Table 5.
The interactions of the top 10 ranked phytochemicals of Vernonia amygdalina and Occinum gratissimum and positive control (Ritonavir and Lopinavir) for the best representative conformation from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories.
| Compound | Binding energies (kcal/mol) |
H-bonding |
Hydrophobic interactions |
||
|---|---|---|---|---|---|
| Number | Residues from SARS-CoV-2 3CLpro | Number | Residues from SARS-CoV-2 3CLpro | ||
| Ritonavir | −6.4 | 6 | ASN142(2), GLY143, SER144, CYS145, and GLU166 | 1 | MET165 |
| Lopinavir | −6.3 | 5 | ASN142, GLY143, ASP178(2), and GLN189 | 1 | THR25 |
| Vernolide | −7.5 | 3 | GLY143, SER144, and CYS145 | 1 | MET165 |
| Vernomygdin | −6.9 | 5 | ASN142, GLY143, SER144, CYS145, and GLN189 | 2 | MET165, and GLU166 |
| 11, 13-dihydrovernodalin | −6.6 | 6 | ASN28(2), GLY143, SER144, CYS145, and GLU166 | 3 | LEU27 (2), and MET165 |
| Neoandrographolide | −7.7 | 7 | THR45, SER46, LEU50, ASN142, GLY143, SER144, and CYS145 | 1 | THR25 |
| Vernomenin | −6.4 | 3 | GLY143, SER144, and CYS145 | 2 | THR25, and LEU27 |
| Myricetin | −7.1 | 7 | LEU141, ASN142, GLY143, SER144(3), and GLU166 | 0 | |
| Chicoric acid | −7.3 | 6 | LEU141, ASN142, GLY143, SER144(2), and CYS145 | 1 | GLN189 |
| Luteolin | −7.2 | 4 | SER144, GLU166(2), and GLN189 | 0 | |
| Rosmarinic acid | −6.8 | 7 | THR26 (2), PHE140, LEU141, GLY143, SER144, and CYS145 | 0 | |
| Isorhamnetin | −7.4 | 6 | ASN142, GLY143, SER144(3), and CYS145 | 0 | |
Residues in bold represent the most reported residues that interacted with the compounds.