Molecular docking and dynamic simulations of some medicinal plants compounds against SARS-CoV-2: an in silico study

Figures & data

Table 1. Docking score result for SARS–CoV-2 receptors binding with the potential inhibitors.

Ligand	Binding affinity (kcal/mol) 6LU7	Binding affinity (kcal/mol) 6ZLG	Binding affinity (kcal/mol) 6VXX
5-hydroxy-7,8,2′-trimethoxyflavone	−7.5	−8.4	−7.4
Andrographolide	−7.1	−7.8	−7.0
Ascorbigen	−7.4	−8.3	−7.5
Astragalin	−8.5	−8.8	−7.6
Azadiradione	−7.6	−8.8	−7.9
Beta-amyrin	−7.4	−9.7	−7.8
Chloroquine	−5.9	−7.6	−5.3
Cucurbitacin-B	−7.5	−9.0	−6.6
Cucurbitacin-K	−7.6	−8.6	−6.9
Diosgenin	−7.3	−9.2	−8.3
Epiazadiradione	−7.5	−8.2	−7.6
Epoxyazadiradione	−7.4	−9.1	−7.7
Friedelin	−8.2	−9.0	−8.5
Gallocatechin	−7.2	−9.2	−6.8
Gamma-cadinene	−6.1	−8.6	−7.4
Gedunin	−7.7	−8.4	−7.4
Hydroxychloroquine	−6.1	−7.2	−5.7
Isoquercitrin	−8.5	−8.1	−6.7
Ivermectin	−5.6	−9.9	−8.5
Kaempferol	−7.8	−7.7	−7.1
Lectin	−7.4	−9.7	−6.8
Lopinavir	−7.1	−8.5	−6.4
Meldenin	−7.7	−7.9	−7.5
Meliantriol	−7.4	−8.3	−8.2
Momordicin	−8.4	−8.6	−7.7
Momordicoside-I	−7.9	−8.9	−8.0
Multiflorenol	−7.4	−9.2	−8.2
Myricetin	−7.3	−8.5	−7.2
Nelfinavir	−8.2	−9.2	−6.5
Neoandrographolide	−7.6	−8.7	−7.1
Nimbaflavone	−8.1s	−8.3	−7.8
Nimbinin	−7.5	−8.8	−7.6
Nimbolin-B	−7.6	−9.0	−7.2
Nimolicinol	−7.2	−9.1	−8.3
Nimolinone	−7.6	−8.7	−7.8
Oseltamivir	−6.1	−5.9	−6.0
Phyllanthusin E	−7.2	−7.7	−6.8
Quercetin	−7.3	−9.5	−7.1
Quercitrin	−7.7	−8.6	−7.2
Remdesivir	−7.7	−8.6	−6.9
Taraxerol	−7.4	−9.0	−8.0

Figure 1. RMSD plots for the studied complexes.

Figure 2. RMSF plots for the α-Carbon backbone of the main protease for three systems.

Table 2. The calculated binding free energies and their relative components for the complexes using MM-GBSA method obtained from the last 1000 frames of 50 ns. The energy components are in kcal/mol.

Compound	ΔEvdw	ΔEele	ΔGgas	ΔGpolar	ΔGnon-polar	ΔGsolvation	ΔGbind
Astra-6LU7	$-44.56$	$-8.63$	$-53.19$	$25.15$	$-5.28$	$19.87$	$-33.32$
Nimb-6LU7	$-42.69$	$-4.24$	$-46.92$	$19.98$	$-4.92$	$15.06$	$-31.86$
Kaem-6LU7	$-32.23$	$-6.34$	$-38.57$	$17.46$	$-4.24$	$13.22$	$-25.35$

Figure 3. Ligand-protein interactions resulting from MM-GBSA calculations.