Table 1.
Docking results of natural products in terms of binding affinity (kcal/mol), interaction of natural products with the COVID-19 main protease (PDB ID: 6LU7) and the drug like properties
| Natural products | Affinity (kcal/mol) | Structure of compounds and its interaction with COVID-19 main protease | Drug like properties (Lipinski’s rule of five) |
|---|---|---|---|
| Glycyrrhizin | − 8.1 |
|
Molecular weight (< 500 Da): 822.93 Log P (< 5): 1.55 H-bond donor (5): 8 H-bond acceptor (< 10): 16 MlogP (< 4.15): 0.02 Violations: 3 |
| Bicylogermecrene | − 6.5 |
|
Molecular weight (< 500 Da): 204.35 Log P (< 5): 4.15 H-bond donor (5): 0 H-bond acceptor (< 10): 0 MlogP (< 4.15): 4.63 Violations: 1 |
| Tryptanthrine | − 8.2 |
|
Molecular weight (< 500 Da): 248.24 Log P (< 5): 2.16 H-bond donor (5): 0 H-bond acceptor (< 10): 3 MlogP (< 4.15): 2.22 Violations: 0 |
| β-sitosterol | − 7.2 |
|
Molecular weight (< 500 Da): 414.71 Log P (< 5): 7.19 H-bond donor (5): 1 H-bond acceptor (< 10): 1 MlogP (< 4.15): 6.73 Violations: 1 |
| Indirubin | − 7.6 |
|
Molecular weight (< 500 Da): 260.26 Log P (< 5): 2.69 H-bond donor (5): 2 H-bond acceptor (< 10): 3 MlogP (< 4.15): 1.70 Violations: 0 |
| Indican | − 7.5 |
|
Molecular weight (< 500 Da): 295.29 Log P (< 5): − 0.16 H-bond donor (5): 5 H-bond acceptor (< 10): 6 MlogP (< 4.15): − 1.13 Violations: 0 |
| Indigo | − 7.5 |
|
Molecular weight (< 500 Da): 262.26 Log P (< 5): 2.63 H-bond donor (5): 2 H-bond acceptor (< 10): 3 MlogP (< 4.15): 1.23 Violations: 0 |
| Hesperetin | − 7.9 |
|
Molecular weight (< 500 Da): 302.28 Log P (< 5): 1.91 H-bond donor (5): 6 H-bond acceptor (< 10): 6 MlogP (< 4.15): 0.41 Violations: 0 |
| Crysophanic acid | − 7.3 |
|
Molecular weight (< 500 Da): 254.24 Log P (< 5): 2.38 H-bond donor (5): 2 H-bond acceptor (< 10): 4 MlogP (< 4.15): 0.92 Violations: 0 |
| Rhein | − 8.9 |
|
Molecular weight (< 500 Da): 284.22 Log P (< 5): 1.48 H-bond donor (5): 3 H-bond acceptor (< 10): 6 MlogP (< 4.15): 0.29 Violations: 0 |
| Berberine | − 8.1 |
|
Molecular weight (< 500 Da): 336.36 Log P (< 5): 2.53 H-bond donor (5): 0 H-bond acceptor (< 10): 4 MlogP (< 4.15): 2.19 Violations: 0 |
| β-caryophyllene | − 7.2 |
|
Molecular weight (< 500 Da): 204.35 Log P (< 5): 4.24 H-bond donor (5): 0 H-bond acceptor (< 10): 0 MlogP (< 4.15): 4.63 Violations: 1 |