure 4. RMSF plot of SARS-CoV-2 Mpro in two complexes.

RMSF plot of SARS-CoV-2 Mpro (C-alpha atom) in two complexes during 100 ns MD simulations, respectively: (A) Mpro in complex with Japonicone G; (B) Mpro in complex with Picrasidine T.

Figure 5. Rg plot of two complexes.

Rg plot of complex Japonicone G and Picrasidine T with SARS-CoV-2 Mpro during 100 ns MD simulation, respectively: (A) Mpro in complex with Japonicone G; (B) Japonicone G in complex; (C) Mpro in complex with Picrasidine T; (D) Picrasidine T in complex.

Figure 6. Hydrogen bond number plot of two complexes.

Hydrogen bond number plot of complex (A) Japonicone G and (B) Picrasidine T with SARS-CoV-2 Mpro during 100 ns MD simulation, respectively.

Table 2. Contribution of each energy element (in kcal/mol) for the interaction of SARS-CoV-2 Mpro with Japonicone G.

van der Waal energy	Electrostatic energy	Polar solvation energy	SASA energy	Binding energy
-39.12	-11.11	31.94	-3.85	-22.13

Figure 7. Contribution energy per amino acid residue of SARS-CoV-2 Mpro upon interaction with Japonicone G.