Table 2.
Molecular docking results and interactions of the top scoring compounds of Saussurea species with SARS-CoV-2 proteins and ACE-2.
| Protein | ligand | Binding energy Score (Kcal/mol) | RMSD refine |
Bonds between atoms of compounds and residues of active site |
|||
|---|---|---|---|---|---|---|---|
| Atom of ligand |
Involved Receptor residues |
Bond type |
Bond length (A°) |
||||
| Tangshenoside III | −9.3479 | 1.6416 | O6 O11 C49 C39 |
Thr 24 Asn 142 Met 49 His 41 |
H-donor H-donor H-donor H-Pi |
2.90 3.06 3.94 4.35 |
|
| Rutin | −9.1420 | 1.2988 | O4 O8 O9 O12 O4 O7 O10 6-ring |
Cys 145 Cys 145 Thr 26 Cys 145 Gly 143 His 163 Thr 26 Gln 189 |
H-donor H-donor H-donor H-donor H-acceptor H-acceptor H-acceptor Pi-H |
4.08 3.55 2.89 3.71 2.77 3.23 3.02 3.67 |
|
| Hesperidin | −8.5672 | 1.6829 | O7 O8 O10 O13 O12 6-ring 6-ring |
Asn 142 Met 165 Thr 190 Cys 145 Cys 145 Thr 25 Asn 142 |
H-donor H-donor H-donor H-donor H-acceptor Pi-H Pi-H |
3.04 3.61 2.86 3.97 3.05 4.13 3.87 |
|
| Arctiin | −8.5658 | 1.5173 | O6 | Met 165 | H-donor | 3.31 | |
| Quercitrin | −8.4104 | 1.2280 | O5 O11 O3 6-ring |
Cys 145 Thr 26 His 163 Gln 189 |
H-donor H-donor H-acceptor Pi-H |
3.57 3.28 3.01 4.09 |
|
| Luteolin-7-glucoside | −8.0322 | 1.8745 | O3 O5 O28 O3 O4 O8 6-ring |
Leu 141 Cys 145 Met 165 Ser 144 His 163 His 41 Gln 189 |
H-donor H-donor H-donor H-acceptor H-acceptor H-pi pi-H |
2.67 3.13 3.89 2.91 3.14 3.28 3.48 |
|
| Quercetin-3-glucoside | −7.9070 | 1.5491 | O4 O8 O13 O3 O4 O6 6-ring 6-ring 6-ring |
Cys 145 Cys 145 Cys 145 Gly 143 Ser 144 His 163 Gln 189 Gln 189 Gln 189 |
H-donor H-donor H-donor H-acceptor H-acceptor H-acceptor pi-H pi-H pi-H |
3.54 3.63 4.10 3.37 3.08 3.12 4.79 3.71 4.24 |
|
| Daucosterol | −7.8411 | 1.3721 | O1 | Glu 166 | H-acceptor | 3.21 | |
| Hispidulin-7-glucoside | −7.7856 | 1.9530 | O4 C12 O3 O6 |
Cys 145 Cys 145 Gly 143 His 163 |
H-donor H-donor H-acceptor H-acceptor |
3.44 3.55 3.09 3.05 |
|
| β-sitosterol | −7.5755 | 1.9469 | O1 | Thr 26 | H-donor | 2.81 | |
| 7ORB | Rutin | −9.0665 | 1.7144 | O4 O15 O4 |
Phe 347 Ser 399 Ser 349 |
H-donor H-donor H-acceptor |
2.91 2.82 2.83 |
| Tangshenoside III | −7.7140 | 1.9781 | O11 O12 |
Lys 356 Tyr 351 Ala 348 |
H-acceptor H-acceptor pi-H |
3.11 3.27 3.95 |
|
| Hesperidin | −7.5719 | 1.7773 | O6 O8 O9 O10 |
Arg 346 Glu 340 Lys 356 Lys 356 |
H-donor H-donor H-acceptor H-acceptor |
2.76 2.92 3.25 3.14 |
|
| Arctiin | −7.2114 | 1.4840 | O4 O6 O7 |
Ser 399 Arg 346 Arg 346 |
H-donor H-donor H-acceptor |
2.83 3.10 2.94 |
|
| Daucosterol | −7.1701 | 1.9301 | O5 O3 |
Glu 340 Asn 354 |
H-donor H-acceptor |
2.81 3.11 |
|
| Epicatechin gallate | −6.9823 | 1.7679 | O4 O6 O9 O11 |
Ser 349 Ala 352 Ser 399 Ser 399 |
H-donor H-donor H-donor H-donor |
2.77 2.87 2.92 3.04 |
|
| Quercitrin | −6.8851 | 1.8457 | O8 | Ser 399 | H-donor | 2.86 | |
| Quercetin-3-glucoside | −6.694 | 1.5691 | O10 O1 O6 |
Ser 399 Arg 346 Arg 346 |
H-donor H-acceptor H-acceptor |
2.91 2.93 3.20 |
|
| Hispidulin-7-glucoside | −6.6385 | 1.6345 | O3 O7 6-ring |
Ser 399 Arg 346 Arg 346 |
H-donor H-donor Pi-cation |
2.85 3.09 2.99 |
|
| Edultin | −6.4001 | 1.9467 | O2 O7 |
Asn 354 Arg 346 |
H-acceptor H-acceptor |
2.64 3.18 |
|
| 1R42 | Rutin | −8.9636 | 1.239 | O5 O10 C20 O7 O9 |
Glu 406 Asp 367 Glu 406 Gln 442 Lys 441 |
H-donor H-donor H-donor H-acceptor H-acceptor |
2.80 3.15 3.31 3.27 2.94 |
| Hesperidin | −8.4456 | 1.421 | O4 O8 C21 O1 O13 |
Asp 367 Asp 367 Asp 367 Lys 441 Gln 522 |
H-donor H-donor H-donor H-acceptor H-acceptor |
2.84 2.87 3.56 2.94 3.15 |
|
| Tangshenoside III | −8.1305 | 1.176 | O10 C5 O5 |
Glu 375 Asn 290 Lys 441 |
H-donor H-acceptor H-acceptor |
2.84 3.07 3.12 |
|