Table 6.
Calculated molecular docking scores (in kcal/mol), binding features and MM/GBSA binding energies over 150 ns MD simulation for the identified potent flavones, lopinavir and baicalein in complex with SARS-CoV-2 main protease (Mpro).
| PubChem code | Docking Score (kcal/mol) | Binding Features (Hydrogen bond length in Å) | Calculated MM/GBSA binding energy (kcal/mol) |
||||||
|---|---|---|---|---|---|---|---|---|---|
| ΔEVDW | ΔEele | ΔEGB | ΔESUR | ΔGgas | ΔGSolv | ΔGbinding | |||
| PubChem-129-716-607 | −10.7 | THR26 (2.07 Å), GLU166 (2.06 Å), HIS164 (2.03 Å), TYR54 (2.33 Å), ASP187 (2.32 Å), THR190 (2.20, 2.02 Å) |
−74.3 | −64.9 | 77.8 | −7.6 | −132.0 | 70.2 | −69.0 |
| PubChem-885-071-27 | −9.5 | THR26 (2.07 Å), ASN142 (2.06 Å), PHE140 (2.8 Å), HIS163 (1.99 Å), GLU166 (2.07 Å), MET165 (2.4, 2.72 Å), GLN192 (2.73 Å), THR190 (2.21, 1.73 Å), PRO168 (2.20, 1.89 Å) |
−86.1 | −71.2 | 98.0 | −8.9 | −147.8 | 89.0 | −68.1 |
| Lopinavir (PubChem-927-27) | −9.8 | HIS164 (2.62 Å), GLY143 (2.01 Å), LEU141 (1.96 Å), SER144 (3.09 Å) |
−45.6 | −22.1 | 39.9 | −5.6 | −67.8 | 34.2 | −33.6 |
| Baicalein | −7.3 | LEU141 (3.06 Å), ASN142 (2.70 Å), GLY143 (2.09, 2.26 Å), SER144 (2.99 Å), GLU166 (2.14 Å). |
−27.2 | −6.3 | 20.2 | −3.4 | −33.6 | 16.8 | −16.8 |