Table 3.
The binding scores and binding modes of the examined compounds from Cuphea ignea A. DC leaves extract (1-15) and N3 (docked, 16) inside the binding site of the SARS-CoV-2 main protease (Mpro).
| No. | Compound | Sa | RMSDb | Amino acid bond | Distance (A֯) |
|---|---|---|---|---|---|
| 1 | p-Coumaric acid | −4.75 | 1.81 | Glu166/H-donor His41/H-pi |
2.91 3.35 |
| 2 | Myricetin 3-O-rhamnoside | −7.86 | 1.11 |
Glu166/H-donor Met165/H-donor |
3.01 3.23 |
| 3 | Gallic acid | −4.52 | 0.85 | His164/H-donor | 3.04 |
| 4 | Rutin | −9.28 | 1.19 |
Glu166/H-donor Thr26/H-donor |
3.01 3.05 |
| 5 | Syringic acid | −5.18 | 1.52 | His164/H-donor | 3.03 |
| 6 | O-Coumaric acid | −4.78 | 1.02 | Glu166/H-donor | 2.92 |
| 7 | Resveratol | −5.79 | 1.44 | Glu 166/pi-H | 4.61 |
| 8 | Quercetin | −6.33 | 1.43 | Leu141/H-donor Gly143/H-acceptor Met165/H-donor Met165/pi-H |
2.69 3.46 3.78 4.57 |
| 9 | Naringenin | −6.15 | 1.05 | Glu166/H-acceptor Asn187/H-donor |
3.03 3.20 |
| 10 | Rosmarinic acid | −7.05 | 1.56 |
His41/H-acceptor Cys145/H-donor Thr25/pi-H |
3.12 4.38 4.08 |
| 11 | Cinnamic acid | −4.59 | 1.26 | Met166/pi-H Glu166/pi-H |
3.45 4.53 |
| 12 | Caffeic acid | −4.84 | 0.92 | Glu166/H-donor | 2.88 |
| 13 | Chlorogenic acid | −6.58 | 1.26 | Leu141/H-donor Glu166/H-acceptor Gln192/H-acceptor |
2.92 3.05 3.13 |
| 14 | Vanillic acid | −4.73 | 1.85 | – | – |
| 15 | Catechin | −6.23 | 1.64 | Arg188/H-donor Phe140/H-donor Glu166/H-donor |
2.91 3.05 3.12 |
| 16 | N3 | −10.11 | 1.86 | Gln189/H-donor Glu166/H-acceptor His41/H-pi Asn142/pi-H |
2.99 3.04 3.63 4.47 |
a
S: the score of a compound inside the protein binding pocket (Kcal/mol).
b
RMSD: The Root Mean Squared Deviation between the predicted pose and the crystal structure.